Starting phenix.real_space_refine on Wed Mar 27 11:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wyk_6696/03_2024/5wyk_6696_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wyk_6696/03_2024/5wyk_6696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wyk_6696/03_2024/5wyk_6696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wyk_6696/03_2024/5wyk_6696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wyk_6696/03_2024/5wyk_6696_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wyk_6696/03_2024/5wyk_6696_neut.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1619 5.49 5 S 323 5.16 5 C 88689 2.51 5 N 27015 2.21 5 O 33114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D ARG 132": "NH1" <-> "NH2" Residue "3D ARG 149": "NH1" <-> "NH2" Residue "3D ARG 194": "NH1" <-> "NH2" Residue "3D ARG 256": "NH1" <-> "NH2" Residue "3D ARG 277": "NH1" <-> "NH2" Residue "3D ARG 314": "NH1" <-> "NH2" Residue "3D ARG 374": "NH1" <-> "NH2" Residue "3D ARG 411": "NH1" <-> "NH2" Residue "3D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E ARG 183": "NH1" <-> "NH2" Residue "3E ARG 207": "NH1" <-> "NH2" Residue "3E ARG 215": "NH1" <-> "NH2" Residue "3E ARG 279": "NH1" <-> "NH2" Residue "3E ARG 298": "NH1" <-> "NH2" Residue "3E ARG 328": "NH1" <-> "NH2" Residue "3E ARG 380": "NH1" <-> "NH2" Residue "3E ARG 391": "NH1" <-> "NH2" Residue "3E ARG 397": "NH1" <-> "NH2" Residue "3F ARG 344": "NH1" <-> "NH2" Residue "3F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3G ARG 46": "NH1" <-> "NH2" Residue "3H ARG 46": "NH1" <-> "NH2" Residue "AE ARG 71": "NH1" <-> "NH2" Residue "AE ARG 83": "NH1" <-> "NH2" Residue "AE ARG 150": "NH1" <-> "NH2" Residue "AE ARG 169": "NH1" <-> "NH2" Residue "AE ARG 353": "NH1" <-> "NH2" Residue "AE ARG 357": "NH1" <-> "NH2" Residue "AE ARG 360": "NH1" <-> "NH2" Residue "AE ARG 374": "NH1" <-> "NH2" Residue "AE ARG 377": "NH1" <-> "NH2" Residue "AE ARG 381": "NH1" <-> "NH2" Residue "B1 ARG 40": "NH1" <-> "NH2" Residue "B1 ARG 66": "NH1" <-> "NH2" Residue "B1 ARG 70": "NH1" <-> "NH2" Residue "B1 ARG 71": "NH1" <-> "NH2" Residue "B1 ARG 92": "NH1" <-> "NH2" Residue "B1 ARG 93": "NH1" <-> "NH2" Residue "B1 ARG 145": "NH1" <-> "NH2" Residue "B1 ARG 163": "NH1" <-> "NH2" Residue "B1 ARG 168": "NH1" <-> "NH2" Residue "B1 ARG 172": "NH1" <-> "NH2" Residue "B1 ARG 193": "NH1" <-> "NH2" Residue "B1 ARG 197": "NH1" <-> "NH2" Residue "B1 ARG 227": "NH1" <-> "NH2" Residue "B1 ARG 246": "NH1" <-> "NH2" Residue "B1 ARG 266": "NH1" <-> "NH2" Residue "B1 ARG 828": "NH1" <-> "NH2" Residue "B1 ARG 830": "NH1" <-> "NH2" Residue "B1 ARG 833": "NH1" <-> "NH2" Residue "B1 ARG 866": "NH1" <-> "NH2" Residue "B1 ARG 868": "NH1" <-> "NH2" Residue "B1 ARG 870": "NH1" <-> "NH2" Residue "B1 ARG 912": "NH1" <-> "NH2" Residue "B1 ARG 960": "NH1" <-> "NH2" Residue "B1 ARG 973": "NH1" <-> "NH2" Residue "B1 ARG 978": "NH1" <-> "NH2" Residue "B1 ARG 988": "NH1" <-> "NH2" Residue "B1 ARG 1004": "NH1" <-> "NH2" Residue "B1 ARG 1010": "NH1" <-> "NH2" Residue "BA ARG 131": "NH1" <-> "NH2" Residue "BB TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ARG 292": "NH1" <-> "NH2" Residue "BE ARG 341": "NH1" <-> "NH2" Residue "BE ARG 446": "NH1" <-> "NH2" Residue "CA PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB ARG 223": "NH1" <-> "NH2" Residue "CB ARG 761": "NH1" <-> "NH2" Residue "CB ARG 822": "NH1" <-> "NH2" Residue "CB ARG 853": "NH1" <-> "NH2" Residue "E1 ARG 82": "NH1" <-> "NH2" Residue "E1 ARG 132": "NH1" <-> "NH2" Residue "E1 ARG 176": "NH1" <-> "NH2" Residue "E1 ARG 188": "NH1" <-> "NH2" Residue "E2 ARG 82": "NH1" <-> "NH2" Residue "E2 ARG 132": "NH1" <-> "NH2" Residue "E2 ARG 176": "NH1" <-> "NH2" Residue "E2 ARG 188": "NH1" <-> "NH2" Residue "E2 ARG 211": "NH1" <-> "NH2" Residue "K1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 ARG 184": "NH1" <-> "NH2" Residue "MA ARG 41": "NH1" <-> "NH2" Residue "MB ARG 94": "NH1" <-> "NH2" Residue "MB ARG 99": "NH1" <-> "NH2" Residue "MB ARG 116": "NH1" <-> "NH2" Residue "MB ARG 119": "NH1" <-> "NH2" Residue "MB ARG 146": "NH1" <-> "NH2" Residue "MB ARG 173": "NH1" <-> "NH2" Residue "MB ARG 201": "NH1" <-> "NH2" Residue "MB ARG 220": "NH1" <-> "NH2" Residue "MB ARG 227": "NH1" <-> "NH2" Residue "MB ARG 240": "NH1" <-> "NH2" Residue "MB ARG 242": "NH1" <-> "NH2" Residue "MB ARG 253": "NH1" <-> "NH2" Residue "MB ARG 257": "NH1" <-> "NH2" Residue "MB ARG 262": "NH1" <-> "NH2" Residue "P1 ARG 97": "NH1" <-> "NH2" Residue "P1 ARG 110": "NH1" <-> "NH2" Residue "P1 ARG 129": "NH1" <-> "NH2" Residue "P1 ARG 140": "NH1" <-> "NH2" Residue "P1 ARG 176": "NH1" <-> "NH2" Residue "P1 ARG 221": "NH1" <-> "NH2" Residue "P1 ARG 223": "NH1" <-> "NH2" Residue "P1 ARG 241": "NH1" <-> "NH2" Residue "P1 ARG 244": "NH1" <-> "NH2" Residue "P1 ARG 264": "NH1" <-> "NH2" Residue "SC ARG 87": "NH1" <-> "NH2" Residue "SC ARG 144": "NH1" <-> "NH2" Residue "SC ARG 152": "NH1" <-> "NH2" Residue "SC ARG 213": "NH1" <-> "NH2" Residue "SF ARG 11": "NH1" <-> "NH2" Residue "SF ARG 49": "NH1" <-> "NH2" Residue "SF ARG 59": "NH1" <-> "NH2" Residue "SF ARG 108": "NH1" <-> "NH2" Residue "SF ARG 148": "NH1" <-> "NH2" Residue "SF ARG 200": "NH1" <-> "NH2" Residue "SG ARG 65": "NH1" <-> "NH2" Residue "SG ARG 76": "NH1" <-> "NH2" Residue "SG ARG 148": "NH1" <-> "NH2" Residue "SG ARG 219": "NH1" <-> "NH2" Residue "SI ARG 39": "NH1" <-> "NH2" Residue "SI TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ARG 8": "NH1" <-> "NH2" Residue "SJ ARG 22": "NH1" <-> "NH2" Residue "SJ ARG 47": "NH1" <-> "NH2" Residue "SJ ARG 59": "NH1" <-> "NH2" Residue "SJ ARG 110": "NH1" <-> "NH2" Residue "SJ ARG 164": "NH1" <-> "NH2" Residue "SJ ARG 178": "NH1" <-> "NH2" Residue "SJ ARG 194": "NH1" <-> "NH2" Residue "SK ARG 17": "NH1" <-> "NH2" Residue "SK ARG 53": "NH1" <-> "NH2" Residue "SK ARG 54": "NH1" <-> "NH2" Residue "SK ARG 62": "NH1" <-> "NH2" Residue "SK ARG 78": "NH1" <-> "NH2" Residue "SK ARG 168": "NH1" <-> "NH2" Residue "SK ARG 171": "NH1" <-> "NH2" Residue "SM ARG 30": "NH1" <-> "NH2" Residue "SM ARG 33": "NH1" <-> "NH2" Residue "SM ARG 116": "NH1" <-> "NH2" Residue "SO ARG 104": "NH1" <-> "NH2" Residue "SO ARG 106": "NH1" <-> "NH2" Residue "SP ARG 90": "NH1" <-> "NH2" Residue "SP ARG 103": "NH1" <-> "NH2" Residue "SP ARG 107": "NH1" <-> "NH2" Residue "SR ARG 114": "NH1" <-> "NH2" Residue "SY ARG 144": "NH1" <-> "NH2" Residue "SZ ARG 20": "NH1" <-> "NH2" Residue "SZ ARG 32": "NH1" <-> "NH2" Residue "Sd ARG 65": "NH1" <-> "NH2" Residue "U4 ARG 84": "NH1" <-> "NH2" Residue "U4 ARG 114": "NH1" <-> "NH2" Residue "U4 ARG 121": "NH1" <-> "NH2" Residue "U4 ARG 124": "NH1" <-> "NH2" Residue "U4 ARG 144": "NH1" <-> "NH2" Residue "U4 ARG 163": "NH1" <-> "NH2" Residue "U5 ARG 50": "NH1" <-> "NH2" Residue "U5 ARG 55": "NH1" <-> "NH2" Residue "U5 ARG 68": "NH1" <-> "NH2" Residue "U5 ARG 84": "NH1" <-> "NH2" Residue "U5 ARG 107": "NH1" <-> "NH2" Residue "U5 ARG 108": "NH1" <-> "NH2" Residue "U5 ARG 109": "NH1" <-> "NH2" Residue "U5 ARG 130": "NH1" <-> "NH2" Residue "U5 ARG 142": "NH1" <-> "NH2" Residue "U5 ARG 155": "NH1" <-> "NH2" Residue "U5 ARG 164": "NH1" <-> "NH2" Residue "U5 ARG 177": "NH1" <-> "NH2" Residue "U5 ARG 181": "NH1" <-> "NH2" Residue "U5 ARG 200": "NH1" <-> "NH2" Residue "U5 ARG 229": "NH1" <-> "NH2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150760 Number of models: 1 Model: "" Number of chains: 58 Chain: "3A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3327 Classifications: {'RNA': 157} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 65, 'rna3p_pyr': 74} Link IDs: {'rna2p': 17, 'rna3p': 139} Chain breaks: 5 Chain: "3B" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1866 Classifications: {'peptide': 239} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 222} Chain: "3C" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1866 Classifications: {'peptide': 239} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 222} Chain: "3D" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2915 Classifications: {'peptide': 370} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 357} Chain breaks: 1 Chain: "3E" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2935 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 7, 'TRANS': 374} Chain breaks: 1 Chain: "3F" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2916 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 5 Chain: "3G" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "3H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "5A" Number of atoms: 9867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 9867 Classifications: {'RNA': 462} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 12, 'rna3p_pur': 231, 'rna3p_pyr': 202} Link IDs: {'rna2p': 29, 'rna3p': 432} Chain breaks: 9 Chain: "AA" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 2845 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 569} Link IDs: {'CIS': 2, 'TRANS': 566} Unresolved non-hydrogen bonds: 1138 Unresolved non-hydrogen angles: 1707 Unresolved non-hydrogen dihedrals: 569 Planarities with less than four sites: {'UNK:plan-1': 569} Unresolved non-hydrogen planarities: 569 Chain: "AB" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2015 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 403} Link IDs: {'CIS': 1, 'TRANS': 401} Chain breaks: 6 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1209 Unresolved non-hydrogen dihedrals: 403 Planarities with less than four sites: {'UNK:plan-1': 403} Unresolved non-hydrogen planarities: 403 Chain: "AC" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 2360 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 472} Link IDs: {'CIS': 1, 'TRANS': 470} Chain breaks: 11 Unresolved non-hydrogen bonds: 944 Unresolved non-hydrogen angles: 1416 Unresolved non-hydrogen dihedrals: 472 Planarities with less than four sites: {'UNK:plan-1': 472} Unresolved non-hydrogen planarities: 472 Chain: "AD" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 505 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'CIS': 1, 'TRANS': 99} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'UNK:plan-1': 101} Unresolved non-hydrogen planarities: 101 Chain: "AE" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3331 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 400} Chain breaks: 2 Chain: "AF" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 1880 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 376} Link IDs: {'TRANS': 375} Chain breaks: 6 Unresolved non-hydrogen bonds: 752 Unresolved non-hydrogen angles: 1128 Unresolved non-hydrogen dihedrals: 376 Planarities with less than four sites: {'UNK:plan-1': 376} Unresolved non-hydrogen planarities: 376 Chain: "AG" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 3060 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 612} Link IDs: {'CIS': 2, 'TRANS': 609} Chain breaks: 1 Unresolved non-hydrogen bonds: 1224 Unresolved non-hydrogen angles: 1836 Unresolved non-hydrogen dihedrals: 612 Planarities with less than four sites: {'UNK:plan-1': 612} Unresolved non-hydrogen planarities: 612 Chain: "B1" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4325 Classifications: {'peptide': 536} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 500} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "BA" Number of atoms: 6026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6026 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 733} Chain breaks: 3 Chain: "BB" Number of atoms: 6138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6138 Classifications: {'peptide': 778} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 757} Chain breaks: 3 Chain: "BC" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6117 Classifications: {'peptide': 783} Link IDs: {'CIS': 3, 'PTRANS': 24, 'TRANS': 755} Chain breaks: 1 Chain: "BD" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2539 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 311} Chain breaks: 3 Chain: "BE" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5936 Classifications: {'peptide': 753} Link IDs: {'PTRANS': 21, 'TRANS': 731} Chain breaks: 5 Chain: "CA" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain breaks: 2 Chain: "CB" Number of atoms: 8870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8870 Classifications: {'peptide': 1098} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1044} Chain breaks: 5 Chain: "E1" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1689 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E2" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1695 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E4" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1425 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'TRANS': 284} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 285 Planarities with less than four sites: {'UNK:plan-1': 285} Unresolved non-hydrogen planarities: 285 Chain: "K1" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1410 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "MA" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "MB" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1465 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain: "MC" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 307 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 45} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "P1" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1368 Classifications: {'peptide': 173} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 162} Chain: "R1" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2742 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 337} Chain: "S1" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1425 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'TRANS': 284} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 285 Planarities with less than four sites: {'UNK:plan-1': 285} Unresolved non-hydrogen planarities: 285 Chain: "SA" Number of atoms: 21307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 21307 Classifications: {'RNA': 1000} Modifications used: {'rna2p_pur': 67, 'rna2p_pyr': 56, 'rna3p_pur': 462, 'rna3p_pyr': 415} Link IDs: {'rna2p': 122, 'rna3p': 877} Chain breaks: 21 Chain: "SC" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "SF" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1881 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "SG" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 196} Chain: "SI" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1322 Classifications: {'peptide': 165} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Chain: "SJ" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1350 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "SK" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1412 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "SM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1143 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "SO" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1087 Classifications: {'peptide': 134} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 126} Chain: "SP" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 771 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "SR" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "SX" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SY" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "SZ" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 801 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "Sc" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 595 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Sd" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Sf" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "U1" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1425 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'TRANS': 284} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 285 Planarities with less than four sites: {'UNK:plan-1': 285} Unresolved non-hydrogen planarities: 285 Chain: "U2" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "U4" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "U5" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2009 Classifications: {'peptide': 248} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 233} Chain: "UA" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1690 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 338} Link IDs: {'TRANS': 337} Chain breaks: 15 Unresolved non-hydrogen bonds: 676 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 338 Planarities with less than four sites: {'UNK:plan-1': 338} Unresolved non-hydrogen planarities: 338 Chain: "UB" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 2775 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 555} Link IDs: {'TRANS': 554} Chain breaks: 31 Unresolved non-hydrogen bonds: 1110 Unresolved non-hydrogen angles: 1665 Unresolved non-hydrogen dihedrals: 555 Planarities with less than four sites: {'UNK:plan-1': 555} Unresolved non-hydrogen planarities: 555 Chain: "UC" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 3300 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 660} Link IDs: {'CIS': 4, 'TRANS': 655} Chain breaks: 25 Unresolved non-hydrogen bonds: 1320 Unresolved non-hydrogen angles: 1980 Unresolved non-hydrogen dihedrals: 660 Planarities with less than four sites: {'UNK:plan-1': 660} Unresolved non-hydrogen planarities: 660 Time building chain proxies: 57.93, per 1000 atoms: 0.38 Number of scatterers: 150760 At special positions: 0 Unit cell: (364.32, 299.2, 308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 323 16.00 P 1619 15.00 O 33114 8.00 N 27015 7.00 C 88689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 49.82 Conformation dependent library (CDL) restraints added in 11.8 seconds 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31760 Finding SS restraints... Secondary structure from input PDB file: 472 helices and 214 sheets defined 47.3% alpha, 24.7% beta 425 base pairs and 805 stacking pairs defined. Time for finding SS restraints: 38.98 Creating SS restraints... Processing helix chain '3B' and resid 149 through 157 removed outlier: 3.969A pdb=" N ALA3B 153 " --> pdb=" O SER3B 149 " (cutoff:3.500A) Processing helix chain '3B' and resid 178 through 188 removed outlier: 3.998A pdb=" N HIS3B 183 " --> pdb=" O THR3B 179 " (cutoff:3.500A) Processing helix chain '3B' and resid 200 through 214 removed outlier: 3.815A pdb=" N GLY3B 204 " --> pdb=" O SER3B 200 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG3B 205 " --> pdb=" O HIS3B 201 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU3B 206 " --> pdb=" O ARG3B 202 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU3B 207 " --> pdb=" O PRO3B 203 " (cutoff:3.500A) Processing helix chain '3B' and resid 226 through 234 removed outlier: 3.577A pdb=" N ARG3B 231 " --> pdb=" O GLN3B 228 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N MET3B 232 " --> pdb=" O LYS3B 229 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE3B 234 " --> pdb=" O ARG3B 231 " (cutoff:3.500A) Processing helix chain '3B' and resid 248 through 260 removed outlier: 4.031A pdb=" N ILE3B 252 " --> pdb=" O ASP3B 248 " (cutoff:3.500A) Processing helix chain '3B' and resid 273 through 277 removed outlier: 3.760A pdb=" N ASP3B 277 " --> pdb=" O ALA3B 273 " (cutoff:3.500A) No H-bonds generated for 'chain '3B' and resid 273 through 277' Processing helix chain '3B' and resid 281 through 296 removed outlier: 3.883A pdb=" N VAL3B 285 " --> pdb=" O ASP3B 281 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU3B 296 " --> pdb=" O LYS3B 292 " (cutoff:3.500A) Processing helix chain '3C' and resid 149 through 158 removed outlier: 3.632A pdb=" N ALA3C 153 " --> pdb=" O SER3C 149 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY3C 158 " --> pdb=" O GLY3C 154 " (cutoff:3.500A) Processing helix chain '3C' and resid 180 through 188 removed outlier: 3.602A pdb=" N VAL3C 184 " --> pdb=" O SER3C 180 " (cutoff:3.500A) Processing helix chain '3C' and resid 200 through 212 removed outlier: 3.728A pdb=" N GLY3C 204 " --> pdb=" O SER3C 200 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG3C 205 " --> pdb=" O HIS3C 201 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU3C 206 " --> pdb=" O ARG3C 202 " (cutoff:3.500A) Processing helix chain '3C' and resid 226 through 230 removed outlier: 3.558A pdb=" N TYR3C 230 " --> pdb=" O PRO3C 227 " (cutoff:3.500A) Processing helix chain '3C' and resid 248 through 253 Processing helix chain '3C' and resid 253 through 258 Processing helix chain '3C' and resid 273 through 277 removed outlier: 3.695A pdb=" N ASP3C 277 " --> pdb=" O ALA3C 273 " (cutoff:3.500A) No H-bonds generated for 'chain '3C' and resid 273 through 277' Processing helix chain '3C' and resid 281 through 296 removed outlier: 4.182A pdb=" N VAL3C 285 " --> pdb=" O ASP3C 281 " (cutoff:3.500A) Processing helix chain '3D' and resid 36 through 42 Processing helix chain '3D' and resid 58 through 71 removed outlier: 4.191A pdb=" N LEU3D 63 " --> pdb=" O ALA3D 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU3D 64 " --> pdb=" O ALA3D 60 " (cutoff:3.500A) Processing helix chain '3D' and resid 75 through 82 Processing helix chain '3D' and resid 85 through 89 Processing helix chain '3D' and resid 104 through 113 removed outlier: 3.903A pdb=" N SER3D 108 " --> pdb=" O ASN3D 104 " (cutoff:3.500A) Processing helix chain '3D' and resid 125 through 133 removed outlier: 3.719A pdb=" N ARG3D 129 " --> pdb=" O GLN3D 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG3D 132 " --> pdb=" O ILE3D 128 " (cutoff:3.500A) Processing helix chain '3D' and resid 135 through 139 Processing helix chain '3D' and resid 146 through 164 removed outlier: 3.969A pdb=" N VAL3D 163 " --> pdb=" O SER3D 159 " (cutoff:3.500A) Processing helix chain '3D' and resid 172 through 203 removed outlier: 3.508A pdb=" N PHE3D 191 " --> pdb=" O ASP3D 187 " (cutoff:3.500A) Processing helix chain '3D' and resid 212 through 222 removed outlier: 3.695A pdb=" N PHE3D 216 " --> pdb=" O ASP3D 212 " (cutoff:3.500A) Processing helix chain '3D' and resid 247 through 255 Processing helix chain '3D' and resid 264 through 300 removed outlier: 3.588A pdb=" N MET3D 268 " --> pdb=" O SER3D 264 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN3D 270 " --> pdb=" O THR3D 266 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL3D 271 " --> pdb=" O ASP3D 267 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA3D 300 " --> pdb=" O MET3D 296 " (cutoff:3.500A) Processing helix chain '3D' and resid 300 through 307 Processing helix chain '3D' and resid 309 through 320 Processing helix chain '3D' and resid 321 through 328 removed outlier: 3.818A pdb=" N GLN3D 328 " --> pdb=" O ASN3D 324 " (cutoff:3.500A) Processing helix chain '3D' and resid 372 through 392 removed outlier: 3.948A pdb=" N TYR3D 392 " --> pdb=" O ARG3D 388 " (cutoff:3.500A) Processing helix chain '3D' and resid 394 through 398 Processing helix chain '3D' and resid 399 through 415 Processing helix chain '3E' and resid 52 through 66 removed outlier: 3.624A pdb=" N ILE3E 64 " --> pdb=" O ALA3E 60 " (cutoff:3.500A) Processing helix chain '3E' and resid 69 through 79 removed outlier: 3.891A pdb=" N ILE3E 79 " --> pdb=" O LEU3E 75 " (cutoff:3.500A) Processing helix chain '3E' and resid 92 through 100 removed outlier: 3.984A pdb=" N ASN3E 96 " --> pdb=" O THR3E 92 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA3E 97 " --> pdb=" O LYS3E 93 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE3E 98 " --> pdb=" O LEU3E 94 " (cutoff:3.500A) Processing helix chain '3E' and resid 114 through 119 Processing helix chain '3E' and resid 120 through 122 No H-bonds generated for 'chain '3E' and resid 120 through 122' Processing helix chain '3E' and resid 123 through 128 Processing helix chain '3E' and resid 132 through 152 removed outlier: 3.913A pdb=" N LEU3E 136 " --> pdb=" O SER3E 132 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER3E 137 " --> pdb=" O ASP3E 133 " (cutoff:3.500A) Processing helix chain '3E' and resid 160 through 189 removed outlier: 4.112A pdb=" N ILE3E 164 " --> pdb=" O ASP3E 160 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA3E 168 " --> pdb=" O ILE3E 164 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP3E 171 " --> pdb=" O ILE3E 167 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP3E 172 " --> pdb=" O ALA3E 168 " (cutoff:3.500A) Processing helix chain '3E' and resid 192 through 196 removed outlier: 3.966A pdb=" N LEU3E 195 " --> pdb=" O PHE3E 192 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA3E 196 " --> pdb=" O PRO3E 193 " (cutoff:3.500A) No H-bonds generated for 'chain '3E' and resid 192 through 196' Processing helix chain '3E' and resid 201 through 213 removed outlier: 3.630A pdb=" N ILE3E 209 " --> pdb=" O TYR3E 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY3E 213 " --> pdb=" O ILE3E 209 " (cutoff:3.500A) Processing helix chain '3E' and resid 214 through 218 removed outlier: 3.698A pdb=" N ALA3E 218 " --> pdb=" O ARG3E 215 " (cutoff:3.500A) Processing helix chain '3E' and resid 220 through 225 Processing helix chain '3E' and resid 228 through 242 removed outlier: 4.060A pdb=" N ARG3E 234 " --> pdb=" O GLU3E 230 " (cutoff:3.500A) Processing helix chain '3E' and resid 248 through 284 removed outlier: 3.986A pdb=" N LEU3E 252 " --> pdb=" O THR3E 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU3E 270 " --> pdb=" O ALA3E 266 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA3E 278 " --> pdb=" O ASN3E 274 " (cutoff:3.500A) Processing helix chain '3E' and resid 284 through 292 Processing helix chain '3E' and resid 293 through 304 Processing helix chain '3E' and resid 306 through 311 removed outlier: 3.570A pdb=" N LYS3E 311 " --> pdb=" O ILE3E 307 " (cutoff:3.500A) Processing helix chain '3E' and resid 313 through 319 removed outlier: 3.515A pdb=" N ILE3E 319 " --> pdb=" O SER3E 315 " (cutoff:3.500A) Processing helix chain '3E' and resid 322 through 333 removed outlier: 3.554A pdb=" N LEU3E 326 " --> pdb=" O ALA3E 322 " (cutoff:3.500A) Processing helix chain '3E' and resid 347 through 351 removed outlier: 3.507A pdb=" N ALA3E 351 " --> pdb=" O VAL3E 348 " (cutoff:3.500A) Processing helix chain '3E' and resid 355 through 376 removed outlier: 4.654A pdb=" N VAL3E 369 " --> pdb=" O ALA3E 365 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU3E 376 " --> pdb=" O ARG3E 372 " (cutoff:3.500A) Processing helix chain '3E' and resid 387 through 401 Processing helix chain '3F' and resid 217 through 221 removed outlier: 3.778A pdb=" N TYR3F 220 " --> pdb=" O GLY3F 217 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE3F 221 " --> pdb=" O ALA3F 218 " (cutoff:3.500A) No H-bonds generated for 'chain '3F' and resid 217 through 221' Processing helix chain '3F' and resid 364 through 375 removed outlier: 3.694A pdb=" N LEU3F 368 " --> pdb=" O GLU3F 364 " (cutoff:3.500A) Processing helix chain '3G' and resid 13 through 30 Processing helix chain '3G' and resid 36 through 46 Processing helix chain '3G' and resid 61 through 64 Processing helix chain '3G' and resid 65 through 75 removed outlier: 4.125A pdb=" N LEU3G 69 " --> pdb=" O LEU3G 65 " (cutoff:3.500A) Processing helix chain '3G' and resid 83 through 90 removed outlier: 3.536A pdb=" N LEU3G 87 " --> pdb=" O SER3G 83 " (cutoff:3.500A) Processing helix chain '3G' and resid 110 through 126 removed outlier: 3.989A pdb=" N ILE3G 126 " --> pdb=" O GLU3G 122 " (cutoff:3.500A) Processing helix chain '3H' and resid 14 through 30 Processing helix chain '3H' and resid 36 through 47 Processing helix chain '3H' and resid 60 through 64 removed outlier: 3.799A pdb=" N ILE3H 63 " --> pdb=" O PRO3H 60 " (cutoff:3.500A) Processing helix chain '3H' and resid 65 through 75 removed outlier: 4.177A pdb=" N LEU3H 69 " --> pdb=" O LEU3H 65 " (cutoff:3.500A) Processing helix chain '3H' and resid 84 through 92 Processing helix chain '3H' and resid 110 through 126 removed outlier: 3.661A pdb=" N ILE3H 126 " --> pdb=" O GLU3H 122 " (cutoff:3.500A) Processing helix chain 'AB' and resid 415 through 422 removed outlier: 3.759A pdb=" N UNKAB 421 " --> pdb=" O UNKAB 417 " (cutoff:3.500A) Processing helix chain 'AB' and resid 423 through 433 Processing helix chain 'AB' and resid 441 through 452 Processing helix chain 'AB' and resid 455 through 464 Processing helix chain 'AB' and resid 468 through 484 removed outlier: 4.903A pdb=" N UNKAB 475 " --> pdb=" O UNKAB 471 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N UNKAB 484 " --> pdb=" O UNKAB 480 " (cutoff:3.500A) Processing helix chain 'AB' and resid 490 through 508 Processing helix chain 'AB' and resid 521 through 551 removed outlier: 4.329A pdb=" N UNKAB 545 " --> pdb=" O UNKAB 541 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N UNKAB 546 " --> pdb=" O UNKAB 542 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N UNKAB 547 " --> pdb=" O UNKAB 543 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNKAB 551 " --> pdb=" O UNKAB 547 " (cutoff:3.500A) Processing helix chain 'AC' and resid 409 through 418 Processing helix chain 'AC' and resid 437 through 447 Processing helix chain 'AC' and resid 460 through 476 Processing helix chain 'AC' and resid 481 through 495 Processing helix chain 'AC' and resid 501 through 510 removed outlier: 3.544A pdb=" N UNKAC 510 " --> pdb=" O UNKAC 506 " (cutoff:3.500A) Processing helix chain 'AC' and resid 526 through 536 Processing helix chain 'AC' and resid 544 through 554 Processing helix chain 'AC' and resid 567 through 576 Processing helix chain 'AC' and resid 596 through 606 Processing helix chain 'AC' and resid 609 through 624 Processing helix chain 'AC' and resid 634 through 652 Processing helix chain 'AC' and resid 661 through 688 removed outlier: 3.764A pdb=" N UNKAC 684 " --> pdb=" O UNKAC 680 " (cutoff:3.500A) Processing helix chain 'AD' and resid 382 through 389 Processing helix chain 'AD' and resid 408 through 417 Processing helix chain 'AD' and resid 429 through 439 removed outlier: 3.676A pdb=" N UNKAD 439 " --> pdb=" O UNKAD 435 " (cutoff:3.500A) Processing helix chain 'AD' and resid 442 through 447 removed outlier: 3.591A pdb=" N UNKAD 447 " --> pdb=" O UNKAD 443 " (cutoff:3.500A) Processing helix chain 'AD' and resid 459 through 467 Processing helix chain 'AD' and resid 473 through 497 Processing helix chain 'AD' and resid 500 through 505 removed outlier: 3.962A pdb=" N UNKAD 504 " --> pdb=" O UNKAD 500 " (cutoff:3.500A) Processing helix chain 'AD' and resid 505 through 513 removed outlier: 3.773A pdb=" N UNKAD 509 " --> pdb=" O UNKAD 505 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N UNKAD 511 " --> pdb=" O UNKAD 507 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N UNKAD 512 " --> pdb=" O UNKAD 508 " (cutoff:3.500A) Processing helix chain 'AE' and resid 4 through 15 removed outlier: 3.785A pdb=" N ALAAE 9 " --> pdb=" O SERAE 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNAE 10 " --> pdb=" O ASPAE 6 " (cutoff:3.500A) Processing helix chain 'AE' and resid 22 through 30 removed outlier: 3.624A pdb=" N GLNAE 26 " --> pdb=" O ARGAE 22 " (cutoff:3.500A) Processing helix chain 'AE' and resid 36 through 43 removed outlier: 3.599A pdb=" N ALAAE 40 " --> pdb=" O ASNAE 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THRAE 42 " --> pdb=" O LYSAE 38 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLNAE 43 " --> pdb=" O THRAE 39 " (cutoff:3.500A) Processing helix chain 'AE' and resid 44 through 59 removed outlier: 4.056A pdb=" N ILEAE 48 " --> pdb=" O ASPAE 44 " (cutoff:3.500A) Processing helix chain 'AE' and resid 68 through 73 Processing helix chain 'AE' and resid 75 through 79 removed outlier: 3.725A pdb=" N ILEAE 79 " --> pdb=" O GLUAE 76 " (cutoff:3.500A) Processing helix chain 'AE' and resid 87 through 105 Processing helix chain 'AE' and resid 111 through 124 removed outlier: 3.808A pdb=" N LEUAE 115 " --> pdb=" O LEUAE 111 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TRPAE 120 " --> pdb=" O HISAE 116 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEUAE 121 " --> pdb=" O ALAAE 117 " (cutoff:3.500A) Processing helix chain 'AE' and resid 126 through 131 Processing helix chain 'AE' and resid 131 through 139 removed outlier: 4.257A pdb=" N LEUAE 137 " --> pdb=" O GLUAE 133 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THRAE 139 " --> pdb=" O LEUAE 135 " (cutoff:3.500A) Processing helix chain 'AE' and resid 145 through 155 removed outlier: 3.554A pdb=" N LYSAE 149 " --> pdb=" O THRAE 145 " (cutoff:3.500A) Processing helix chain 'AE' and resid 165 through 171 removed outlier: 3.845A pdb=" N ARGAE 169 " --> pdb=" O SERAE 165 " (cutoff:3.500A) Processing helix chain 'AE' and resid 175 through 180 Processing helix chain 'AE' and resid 185 through 202 removed outlier: 3.777A pdb=" N TYRAE 192 " --> pdb=" O PHEAE 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYRAE 195 " --> pdb=" O LEUAE 191 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUAE 196 " --> pdb=" O TYRAE 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAE 200 " --> pdb=" O LEUAE 196 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYSAE 201 " --> pdb=" O ASPAE 197 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HISAE 202 " --> pdb=" O GLNAE 198 " (cutoff:3.500A) Processing helix chain 'AE' and resid 206 through 223 removed outlier: 3.672A pdb=" N ILEAE 218 " --> pdb=" O THRAE 214 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASNAE 219 " --> pdb=" O CYSAE 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHEAE 223 " --> pdb=" O ASNAE 219 " (cutoff:3.500A) Processing helix chain 'AE' and resid 233 through 246 removed outlier: 3.982A pdb=" N ILEAE 237 " --> pdb=" O GLNAE 233 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEUAE 238 " --> pdb=" O LEUAE 234 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEUAE 239 " --> pdb=" O VALAE 235 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLUAE 240 " --> pdb=" O PROAE 236 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEUAE 246 " --> pdb=" O SERAE 242 " (cutoff:3.500A) Processing helix chain 'AE' and resid 250 through 267 removed outlier: 3.887A pdb=" N GLNAE 254 " --> pdb=" O SERAE 250 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUAE 261 " --> pdb=" O ALAAE 257 " (cutoff:3.500A) Processing helix chain 'AE' and resid 271 through 283 removed outlier: 3.535A pdb=" N METAE 279 " --> pdb=" O ILEAE 275 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLUAE 280 " --> pdb=" O LEUAE 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THRAE 281 " --> pdb=" O ALAAE 277 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILEAE 282 " --> pdb=" O ALAAE 278 " (cutoff:3.500A) Processing helix chain 'AE' and resid 291 through 307 removed outlier: 3.847A pdb=" N THRAE 305 " --> pdb=" O LYSAE 301 " (cutoff:3.500A) Processing helix chain 'AE' and resid 308 through 310 No H-bonds generated for 'chain 'AE' and resid 308 through 310' Processing helix chain 'AE' and resid 317 through 322 Processing helix chain 'AE' and resid 328 through 339 removed outlier: 3.668A pdb=" N LEUAE 333 " --> pdb=" O THRAE 329 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHEAE 335 " --> pdb=" O SERAE 331 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAE 339 " --> pdb=" O PHEAE 335 " (cutoff:3.500A) Processing helix chain 'AE' and resid 344 through 356 Processing helix chain 'AE' and resid 363 through 373 removed outlier: 4.047A pdb=" N ILEAE 373 " --> pdb=" O LEUAE 369 " (cutoff:3.500A) Processing helix chain 'AE' and resid 379 through 389 removed outlier: 3.858A pdb=" N ILEAE 383 " --> pdb=" O GLUAE 379 " (cutoff:3.500A) Processing helix chain 'AE' and resid 395 through 408 removed outlier: 3.568A pdb=" N ILEAE 408 " --> pdb=" O PHEAE 404 " (cutoff:3.500A) Processing helix chain 'AE' and resid 413 through 420 Processing helix chain 'AF' and resid 383 through 391 removed outlier: 3.874A pdb=" N UNKAF 391 " --> pdb=" O UNKAF 387 " (cutoff:3.500A) Processing helix chain 'AF' and resid 405 through 414 Processing helix chain 'AF' and resid 425 through 433 Processing helix chain 'AF' and resid 441 through 452 Processing helix chain 'AF' and resid 469 through 479 Processing helix chain 'AF' and resid 484 through 498 Processing helix chain 'AF' and resid 499 through 512 removed outlier: 4.195A pdb=" N UNKAF 503 " --> pdb=" O UNKAF 499 " (cutoff:3.500A) Processing helix chain 'AG' and resid 819 through 829 Processing helix chain 'AG' and resid 835 through 847 removed outlier: 3.564A pdb=" N UNKAG 839 " --> pdb=" O UNKAG 835 " (cutoff:3.500A) Processing helix chain 'B1' and resid 36 through 41 removed outlier: 3.750A pdb=" N ARGB1 40 " --> pdb=" O PROB1 36 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THRB1 41 " --> pdb=" O METB1 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 36 through 41' Processing helix chain 'B1' and resid 60 through 73 removed outlier: 3.719A pdb=" N ARGB1 71 " --> pdb=" O SERB1 67 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N METB1 72 " --> pdb=" O LEUB1 68 " (cutoff:3.500A) Processing helix chain 'B1' and resid 104 through 112 removed outlier: 3.865A pdb=" N ILEB1 108 " --> pdb=" O LEUB1 104 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALAB1 111 " --> pdb=" O METB1 107 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYSB1 112 " --> pdb=" O ILEB1 108 " (cutoff:3.500A) Processing helix chain 'B1' and resid 133 through 141 removed outlier: 3.772A pdb=" N ILEB1 137 " --> pdb=" O GLUB1 133 " (cutoff:3.500A) Processing helix chain 'B1' and resid 160 through 173 removed outlier: 4.319A pdb=" N ALAB1 164 " --> pdb=" O SERB1 160 " (cutoff:3.500A) Processing helix chain 'B1' and resid 197 through 209 Processing helix chain 'B1' and resid 548 through 553 Processing helix chain 'B1' and resid 559 through 568 Processing helix chain 'B1' and resid 617 through 625 Processing helix chain 'B1' and resid 628 through 635 removed outlier: 3.805A pdb=" N ILEB1 631 " --> pdb=" O VALB1 628 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLUB1 633 " --> pdb=" O ALAB1 630 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHEB1 635 " --> pdb=" O LYSB1 632 " (cutoff:3.500A) Processing helix chain 'B1' and resid 797 through 801 Processing helix chain 'B1' and resid 954 through 961 removed outlier: 4.172A pdb=" N VALB1 958 " --> pdb=" O SERB1 954 " (cutoff:3.500A) Processing helix chain 'B1' and resid 962 through 964 No H-bonds generated for 'chain 'B1' and resid 962 through 964' Processing helix chain 'BA' and resid 179 through 183 Processing helix chain 'BA' and resid 716 through 720 removed outlier: 3.659A pdb=" N VALBA 719 " --> pdb=" O ASPBA 716 " (cutoff:3.500A) Processing helix chain 'BA' and resid 724 through 733 removed outlier: 3.668A pdb=" N GLUBA 732 " --> pdb=" O GLUBA 728 " (cutoff:3.500A) Processing helix chain 'BA' and resid 734 through 745 removed outlier: 3.782A pdb=" N LEUBA 739 " --> pdb=" O PHEBA 735 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALBA 740 " --> pdb=" O LEUBA 736 " (cutoff:3.500A) Processing helix chain 'BA' and resid 747 through 757 removed outlier: 3.909A pdb=" N ASNBA 752 " --> pdb=" O GLUBA 748 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYSBA 753 " --> pdb=" O TYRBA 749 " (cutoff:3.500A) Processing helix chain 'BA' and resid 762 through 769 Processing helix chain 'BA' and resid 774 through 786 removed outlier: 4.274A pdb=" N ILEBA 778 " --> pdb=" O TYRBA 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLYBA 783 " --> pdb=" O LEUBA 779 " (cutoff:3.500A) Processing helix chain 'BA' and resid 791 through 806 Processing helix chain 'BA' and resid 806 through 813 Processing helix chain 'BA' and resid 816 through 841 removed outlier: 3.848A pdb=" N PHEBA 827 " --> pdb=" O SERBA 823 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLUBA 834 " --> pdb=" O ARGBA 830 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASNBA 837 " --> pdb=" O LYSBA 833 " (cutoff:3.500A) Processing helix chain 'BA' and resid 844 through 852 removed outlier: 3.985A pdb=" N THRBA 852 " --> pdb=" O PHEBA 848 " (cutoff:3.500A) Processing helix chain 'BB' and resid 748 through 768 removed outlier: 3.811A pdb=" N GLYBB 765 " --> pdb=" O ALABB 761 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALABB 768 " --> pdb=" O GLUBB 764 " (cutoff:3.500A) Processing helix chain 'BB' and resid 801 through 812 removed outlier: 3.601A pdb=" N ASPBB 807 " --> pdb=" O GLNBB 803 " (cutoff:3.500A) Processing helix chain 'BB' and resid 817 through 824 removed outlier: 4.135A pdb=" N METBB 824 " --> pdb=" O ALABB 820 " (cutoff:3.500A) Processing helix chain 'BB' and resid 825 through 843 removed outlier: 4.322A pdb=" N LYSBB 834 " --> pdb=" O LEUBB 830 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHEBB 835 " --> pdb=" O LYSBB 831 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILEBB 836 " --> pdb=" O PHEBB 832 " (cutoff:3.500A) Processing helix chain 'BB' and resid 849 through 864 removed outlier: 4.042A pdb=" N PHEBB 859 " --> pdb=" O LYSBB 855 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYSBB 862 " --> pdb=" O PHEBB 858 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNBB 864 " --> pdb=" O ILEBB 860 " (cutoff:3.500A) Processing helix chain 'BB' and resid 874 through 912 removed outlier: 3.590A pdb=" N ASNBB 881 " --> pdb=" O LYSBB 877 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARGBB 882 " --> pdb=" O LEUBB 878 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THRBB 894 " --> pdb=" O ALABB 890 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLNBB 903 " --> pdb=" O GLYBB 899 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHEBB 907 " --> pdb=" O GLNBB 903 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VALBB 908 " --> pdb=" O GLYBB 904 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYSBB 909 " --> pdb=" O LEUBB 905 " (cutoff:3.500A) Processing helix chain 'BC' and resid 661 through 674 removed outlier: 3.818A pdb=" N SERBC 674 " --> pdb=" O GLNBC 670 " (cutoff:3.500A) Processing helix chain 'BC' and resid 678 through 687 Processing helix chain 'BC' and resid 690 through 703 removed outlier: 3.627A pdb=" N LEUBC 694 " --> pdb=" O HISBC 690 " (cutoff:3.500A) Processing helix chain 'BC' and resid 722 through 730 Processing helix chain 'BC' and resid 732 through 747 removed outlier: 3.633A pdb=" N ARGBC 742 " --> pdb=" O LEUBC 738 " (cutoff:3.500A) Processing helix chain 'BC' and resid 752 through 767 removed outlier: 3.544A pdb=" N ALABC 756 " --> pdb=" O THRBC 752 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THRBC 759 " --> pdb=" O ILEBC 755 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILEBC 760 " --> pdb=" O ALABC 756 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEUBC 764 " --> pdb=" O ILEBC 760 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N METBC 765 " --> pdb=" O ARGBC 761 " (cutoff:3.500A) Processing helix chain 'BC' and resid 778 through 804 removed outlier: 4.347A pdb=" N ILEBC 786 " --> pdb=" O VALBC 782 " (cutoff:3.500A) Proline residue: BC 787 - end of helix removed outlier: 4.134A pdb=" N THRBC 794 " --> pdb=" O GLNBC 790 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARGBC 795 " --> pdb=" O ARGBC 791 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VALBC 796 " --> pdb=" O HISBC 792 " (cutoff:3.500A) Processing helix chain 'BC' and resid 804 through 809 removed outlier: 3.726A pdb=" N ALABC 809 " --> pdb=" O ILEBC 805 " (cutoff:3.500A) Processing helix chain 'BD' and resid 495 through 500 removed outlier: 3.585A pdb=" N ASNBD 498 " --> pdb=" O ASPBD 495 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N METBD 500 " --> pdb=" O ASNBD 497 " (cutoff:3.500A) Processing helix chain 'BE' and resid 795 through 801 Processing helix chain 'BE' and resid 817 through 824 removed outlier: 3.690A pdb=" N LEUBE 821 " --> pdb=" O PHEBE 817 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARGBE 822 " --> pdb=" O THRBE 818 " (cutoff:3.500A) Processing helix chain 'BE' and resid 829 through 840 removed outlier: 3.980A pdb=" N LEUBE 833 " --> pdb=" O ASPBE 829 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHEBE 840 " --> pdb=" O THRBE 836 " (cutoff:3.500A) Processing helix chain 'BE' and resid 845 through 849 Processing helix chain 'BE' and resid 860 through 874 removed outlier: 3.785A pdb=" N SERBE 874 " --> pdb=" O GLNBE 870 " (cutoff:3.500A) Processing helix chain 'BE' and resid 877 through 892 removed outlier: 4.181A pdb=" N THRBE 883 " --> pdb=" O GLUBE 879 " (cutoff:3.500A) Processing helix chain 'BE' and resid 903 through 919 removed outlier: 3.879A pdb=" N SERBE 907 " --> pdb=" O GLNBE 903 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALABE 908 " --> pdb=" O ASPBE 904 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASPBE 914 " --> pdb=" O GLNBE 910 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VALBE 915 " --> pdb=" O ASNBE 911 " (cutoff:3.500A) Processing helix chain 'BE' and resid 921 through 939 removed outlier: 4.195A pdb=" N LEUBE 925 " --> pdb=" O ARGBE 921 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VALBE 926 " --> pdb=" O LEUBE 922 " (cutoff:3.500A) Processing helix chain 'CA' and resid 63 through 79 Processing helix chain 'CA' and resid 100 through 105 removed outlier: 3.783A pdb=" N SERCA 105 " --> pdb=" O SERCA 101 " (cutoff:3.500A) Processing helix chain 'CA' and resid 130 through 145 removed outlier: 3.847A pdb=" N ILECA 134 " --> pdb=" O ASPCA 130 " (cutoff:3.500A) Processing helix chain 'CA' and resid 164 through 169 Processing helix chain 'CA' and resid 170 through 173 Processing helix chain 'CA' and resid 176 through 198 removed outlier: 3.785A pdb=" N ILECA 190 " --> pdb=" O THRCA 186 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLNCA 193 " --> pdb=" O ALACA 189 " (cutoff:3.500A) Processing helix chain 'CA' and resid 200 through 208 Processing helix chain 'CA' and resid 208 through 216 removed outlier: 3.591A pdb=" N VALCA 216 " --> pdb=" O PHECA 212 " (cutoff:3.500A) Processing helix chain 'CB' and resid 82 through 96 Processing helix chain 'CB' and resid 96 through 114 Processing helix chain 'CB' and resid 117 through 137 removed outlier: 3.674A pdb=" N VALCB 121 " --> pdb=" O LYSCB 117 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHECB 127 " --> pdb=" O LYSCB 123 " (cutoff:3.500A) Processing helix chain 'CB' and resid 145 through 153 Processing helix chain 'CB' and resid 210 through 214 removed outlier: 3.545A pdb=" N LEUCB 213 " --> pdb=" O PROCB 210 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHECB 214 " --> pdb=" O LYSCB 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 210 through 214' Processing helix chain 'CB' and resid 222 through 246 Processing helix chain 'CB' and resid 247 through 250 removed outlier: 4.165A pdb=" N SERCB 250 " --> pdb=" O LYSCB 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 247 through 250' Processing helix chain 'CB' and resid 260 through 262 No H-bonds generated for 'chain 'CB' and resid 260 through 262' Processing helix chain 'CB' and resid 305 through 309 removed outlier: 3.634A pdb=" N LEUCB 309 " --> pdb=" O LYSCB 306 " (cutoff:3.500A) Processing helix chain 'CB' and resid 329 through 339 Processing helix chain 'CB' and resid 341 through 355 Processing helix chain 'CB' and resid 358 through 372 Processing helix chain 'CB' and resid 379 through 383 removed outlier: 3.508A pdb=" N SERCB 382 " --> pdb=" O METCB 379 " (cutoff:3.500A) Processing helix chain 'CB' and resid 389 through 401 Processing helix chain 'CB' and resid 417 through 432 Processing helix chain 'CB' and resid 475 through 480 removed outlier: 3.559A pdb=" N THRCB 478 " --> pdb=" O ASNCB 475 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYSCB 479 " --> pdb=" O ILECB 476 " (cutoff:3.500A) Processing helix chain 'CB' and resid 481 through 500 Processing helix chain 'CB' and resid 506 through 512 Processing helix chain 'CB' and resid 518 through 523 Processing helix chain 'CB' and resid 538 through 543 Processing helix chain 'CB' and resid 548 through 555 Processing helix chain 'CB' and resid 557 through 574 Processing helix chain 'CB' and resid 602 through 606 removed outlier: 4.368A pdb=" N GLYCB 605 " --> pdb=" O ASNCB 602 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASNCB 606 " --> pdb=" O THRCB 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 602 through 606' Processing helix chain 'CB' and resid 639 through 649 removed outlier: 3.568A pdb=" N ALACB 643 " --> pdb=" O SERCB 639 " (cutoff:3.500A) Processing helix chain 'CB' and resid 677 through 690 removed outlier: 3.690A pdb=" N VALCB 690 " --> pdb=" O LEUCB 686 " (cutoff:3.500A) Processing helix chain 'CB' and resid 698 through 707 removed outlier: 3.890A pdb=" N LYSCB 702 " --> pdb=" O ASNCB 698 " (cutoff:3.500A) Processing helix chain 'CB' and resid 724 through 742 removed outlier: 3.655A pdb=" N ILECB 740 " --> pdb=" O ASPCB 736 " (cutoff:3.500A) Processing helix chain 'CB' and resid 758 through 762 Processing helix chain 'CB' and resid 795 through 818 Processing helix chain 'CB' and resid 857 through 870 removed outlier: 4.423A pdb=" N ILECB 861 " --> pdb=" O GLUCB 857 " (cutoff:3.500A) Processing helix chain 'CB' and resid 874 through 889 removed outlier: 3.642A pdb=" N LEUCB 878 " --> pdb=" O LEUCB 874 " (cutoff:3.500A) Processing helix chain 'CB' and resid 890 through 902 removed outlier: 4.235A pdb=" N ARGCB 894 " --> pdb=" O LEUCB 890 " (cutoff:3.500A) Processing helix chain 'CB' and resid 903 through 905 No H-bonds generated for 'chain 'CB' and resid 903 through 905' Processing helix chain 'CB' and resid 908 through 923 Processing helix chain 'CB' and resid 930 through 939 Processing helix chain 'CB' and resid 939 through 944 Processing helix chain 'CB' and resid 953 through 968 Processing helix chain 'CB' and resid 1013 through 1031 removed outlier: 4.063A pdb=" N SERCB1030 " --> pdb=" O ASNCB1026 " (cutoff:3.500A) Processing helix chain 'CB' and resid 1057 through 1078 removed outlier: 3.627A pdb=" N ALACB1061 " --> pdb=" O PROCB1057 " (cutoff:3.500A) Processing helix chain 'CB' and resid 1081 through 1089 removed outlier: 3.567A pdb=" N ILECB1085 " --> pdb=" O ASNCB1081 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHECB1089 " --> pdb=" O ILECB1085 " (cutoff:3.500A) Processing helix chain 'CB' and resid 1109 through 1113 Processing helix chain 'CB' and resid 1135 through 1143 removed outlier: 3.569A pdb=" N SERCB1140 " --> pdb=" O ASNCB1137 " (cutoff:3.500A) Processing helix chain 'CB' and resid 1145 through 1157 Processing helix chain 'CB' and resid 1168 through 1173 removed outlier: 3.816A pdb=" N ASNCB1172 " --> pdb=" O TYRCB1168 " (cutoff:3.500A) Processing helix chain 'CB' and resid 1188 through 1191 removed outlier: 3.865A pdb=" N LYSCB1191 " --> pdb=" O PROCB1188 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 1188 through 1191' Processing helix chain 'CB' and resid 1215 through 1227 removed outlier: 3.839A pdb=" N ILECB1219 " --> pdb=" O ASNCB1215 " (cutoff:3.500A) Processing helix chain 'E1' and resid 73 through 80 removed outlier: 3.579A pdb=" N METE1 80 " --> pdb=" O LEUE1 76 " (cutoff:3.500A) Processing helix chain 'E1' and resid 83 through 87 removed outlier: 3.667A pdb=" N GLUE1 86 " --> pdb=" O ASPE1 83 " (cutoff:3.500A) Processing helix chain 'E1' and resid 88 through 101 removed outlier: 4.263A pdb=" N THRE1 92 " --> pdb=" O ARGE1 88 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASPE1 101 " --> pdb=" O LEUE1 97 " (cutoff:3.500A) Processing helix chain 'E1' and resid 102 through 107 removed outlier: 3.524A pdb=" N LYSE1 106 " --> pdb=" O SERE1 102 " (cutoff:3.500A) Processing helix chain 'E1' and resid 133 through 148 Processing helix chain 'E1' and resid 166 through 170 removed outlier: 3.648A pdb=" N ASPE1 169 " --> pdb=" O PROE1 166 " (cutoff:3.500A) Processing helix chain 'E1' and resid 188 through 195 Processing helix chain 'E1' and resid 214 through 218 removed outlier: 4.243A pdb=" N ALAE1 217 " --> pdb=" O ASPE1 214 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASPE1 218 " --> pdb=" O ASNE1 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E1' and resid 214 through 218' Processing helix chain 'E1' and resid 233 through 249 Processing helix chain 'E2' and resid 84 through 87 Processing helix chain 'E2' and resid 88 through 100 removed outlier: 4.523A pdb=" N THRE2 92 " --> pdb=" O ARGE2 88 " (cutoff:3.500A) Processing helix chain 'E2' and resid 102 through 108 removed outlier: 3.659A pdb=" N LYSE2 106 " --> pdb=" O SERE2 102 " (cutoff:3.500A) Processing helix chain 'E2' and resid 134 through 148 Processing helix chain 'E2' and resid 166 through 170 Processing helix chain 'E2' and resid 188 through 194 removed outlier: 3.789A pdb=" N TYRE2 192 " --> pdb=" O ARGE2 188 " (cutoff:3.500A) Processing helix chain 'E2' and resid 233 through 249 Processing helix chain 'K1' and resid 46 through 48 No H-bonds generated for 'chain 'K1' and resid 46 through 48' Processing helix chain 'K1' and resid 49 through 66 removed outlier: 5.232A pdb=" N ASNK1 58 " --> pdb=" O LYSK1 54 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASPK1 59 " --> pdb=" O THRK1 55 " (cutoff:3.500A) Processing helix chain 'K1' and resid 92 through 106 removed outlier: 3.939A pdb=" N LYSK1 96 " --> pdb=" O ALAK1 92 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARGK1 106 " --> pdb=" O LYSK1 102 " (cutoff:3.500A) Processing helix chain 'K1' and resid 109 through 114 Processing helix chain 'K1' and resid 115 through 118 Processing helix chain 'K1' and resid 135 through 147 Processing helix chain 'K1' and resid 148 through 150 No H-bonds generated for 'chain 'K1' and resid 148 through 150' Processing helix chain 'K1' and resid 151 through 160 Processing helix chain 'K1' and resid 176 through 191 Processing helix chain 'K1' and resid 195 through 212 removed outlier: 4.135A pdb=" N HISK1 199 " --> pdb=" O HISK1 195 " (cutoff:3.500A) Processing helix chain 'MA' and resid 30 through 36 removed outlier: 3.671A pdb=" N TYRMA 36 " --> pdb=" O VALMA 32 " (cutoff:3.500A) Processing helix chain 'MA' and resid 41 through 63 removed outlier: 4.336A pdb=" N HISMA 45 " --> pdb=" O ARGMA 41 " (cutoff:3.500A) Processing helix chain 'MA' and resid 68 through 85 removed outlier: 3.561A pdb=" N ARGMA 72 " --> pdb=" O ASPMA 68 " (cutoff:3.500A) Processing helix chain 'MA' and resid 95 through 100 removed outlier: 3.615A pdb=" N ASNMA 99 " --> pdb=" O SERMA 95 " (cutoff:3.500A) Processing helix chain 'MA' and resid 102 through 108 removed outlier: 4.009A pdb=" N ILEMA 106 " --> pdb=" O THRMA 102 " (cutoff:3.500A) Processing helix chain 'MA' and resid 110 through 118 Processing helix chain 'MA' and resid 123 through 132 Processing helix chain 'MA' and resid 154 through 156 No H-bonds generated for 'chain 'MA' and resid 154 through 156' Processing helix chain 'MB' and resid 97 through 109 removed outlier: 3.746A pdb=" N PHEMB 103 " --> pdb=" O ARGMB 99 " (cutoff:3.500A) Processing helix chain 'MB' and resid 126 through 135 Processing helix chain 'MB' and resid 199 through 210 Processing helix chain 'MC' and resid 46 through 61 Processing helix chain 'MC' and resid 430 through 454 removed outlier: 3.567A pdb=" N TYRMC 446 " --> pdb=" O ALAMC 442 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEUMC 451 " --> pdb=" O LYSMC 447 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SERMC 453 " --> pdb=" O ASPMC 449 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VALMC 454 " --> pdb=" O VALMC 450 " (cutoff:3.500A) Processing helix chain 'P1' and resid 102 through 104 No H-bonds generated for 'chain 'P1' and resid 102 through 104' Processing helix chain 'P1' and resid 105 through 111 Processing helix chain 'P1' and resid 116 through 125 Processing helix chain 'P1' and resid 149 through 164 removed outlier: 4.095A pdb=" N GLNP1 153 " --> pdb=" O PROP1 149 " (cutoff:3.500A) Processing helix chain 'P1' and resid 168 through 173 removed outlier: 3.937A pdb=" N ALAP1 173 " --> pdb=" O ASPP1 169 " (cutoff:3.500A) Processing helix chain 'P1' and resid 174 through 176 No H-bonds generated for 'chain 'P1' and resid 174 through 176' Processing helix chain 'P1' and resid 188 through 191 removed outlier: 3.699A pdb=" N LYSP1 191 " --> pdb=" O LYSP1 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'P1' and resid 188 through 191' Processing helix chain 'P1' and resid 198 through 207 Processing helix chain 'P1' and resid 210 through 220 removed outlier: 4.175A pdb=" N ALAP1 215 " --> pdb=" O LYSP1 211 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILEP1 216 " --> pdb=" O THRP1 212 " (cutoff:3.500A) Processing helix chain 'P1' and resid 237 through 252 removed outlier: 4.012A pdb=" N GLUP1 245 " --> pdb=" O ARGP1 241 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SERP1 246 " --> pdb=" O METP1 242 " (cutoff:3.500A) Processing helix chain 'P1' and resid 255 through 264 removed outlier: 3.643A pdb=" N VALP1 259 " --> pdb=" O PROP1 255 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEUP1 263 " --> pdb=" O VALP1 259 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGP1 264 " --> pdb=" O TYRP1 260 " (cutoff:3.500A) Processing helix chain 'R1' and resid 16 through 28 Processing helix chain 'R1' and resid 46 through 59 removed outlier: 3.554A pdb=" N VALR1 50 " --> pdb=" O LYSR1 46 " (cutoff:3.500A) Processing helix chain 'R1' and resid 96 through 104 Proline residue: R1 102 - end of helix Processing helix chain 'R1' and resid 129 through 137 removed outlier: 3.510A pdb=" N ILER1 133 " --> pdb=" O GLYR1 129 " (cutoff:3.500A) Processing helix chain 'R1' and resid 137 through 144 Processing helix chain 'R1' and resid 203 through 214 Processing helix chain 'R1' and resid 232 through 236 Processing helix chain 'R1' and resid 267 through 285 Processing helix chain 'R1' and resid 293 through 303 Processing helix chain 'R1' and resid 319 through 333 Processing helix chain 'SC' and resid 22 through 26 Processing helix chain 'SC' and resid 56 through 61 removed outlier: 3.789A pdb=" N ALASC 60 " --> pdb=" O SERSC 56 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEUSC 61 " --> pdb=" O ALASC 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 56 through 61' Processing helix chain 'SC' and resid 70 through 75 Processing helix chain 'SC' and resid 106 through 114 removed outlier: 3.880A pdb=" N LEUSC 110 " --> pdb=" O THRSC 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N METSC 113 " --> pdb=" O LYSSC 109 " (cutoff:3.500A) Processing helix chain 'SC' and resid 159 through 176 removed outlier: 4.019A pdb=" N VALSC 167 " --> pdb=" O ALASC 163 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THRSC 173 " --> pdb=" O SERSC 169 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYSSC 174 " --> pdb=" O GLUSC 170 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VALSC 176 " --> pdb=" O LEUSC 172 " (cutoff:3.500A) Processing helix chain 'SC' and resid 181 through 189 Processing helix chain 'SC' and resid 191 through 202 removed outlier: 4.231A pdb=" N LYSSC 195 " --> pdb=" O GLUSC 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLUSC 196 " --> pdb=" O VALSC 192 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALASC 200 " --> pdb=" O GLUSC 196 " (cutoff:3.500A) Processing helix chain 'SC' and resid 227 through 232 removed outlier: 3.529A pdb=" N ALASC 230 " --> pdb=" O ALASC 227 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEUSC 231 " --> pdb=" O LEUSC 228 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HISSC 232 " --> pdb=" O METSC 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 227 through 232' Processing helix chain 'SF' and resid 15 through 19 removed outlier: 3.587A pdb=" N TRPSF 18 " --> pdb=" O PROSF 15 " (cutoff:3.500A) Processing helix chain 'SF' and resid 44 through 49 removed outlier: 3.915A pdb=" N ARGSF 49 " --> pdb=" O ILESF 45 " (cutoff:3.500A) Processing helix chain 'SF' and resid 58 through 66 removed outlier: 3.844A pdb=" N LYSSF 62 " --> pdb=" O GLYSF 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALASF 63 " --> pdb=" O ARGSF 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILESF 64 " --> pdb=" O GLUSF 60 " (cutoff:3.500A) Processing helix chain 'SF' and resid 117 through 121 removed outlier: 3.881A pdb=" N TYRSF 121 " --> pdb=" O GLUSF 118 " (cutoff:3.500A) Processing helix chain 'SF' and resid 133 through 135 No H-bonds generated for 'chain 'SF' and resid 133 through 135' Processing helix chain 'SG' and resid 30 through 36 removed outlier: 3.872A pdb=" N ALASG 36 " --> pdb=" O GLUSG 32 " (cutoff:3.500A) Processing helix chain 'SG' and resid 83 through 87 removed outlier: 3.754A pdb=" N CYSSG 87 " --> pdb=" O LYSSG 84 " (cutoff:3.500A) Processing helix chain 'SG' and resid 88 through 96 Processing helix chain 'SG' and resid 106 through 124 removed outlier: 3.583A pdb=" N ALASG 110 " --> pdb=" O LYSSG 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILESG 114 " --> pdb=" O ALASG 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HISSG 116 " --> pdb=" O ARGSG 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASPSG 119 " --> pdb=" O LYSSG 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASNSG 122 " --> pdb=" O LEUSG 118 " (cutoff:3.500A) Processing helix chain 'SG' and resid 129 through 139 removed outlier: 3.517A pdb=" N VALSG 134 " --> pdb=" O ILESG 130 " (cutoff:3.500A) Processing helix chain 'SG' and resid 163 through 183 removed outlier: 3.657A pdb=" N ALASG 171 " --> pdb=" O ARGSG 167 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEUSG 175 " --> pdb=" O ALASG 171 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARGSG 180 " --> pdb=" O THRSG 176 " (cutoff:3.500A) Processing helix chain 'SG' and resid 189 through 203 Processing helix chain 'SG' and resid 208 through 222 removed outlier: 3.981A pdb=" N LYSSG 212 " --> pdb=" O SERSG 208 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYSSG 213 " --> pdb=" O TYRSG 209 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VALSG 220 " --> pdb=" O GLUSG 216 " (cutoff:3.500A) Processing helix chain 'SI' and resid 14 through 28 removed outlier: 3.508A pdb=" N ALASI 23 " --> pdb=" O GLNSI 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLUSI 26 " --> pdb=" O GLNSI 22 " (cutoff:3.500A) Processing helix chain 'SI' and resid 30 through 35 Processing helix chain 'SI' and resid 66 through 72 removed outlier: 3.738A pdb=" N LYSSI 72 " --> pdb=" O ALASI 68 " (cutoff:3.500A) Processing helix chain 'SI' and resid 73 through 81 removed outlier: 4.255A pdb=" N ARGSI 79 " --> pdb=" O THRSI 75 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLUSI 80 " --> pdb=" O LYSSI 76 " (cutoff:3.500A) Processing helix chain 'SI' and resid 119 through 130 removed outlier: 3.632A pdb=" N VALSI 130 " --> pdb=" O LEUSI 126 " (cutoff:3.500A) Processing helix chain 'SI' and resid 159 through 164 removed outlier: 4.695A pdb=" N TYRSI 164 " --> pdb=" O GLNSI 160 " (cutoff:3.500A) Processing helix chain 'SI' and resid 165 through 177 removed outlier: 3.605A pdb=" N ALASI 171 " --> pdb=" O GLUSI 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VALSI 172 " --> pdb=" O SERSI 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYRSI 173 " --> pdb=" O PHESI 169 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 88 through 94 Processing helix chain 'SJ' and resid 106 through 117 removed outlier: 3.612A pdb=" N ARGSJ 110 " --> pdb=" O ALASJ 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALASJ 115 " --> pdb=" O GLNSJ 111 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 154 through 163 removed outlier: 3.778A pdb=" N SERSJ 161 " --> pdb=" O GLUSJ 157 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALASJ 162 " --> pdb=" O SERSJ 158 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 186 through 198 Processing helix chain 'SK' and resid 20 through 34 removed outlier: 3.693A pdb=" N ALASK 26 " --> pdb=" O SERSK 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEUSK 28 " --> pdb=" O LEUSK 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEUSK 30 " --> pdb=" O ALASK 26 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLUSK 33 " --> pdb=" O LYSSK 29 " (cutoff:3.500A) Processing helix chain 'SK' and resid 39 through 59 removed outlier: 4.643A pdb=" N ILESK 45 " --> pdb=" O GLUSK 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALASK 55 " --> pdb=" O LYSSK 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEUSK 59 " --> pdb=" O ALASK 55 " (cutoff:3.500A) Processing helix chain 'SK' and resid 66 through 83 removed outlier: 3.519A pdb=" N GLYSK 73 " --> pdb=" O ARGSK 69 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALASK 75 " --> pdb=" O PHESK 71 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEUSK 76 " --> pdb=" O GLUSK 72 " (cutoff:3.500A) Processing helix chain 'SK' and resid 87 through 91 removed outlier: 3.589A pdb=" N LYSSK 91 " --> pdb=" O GLUSK 88 " (cutoff:3.500A) Processing helix chain 'SK' and resid 101 through 107 removed outlier: 3.539A pdb=" N LEUSK 105 " --> pdb=" O VALSK 101 " (cutoff:3.500A) Processing helix chain 'SK' and resid 108 through 116 removed outlier: 3.729A pdb=" N VALSK 113 " --> pdb=" O LEUSK 109 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYRSK 114 " --> pdb=" O GLNSK 110 " (cutoff:3.500A) Processing helix chain 'SK' and resid 123 through 130 removed outlier: 3.759A pdb=" N THRSK 130 " --> pdb=" O ARGSK 126 " (cutoff:3.500A) Processing helix chain 'SK' and resid 152 through 156 removed outlier: 3.608A pdb=" N HISSK 155 " --> pdb=" O SERSK 152 " (cutoff:3.500A) Processing helix chain 'SK' and resid 172 through 184 removed outlier: 3.702A pdb=" N LYSSK 180 " --> pdb=" O ASNSK 176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALASK 181 " --> pdb=" O ALASK 177 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLUSK 182 " --> pdb=" O ALASK 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALASK 183 " --> pdb=" O ARGSK 179 " (cutoff:3.500A) Processing helix chain 'SM' and resid 45 through 50 removed outlier: 4.322A pdb=" N ILESM 49 " --> pdb=" O PROSM 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLUSM 50 " --> pdb=" O LYSSM 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SM' and resid 45 through 50' Processing helix chain 'SO' and resid 29 through 44 removed outlier: 3.584A pdb=" N VALSO 33 " --> pdb=" O SERSO 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLNSO 36 " --> pdb=" O SERSO 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALSO 38 " --> pdb=" O ILESO 34 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLYSO 44 " --> pdb=" O TYRSO 40 " (cutoff:3.500A) Processing helix chain 'SO' and resid 46 through 58 removed outlier: 3.677A pdb=" N GLYSO 51 " --> pdb=" O PROSO 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARGSO 55 " --> pdb=" O GLYSO 51 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASPSO 56 " --> pdb=" O VALSO 52 " (cutoff:3.500A) Processing helix chain 'SO' and resid 62 through 67 removed outlier: 3.782A pdb=" N ILESO 66 " --> pdb=" O GLNSO 62 " (cutoff:3.500A) Processing helix chain 'SO' and resid 70 through 78 Processing helix chain 'SO' and resid 85 through 105 removed outlier: 3.874A pdb=" N TYRSO 90 " --> pdb=" O GLUSO 86 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEUSO 91 " --> pdb=" O ASPSO 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARGSO 104 " --> pdb=" O LYSSO 100 " (cutoff:3.500A) Processing helix chain 'SO' and resid 108 through 132 removed outlier: 3.621A pdb=" N LYSSO 112 " --> pdb=" O ASPSO 108 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHESO 113 " --> pdb=" O LYSSO 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARGSO 114 " --> pdb=" O ASPSO 110 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILESO 116 " --> pdb=" O LYSSO 112 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEUSO 117 " --> pdb=" O PHESO 113 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARGSO 121 " --> pdb=" O LEUSO 117 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYRSO 128 " --> pdb=" O ARGSO 124 " (cutoff:3.500A) Processing helix chain 'SP' and resid 43 through 48 removed outlier: 4.113A pdb=" N VALSP 48 " --> pdb=" O GLYSP 45 " (cutoff:3.500A) Processing helix chain 'SP' and resid 56 through 75 removed outlier: 3.512A pdb=" N CYSSP 71 " --> pdb=" O VALSP 67 " (cutoff:3.500A) Processing helix chain 'SP' and resid 95 through 97 No H-bonds generated for 'chain 'SP' and resid 95 through 97' Processing helix chain 'SP' and resid 98 through 108 Processing helix chain 'SR' and resid 37 through 39 No H-bonds generated for 'chain 'SR' and resid 37 through 39' Processing helix chain 'SR' and resid 45 through 54 Proline residue: SR 51 - end of helix Processing helix chain 'SR' and resid 75 through 94 Processing helix chain 'SR' and resid 98 through 112 removed outlier: 3.803A pdb=" N LYSSR 102 " --> pdb=" O ASPSR 98 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SERSR 111 " --> pdb=" O LYSSR 107 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYRSR 112 " --> pdb=" O ALASR 108 " (cutoff:3.500A) Processing helix chain 'SX' and resid 5 through 13 Processing helix chain 'SX' and resid 13 through 20 removed outlier: 3.622A pdb=" N ALASX 17 " --> pdb=" O ALASX 13 " (cutoff:3.500A) Processing helix chain 'SX' and resid 31 through 45 removed outlier: 3.862A pdb=" N VALSX 40 " --> pdb=" O LYSSX 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N METSX 41 " --> pdb=" O PHESX 37 " (cutoff:3.500A) Processing helix chain 'SX' and resid 82 through 84 No H-bonds generated for 'chain 'SX' and resid 82 through 84' Processing helix chain 'SX' and resid 85 through 93 removed outlier: 3.524A pdb=" N ALASX 91 " --> pdb=" O GLUSX 87 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEUSX 93 " --> pdb=" O TRPSX 89 " (cutoff:3.500A) Processing helix chain 'SX' and resid 113 through 120 removed outlier: 3.901A pdb=" N ARGSX 118 " --> pdb=" O GLUSX 114 " (cutoff:3.500A) Processing helix chain 'SY' and resid 92 through 96 removed outlier: 3.501A pdb=" N VALSY 96 " --> pdb=" O LEUSY 93 " (cutoff:3.500A) Processing helix chain 'SY' and resid 131 through 138 removed outlier: 3.689A pdb=" N LEUSY 135 " --> pdb=" O SERSY 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLUSY 138 " --> pdb=" O ALASY 134 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 37 through 44 removed outlier: 3.751A pdb=" N ARGSZ 41 " --> pdb=" O LYSSZ 37 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 78 through 86 removed outlier: 3.597A pdb=" N ALASZ 82 " --> pdb=" O SERSZ 78 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLUSZ 86 " --> pdb=" O ALASZ 82 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 87 through 95 removed outlier: 3.564A pdb=" N LEUSZ 91 " --> pdb=" O PROSZ 87 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALSZ 92 " --> pdb=" O THRSZ 88 " (cutoff:3.500A) Processing helix chain 'Sc' and resid 11 through 17 removed outlier: 3.879A pdb=" N ARGSc 17 " --> pdb=" O ALASc 13 " (cutoff:3.500A) Processing helix chain 'Sf' and resid 32 through 52 removed outlier: 3.951A pdb=" N LYSSf 36 " --> pdb=" O GLYSf 32 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEUSf 38 " --> pdb=" O ALASf 34 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEUSf 49 " --> pdb=" O VALSf 45 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VALSf 50 " --> pdb=" O ASNSf 46 " (cutoff:3.500A) Processing helix chain 'U2' and resid 3 through 26 removed outlier: 3.698A pdb=" N UNKU2 8 " --> pdb=" O UNKU2 4 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N UNKU2 11 " --> pdb=" O UNKU2 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNKU2 15 " --> pdb=" O UNKU2 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNKU2 16 " --> pdb=" O UNKU2 12 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N UNKU2 18 " --> pdb=" O UNKU2 14 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N UNKU2 19 " --> pdb=" O UNKU2 15 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N UNKU2 22 " --> pdb=" O UNKU2 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNKU2 26 " --> pdb=" O UNKU2 22 " (cutoff:3.500A) Processing helix chain 'U2' and resid 27 through 49 removed outlier: 3.878A pdb=" N UNKU2 32 " --> pdb=" O UNKU2 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N UNKU2 40 " --> pdb=" O UNKU2 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNKU2 47 " --> pdb=" O UNKU2 43 " (cutoff:3.500A) Processing helix chain 'U2' and resid 50 through 59 removed outlier: 3.800A pdb=" N UNKU2 56 " --> pdb=" O UNKU2 52 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N UNKU2 57 " --> pdb=" O UNKU2 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNKU2 59 " --> pdb=" O UNKU2 55 " (cutoff:3.500A) Processing helix chain 'U2' and resid 63 through 72 removed outlier: 3.790A pdb=" N UNKU2 72 " --> pdb=" O UNKU2 68 " (cutoff:3.500A) Processing helix chain 'U4' and resid 68 through 76 removed outlier: 4.214A pdb=" N ILEU4 72 " --> pdb=" O ASPU4 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASNU4 73 " --> pdb=" O THRU4 69 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHEU4 74 " --> pdb=" O ASNU4 70 " (cutoff:3.500A) Processing helix chain 'U4' and resid 77 through 79 No H-bonds generated for 'chain 'U4' and resid 77 through 79' Processing helix chain 'U4' and resid 82 through 91 removed outlier: 3.616A pdb=" N ASPU4 88 " --> pdb=" O ARGU4 84 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYSU4 89 " --> pdb=" O GLYU4 85 " (cutoff:3.500A) Processing helix chain 'U4' and resid 99 through 107 removed outlier: 3.609A pdb=" N GLUU4 105 " --> pdb=" O CYSU4 101 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEUU4 106 " --> pdb=" O VALU4 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLUU4 107 " --> pdb=" O METU4 103 " (cutoff:3.500A) Processing helix chain 'U4' and resid 109 through 112 Processing helix chain 'U4' and resid 113 through 121 removed outlier: 3.539A pdb=" N LEUU4 117 " --> pdb=" O TYRU4 113 " (cutoff:3.500A) Processing helix chain 'U4' and resid 136 through 147 removed outlier: 3.841A pdb=" N LEUU4 141 " --> pdb=" O ALAU4 137 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VALU4 142 " --> pdb=" O ASPU4 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HISU4 143 " --> pdb=" O ASPU4 139 " (cutoff:3.500A) Processing helix chain 'U4' and resid 157 through 162 Processing helix chain 'U5' and resid 12 through 23 removed outlier: 3.596A pdb=" N ALAU5 16 " --> pdb=" O LEUU5 12 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILEU5 21 " --> pdb=" O LEUU5 17 " (cutoff:3.500A) Processing helix chain 'U5' and resid 65 through 69 Processing helix chain 'U5' and resid 80 through 87 removed outlier: 3.863A pdb=" N LEUU5 87 " --> pdb=" O TYRU5 83 " (cutoff:3.500A) Processing helix chain 'U5' and resid 107 through 112 Processing helix chain 'U5' and resid 114 through 119 removed outlier: 3.845A pdb=" N TYRU5 119 " --> pdb=" O LEUU5 115 " (cutoff:3.500A) Processing helix chain 'U5' and resid 134 through 139 Processing helix chain 'U5' and resid 139 through 146 Processing helix chain 'U5' and resid 176 through 184 removed outlier: 3.652A pdb=" N CYSU5 184 " --> pdb=" O LEUU5 180 " (cutoff:3.500A) Processing helix chain 'U5' and resid 208 through 223 removed outlier: 3.806A pdb=" N ILEU5 212 " --> pdb=" O SERU5 208 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILEU5 220 " --> pdb=" O ILEU5 216 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEUU5 223 " --> pdb=" O THRU5 219 " (cutoff:3.500A) Processing helix chain 'UA' and resid 102 through 121 removed outlier: 3.890A pdb=" N UNKUA 106 " --> pdb=" O UNKUA 102 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N UNKUA 110 " --> pdb=" O UNKUA 106 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N UNKUA 112 " --> pdb=" O UNKUA 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNKUA 119 " --> pdb=" O UNKUA 115 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNKUA 121 " --> pdb=" O UNKUA 117 " (cutoff:3.500A) Processing helix chain 'UA' and resid 203 through 220 removed outlier: 3.588A pdb=" N UNKUA 210 " --> pdb=" O UNKUA 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N UNKUA 216 " --> pdb=" O UNKUA 212 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N UNKUA 219 " --> pdb=" O UNKUA 215 " (cutoff:3.500A) Processing helix chain 'UA' and resid 304 through 325 removed outlier: 3.782A pdb=" N UNKUA 310 " --> pdb=" O UNKUA 306 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNKUA 318 " --> pdb=" O UNKUA 314 " (cutoff:3.500A) Processing helix chain 'UA' and resid 326 through 330 Processing helix chain 'UA' and resid 402 through 424 removed outlier: 3.946A pdb=" N UNKUA 407 " --> pdb=" O UNKUA 403 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N UNKUA 408 " --> pdb=" O UNKUA 404 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N UNKUA 410 " --> pdb=" O UNKUA 406 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N UNKUA 412 " --> pdb=" O UNKUA 408 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N UNKUA 421 " --> pdb=" O UNKUA 417 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNKUA 422 " --> pdb=" O UNKUA 418 " (cutoff:3.500A) Processing helix chain 'UA' and resid 507 through 515 removed outlier: 3.668A pdb=" N UNKUA 513 " --> pdb=" O UNKUA 509 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N UNKUA 515 " --> pdb=" O UNKUA 511 " (cutoff:3.500A) Processing helix chain 'UA' and resid 602 through 614 removed outlier: 3.778A pdb=" N UNKUA 614 " --> pdb=" O UNKUA 610 " (cutoff:3.500A) Processing helix chain 'UA' and resid 703 through 715 removed outlier: 3.516A pdb=" N UNKUA 710 " --> pdb=" O UNKUA 706 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNKUA 712 " --> pdb=" O UNKUA 708 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N UNKUA 713 " --> pdb=" O UNKUA 709 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N UNKUA 715 " --> pdb=" O UNKUA 711 " (cutoff:3.500A) Processing helix chain 'UA' and resid 802 through 815 removed outlier: 3.522A pdb=" N UNKUA 812 " --> pdb=" O UNKUA 808 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N UNKUA 814 " --> pdb=" O UNKUA 810 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N UNKUA 815 " --> pdb=" O UNKUA 811 " (cutoff:3.500A) Processing helix chain 'UA' and resid 905 through 932 removed outlier: 3.601A pdb=" N UNKUA 918 " --> pdb=" O UNKUA 914 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNKUA 921 " --> pdb=" O UNKUA 917 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N UNKUA 922 " --> pdb=" O UNKUA 918 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNKUA 932 " --> pdb=" O UNKUA 928 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1002 through 1027 removed outlier: 3.508A pdb=" N UNKUA1006 " --> pdb=" O UNKUA1002 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N UNKUA1007 " --> pdb=" O UNKUA1003 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNKUA1008 " --> pdb=" O UNKUA1004 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N UNKUA1021 " --> pdb=" O UNKUA1017 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNKUA1022 " --> pdb=" O UNKUA1018 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N UNKUA1024 " --> pdb=" O UNKUA1020 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1107 through 1129 removed outlier: 3.501A pdb=" N UNKUA1117 " --> pdb=" O UNKUA1113 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N UNKUA1122 " --> pdb=" O UNKUA1118 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N UNKUA1126 " --> pdb=" O UNKUA1122 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNKUA1129 " --> pdb=" O UNKUA1125 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1202 through 1217 removed outlier: 3.832A pdb=" N UNKUA1207 " --> pdb=" O UNKUA1203 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNKUA1215 " --> pdb=" O UNKUA1211 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1307 through 1323 removed outlier: 3.567A pdb=" N UNKUA1311 " --> pdb=" O UNKUA1307 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNKUA1317 " --> pdb=" O UNKUA1313 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNKUA1323 " --> pdb=" O UNKUA1319 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1402 through 1418 removed outlier: 3.564A pdb=" N UNKUA1406 " --> pdb=" O UNKUA1402 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNKUA1409 " --> pdb=" O UNKUA1405 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N UNKUA1411 " --> pdb=" O UNKUA1407 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N UNKUA1412 " --> pdb=" O UNKUA1408 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N UNKUA1414 " --> pdb=" O UNKUA1410 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1505 through 1521 removed outlier: 4.048A pdb=" N UNKUA1510 " --> pdb=" O UNKUA1506 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N UNKUA1514 " --> pdb=" O UNKUA1510 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N UNKUA1518 " --> pdb=" O UNKUA1514 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N UNKUA1519 " --> pdb=" O UNKUA1515 " (cutoff:3.500A) Processing helix chain 'UA' and resid 1604 through 1615 Processing helix chain 'UB' and resid 17 through 30 removed outlier: 3.827A pdb=" N UNKUB 22 " --> pdb=" O UNKUB 18 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N UNKUB 23 " --> pdb=" O UNKUB 19 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N UNKUB 25 " --> pdb=" O UNKUB 21 " (cutoff:3.500A) Processing helix chain 'UB' and resid 61 through 66 removed outlier: 4.369A pdb=" N UNKUB 66 " --> pdb=" O UNKUB 62 " (cutoff:3.500A) Processing helix chain 'UB' and resid 70 through 78 removed outlier: 3.774A pdb=" N UNKUB 74 " --> pdb=" O UNKUB 70 " (cutoff:3.500A) Processing helix chain 'UB' and resid 89 through 99 Processing helix chain 'UB' and resid 107 through 113 Processing helix chain 'UB' and resid 157 through 166 removed outlier: 3.527A pdb=" N UNKUB 162 " --> pdb=" O UNKUB 158 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNKUB 163 " --> pdb=" O UNKUB 159 " (cutoff:3.500A) Processing helix chain 'UB' and resid 179 through 196 removed outlier: 3.635A pdb=" N UNKUB 185 " --> pdb=" O UNKUB 181 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N UNKUB 189 " --> pdb=" O UNKUB 185 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N UNKUB 191 " --> pdb=" O UNKUB 187 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N UNKUB 196 " --> pdb=" O UNKUB 192 " (cutoff:3.500A) Processing helix chain 'UB' and resid 210 through 215 removed outlier: 4.220A pdb=" N UNKUB 215 " --> pdb=" O UNKUB 211 " (cutoff:3.500A) Processing helix chain 'UB' and resid 230 through 245 removed outlier: 3.589A pdb=" N UNKUB 234 " --> pdb=" O UNKUB 230 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N UNKUB 235 " --> pdb=" O UNKUB 231 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N UNKUB 239 " --> pdb=" O UNKUB 235 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N UNKUB 241 " --> pdb=" O UNKUB 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N UNKUB 245 " --> pdb=" O UNKUB 241 " (cutoff:3.500A) Processing helix chain 'UB' and resid 267 through 273 Processing helix chain 'UB' and resid 282 through 299 removed outlier: 3.986A pdb=" N UNKUB 286 " --> pdb=" O UNKUB 282 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N UNKUB 287 " --> pdb=" O UNKUB 283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N UNKUB 291 " --> pdb=" O UNKUB 287 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNKUB 293 " --> pdb=" O UNKUB 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N UNKUB 296 " --> pdb=" O UNKUB 292 " (cutoff:3.500A) Processing helix chain 'UB' and resid 311 through 316 removed outlier: 3.549A pdb=" N UNKUB 315 " --> pdb=" O UNKUB 311 " (cutoff:3.500A) Processing helix chain 'UB' and resid 317 through 326 Processing helix chain 'UB' and resid 338 through 348 removed outlier: 3.704A pdb=" N UNKUB 344 " --> pdb=" O UNKUB 340 " (cutoff:3.500A) Processing helix chain 'UB' and resid 361 through 371 removed outlier: 3.916A pdb=" N UNKUB 368 " --> pdb=" O UNKUB 364 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N UNKUB 369 " --> pdb=" O UNKUB 365 " (cutoff:3.500A) Processing helix chain 'UB' and resid 395 through 400 Processing helix chain 'UB' and resid 403 through 408 removed outlier: 3.743A pdb=" N UNKUB 408 " --> pdb=" O UNKUB 404 " (cutoff:3.500A) Processing helix chain 'UB' and resid 434 through 444 removed outlier: 3.578A pdb=" N UNKUB 439 " --> pdb=" O UNKUB 435 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N UNKUB 444 " --> pdb=" O UNKUB 440 " (cutoff:3.500A) Processing helix chain 'UB' and resid 457 through 460 Processing helix chain 'UB' and resid 461 through 468 Processing helix chain 'UB' and resid 468 through 473 Processing helix chain 'UB' and resid 480 through 491 removed outlier: 3.883A pdb=" N UNKUB 486 " --> pdb=" O UNKUB 482 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N UNKUB 489 " --> pdb=" O UNKUB 485 " (cutoff:3.500A) Processing helix chain 'UB' and resid 504 through 516 removed outlier: 3.521A pdb=" N UNKUB 510 " --> pdb=" O UNKUB 506 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N UNKUB 511 " --> pdb=" O UNKUB 507 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N UNKUB 513 " --> pdb=" O UNKUB 509 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNKUB 514 " --> pdb=" O UNKUB 510 " (cutoff:3.500A) Processing helix chain 'UB' and resid 531 through 542 removed outlier: 3.596A pdb=" N UNKUB 536 " --> pdb=" O UNKUB 532 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N UNKUB 539 " --> pdb=" O UNKUB 535 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N UNKUB 540 " --> pdb=" O UNKUB 536 " (cutoff:3.500A) Processing helix chain 'UB' and resid 561 through 575 removed outlier: 3.792A pdb=" N UNKUB 567 " --> pdb=" O UNKUB 563 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N UNKUB 568 " --> pdb=" O UNKUB 564 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNKUB 575 " --> pdb=" O UNKUB 571 " (cutoff:3.500A) Processing helix chain 'UB' and resid 601 through 616 removed outlier: 3.620A pdb=" N UNKUB 605 " --> pdb=" O UNKUB 601 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N UNKUB 606 " --> pdb=" O UNKUB 602 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N UNKUB 607 " --> pdb=" O UNKUB 603 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNKUB 611 " --> pdb=" O UNKUB 607 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNKUB 612 " --> pdb=" O UNKUB 608 " (cutoff:3.500A) Processing helix chain 'UB' and resid 635 through 640 removed outlier: 3.506A pdb=" N UNKUB 640 " --> pdb=" O UNKUB 636 " (cutoff:3.500A) Processing helix chain 'UB' and resid 646 through 657 removed outlier: 3.666A pdb=" N UNKUB 652 " --> pdb=" O UNKUB 648 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N UNKUB 653 " --> pdb=" O UNKUB 649 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N UNKUB 657 " --> pdb=" O UNKUB 653 " (cutoff:3.500A) Processing helix chain 'UB' and resid 666 through 683 removed outlier: 3.504A pdb=" N UNKUB 676 " --> pdb=" O UNKUB 672 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N UNKUB 677 " --> pdb=" O UNKUB 673 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N UNKUB 679 " --> pdb=" O UNKUB 675 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N UNKUB 683 " --> pdb=" O UNKUB 679 " (cutoff:3.500A) Processing helix chain 'UB' and resid 693 through 698 removed outlier: 4.119A pdb=" N UNKUB 698 " --> pdb=" O UNKUB 694 " (cutoff:3.500A) Processing helix chain 'UB' and resid 699 through 703 Processing helix chain 'UB' and resid 729 through 741 removed outlier: 4.036A pdb=" N UNKUB 733 " --> pdb=" O UNKUB 729 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N UNKUB 741 " --> pdb=" O UNKUB 737 " (cutoff:3.500A) Processing helix chain 'UB' and resid 768 through 773 removed outlier: 3.612A pdb=" N UNKUB 773 " --> pdb=" O UNKUB 769 " (cutoff:3.500A) Processing helix chain 'UB' and resid 817 through 826 removed outlier: 3.843A pdb=" N UNKUB 821 " --> pdb=" O UNKUB 817 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N UNKUB 825 " --> pdb=" O UNKUB 821 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNKUB 826 " --> pdb=" O UNKUB 822 " (cutoff:3.500A) Processing helix chain 'UB' and resid 922 through 938 removed outlier: 4.184A pdb=" N UNKUB 926 " --> pdb=" O UNKUB 922 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N UNKUB 927 " --> pdb=" O UNKUB 923 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNKUB 931 " --> pdb=" O UNKUB 927 " (cutoff:3.500A) Processing helix chain 'UB' and resid 967 through 974 removed outlier: 4.247A pdb=" N UNKUB 971 " --> pdb=" O UNKUB 967 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N UNKUB 972 " --> pdb=" O UNKUB 968 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N UNKUB 974 " --> pdb=" O UNKUB 970 " (cutoff:3.500A) Processing helix chain 'UC' and resid 2 through 11 removed outlier: 4.048A pdb=" N UNKUC 7 " --> pdb=" O UNKUC 3 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N UNKUC 8 " --> pdb=" O UNKUC 4 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNKUC 11 " --> pdb=" O UNKUC 7 " (cutoff:3.500A) Processing helix chain 'UC' and resid 25 through 43 removed outlier: 3.837A pdb=" N UNKUC 29 " --> pdb=" O UNKUC 25 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N UNKUC 30 " --> pdb=" O UNKUC 26 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N UNKUC 33 " --> pdb=" O UNKUC 29 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N UNKUC 35 " --> pdb=" O UNKUC 31 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N UNKUC 39 " --> pdb=" O UNKUC 35 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N UNKUC 40 " --> pdb=" O UNKUC 36 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N UNKUC 42 " --> pdb=" O UNKUC 38 " (cutoff:3.500A) Processing helix chain 'UC' and resid 52 through 61 removed outlier: 3.909A pdb=" N UNKUC 57 " --> pdb=" O UNKUC 53 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N UNKUC 58 " --> pdb=" O UNKUC 54 " (cutoff:3.500A) Processing helix chain 'UC' and resid 141 through 157 removed outlier: 3.798A pdb=" N UNKUC 145 " --> pdb=" O UNKUC 141 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N UNKUC 146 " --> pdb=" O UNKUC 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNKUC 148 " --> pdb=" O UNKUC 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNKUC 149 " --> pdb=" O UNKUC 145 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N UNKUC 150 " --> pdb=" O UNKUC 146 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N UNKUC 153 " --> pdb=" O UNKUC 149 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N UNKUC 154 " --> pdb=" O UNKUC 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N UNKUC 156 " --> pdb=" O UNKUC 152 " (cutoff:3.500A) Processing helix chain 'UC' and resid 161 through 169 removed outlier: 5.035A pdb=" N UNKUC 167 " --> pdb=" O UNKUC 163 " (cutoff:3.500A) Processing helix chain 'UC' and resid 175 through 178 Processing helix chain 'UC' and resid 179 through 187 removed outlier: 3.547A pdb=" N UNKUC 183 " --> pdb=" O UNKUC 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNKUC 184 " --> pdb=" O UNKUC 180 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N UNKUC 185 " --> pdb=" O UNKUC 181 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N UNKUC 186 " --> pdb=" O UNKUC 182 " (cutoff:3.500A) Processing helix chain 'UC' and resid 189 through 200 removed outlier: 3.530A pdb=" N UNKUC 194 " --> pdb=" O UNKUC 190 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N UNKUC 195 " --> pdb=" O UNKUC 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N UNKUC 200 " --> pdb=" O UNKUC 196 " (cutoff:3.500A) Processing helix chain 'UC' and resid 216 through 230 removed outlier: 3.859A pdb=" N UNKUC 220 " --> pdb=" O UNKUC 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNKUC 227 " --> pdb=" O UNKUC 223 " (cutoff:3.500A) Processing helix chain 'UC' and resid 234 through 237 Processing helix chain 'UC' and resid 238 through 247 removed outlier: 3.516A pdb=" N UNKUC 244 " --> pdb=" O UNKUC 240 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNKUC 245 " --> pdb=" O UNKUC 241 " (cutoff:3.500A) Processing helix chain 'UC' and resid 249 through 264 removed outlier: 4.199A pdb=" N UNKUC 262 " --> pdb=" O UNKUC 258 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N UNKUC 263 " --> pdb=" O UNKUC 259 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNKUC 264 " --> pdb=" O UNKUC 260 " (cutoff:3.500A) Processing helix chain 'UC' and resid 276 through 300 removed outlier: 3.690A pdb=" N UNKUC 281 " --> pdb=" O UNKUC 277 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNKUC 282 " --> pdb=" O UNKUC 278 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNKUC 292 " --> pdb=" O UNKUC 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNKUC 296 " --> pdb=" O UNKUC 292 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNKUC 298 " --> pdb=" O UNKUC 294 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N UNKUC 300 " --> pdb=" O UNKUC 296 " (cutoff:3.500A) Processing helix chain 'UC' and resid 306 through 324 removed outlier: 3.936A pdb=" N UNKUC 311 " --> pdb=" O UNKUC 307 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N UNKUC 319 " --> pdb=" O UNKUC 315 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N UNKUC 322 " --> pdb=" O UNKUC 318 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N UNKUC 324 " --> pdb=" O UNKUC 320 " (cutoff:3.500A) Processing helix chain 'UC' and resid 331 through 342 removed outlier: 3.787A pdb=" N UNKUC 335 " --> pdb=" O UNKUC 331 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNKUC 337 " --> pdb=" O UNKUC 333 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNKUC 342 " --> pdb=" O UNKUC 338 " (cutoff:3.500A) Processing helix chain 'UC' and resid 343 through 351 removed outlier: 3.664A pdb=" N UNKUC 350 " --> pdb=" O UNKUC 346 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N UNKUC 351 " --> pdb=" O UNKUC 347 " (cutoff:3.500A) Processing helix chain 'UC' and resid 352 through 361 removed outlier: 3.605A pdb=" N UNKUC 361 " --> pdb=" O UNKUC 357 " (cutoff:3.500A) Processing helix chain 'UC' and resid 382 through 385 removed outlier: 4.070A pdb=" N UNKUC 385 " --> pdb=" O UNKUC 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'UC' and resid 382 through 385' Processing helix chain 'UC' and resid 386 through 397 removed outlier: 3.648A pdb=" N UNKUC 395 " --> pdb=" O UNKUC 391 " (cutoff:3.500A) Processing helix chain 'UC' and resid 408 through 431 removed outlier: 4.555A pdb=" N UNKUC 414 " --> pdb=" O UNKUC 410 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNKUC 415 " --> pdb=" O UNKUC 411 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N UNKUC 418 " --> pdb=" O UNKUC 414 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNKUC 424 " --> pdb=" O UNKUC 420 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N UNKUC 425 " --> pdb=" O UNKUC 421 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N UNKUC 426 " --> pdb=" O UNKUC 422 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNKUC 427 " --> pdb=" O UNKUC 423 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N UNKUC 429 " --> pdb=" O UNKUC 425 " (cutoff:3.500A) Processing helix chain 'UC' and resid 439 through 443 removed outlier: 3.513A pdb=" N UNKUC 443 " --> pdb=" O UNKUC 440 " (cutoff:3.500A) Processing helix chain 'UC' and resid 457 through 469 removed outlier: 4.408A pdb=" N UNKUC 462 " --> pdb=" O UNKUC 458 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N UNKUC 463 " --> pdb=" O UNKUC 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNKUC 464 " --> pdb=" O UNKUC 460 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N UNKUC 467 " --> pdb=" O UNKUC 463 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N UNKUC 469 " --> pdb=" O UNKUC 465 " (cutoff:3.500A) Processing helix chain 'UC' and resid 477 through 492 removed outlier: 3.734A pdb=" N UNKUC 488 " --> pdb=" O UNKUC 484 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNKUC 491 " --> pdb=" O UNKUC 487 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N UNKUC 492 " --> pdb=" O UNKUC 488 " (cutoff:3.500A) Processing helix chain 'UC' and resid 505 through 510 removed outlier: 3.828A pdb=" N UNKUC 510 " --> pdb=" O UNKUC 506 " (cutoff:3.500A) Processing helix chain 'UC' and resid 738 through 750 removed outlier: 3.917A pdb=" N UNKUC 744 " --> pdb=" O UNKUC 740 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNKUC 749 " --> pdb=" O UNKUC 745 " (cutoff:3.500A) Processing helix chain 'UC' and resid 768 through 774 removed outlier: 3.689A pdb=" N UNKUC 772 " --> pdb=" O UNKUC 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNKUC 773 " --> pdb=" O UNKUC 769 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N UNKUC 774 " --> pdb=" O UNKUC 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'UC' and resid 768 through 774' Processing helix chain 'UC' and resid 775 through 777 No H-bonds generated for 'chain 'UC' and resid 775 through 777' Processing helix chain 'UC' and resid 787 through 806 removed outlier: 3.683A pdb=" N UNKUC 792 " --> pdb=" O UNKUC 788 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N UNKUC 793 " --> pdb=" O UNKUC 789 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNKUC 794 " --> pdb=" O UNKUC 790 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N UNKUC 795 " --> pdb=" O UNKUC 791 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N UNKUC 796 " --> pdb=" O UNKUC 792 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N UNKUC 797 " --> pdb=" O UNKUC 793 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N UNKUC 801 " --> pdb=" O UNKUC 797 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N UNKUC 804 " --> pdb=" O UNKUC 800 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N UNKUC 806 " --> pdb=" O UNKUC 802 " (cutoff:3.500A) Processing helix chain 'UC' and resid 851 through 865 removed outlier: 3.625A pdb=" N UNKUC 863 " --> pdb=" O UNKUC 859 " (cutoff:3.500A) Processing helix chain 'UC' and resid 882 through 914 removed outlier: 3.503A pdb=" N UNKUC 904 " --> pdb=" O UNKUC 900 " (cutoff:3.500A) Processing helix chain 'UC' and resid 922 through 937 removed outlier: 3.675A pdb=" N UNKUC 929 " --> pdb=" O UNKUC 925 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNKUC 932 " --> pdb=" O UNKUC 928 " (cutoff:3.500A) Processing helix chain 'UC' and resid 952 through 966 removed outlier: 3.504A pdb=" N UNKUC 964 " --> pdb=" O UNKUC 960 " (cutoff:3.500A) Processing helix chain 'UC' and resid 973 through 983 removed outlier: 3.589A pdb=" N UNKUC 978 " --> pdb=" O UNKUC 974 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNKUC 983 " --> pdb=" O UNKUC 979 " (cutoff:3.500A) Processing helix chain 'UC' and resid 983 through 989 removed outlier: 3.542A pdb=" N UNKUC 989 " --> pdb=" O UNKUC 985 " (cutoff:3.500A) Processing helix chain 'UC' and resid 992 through 1006 Processing helix chain 'UC' and resid 1012 through 1031 removed outlier: 3.701A pdb=" N UNKUC1019 " --> pdb=" O UNKUC1015 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N UNKUC1020 " --> pdb=" O UNKUC1016 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNKUC1021 " --> pdb=" O UNKUC1017 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N UNKUC1027 " --> pdb=" O UNKUC1023 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N UNKUC1028 " --> pdb=" O UNKUC1024 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N UNKUC1029 " --> pdb=" O UNKUC1025 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N UNKUC1031 " --> pdb=" O UNKUC1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3B' and resid 87 through 90 Processing sheet with id=AA2, first strand: chain '3B' and resid 217 through 221 removed outlier: 6.367A pdb=" N VAL3B 194 " --> pdb=" O ILE3B 218 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE3B 220 " --> pdb=" O VAL3B 194 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA3B 196 " --> pdb=" O ILE3B 220 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL3B 197 " --> pdb=" O TYR3B 172 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS3B 169 " --> pdb=" O CYS3B 239 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE3B 241 " --> pdb=" O LYS3B 169 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU3B 171 " --> pdb=" O PHE3B 241 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASP3B 238 " --> pdb=" O GLN3B 264 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY3B 265 " --> pdb=" O TYR3B 320 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS3B 313 " --> pdb=" O THR3B 305 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR3B 305 " --> pdb=" O HIS3B 313 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE3B 315 " --> pdb=" O GLN3B 303 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN3B 303 " --> pdb=" O ILE3B 315 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL3B 317 " --> pdb=" O LEU3B 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3C' and resid 87 through 90 removed outlier: 4.070A pdb=" N LEU3C 106 " --> pdb=" O TRP3C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3C' and resid 217 through 221 removed outlier: 6.398A pdb=" N VAL3C 194 " --> pdb=" O ILE3C 218 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE3C 220 " --> pdb=" O VAL3C 194 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA3C 196 " --> pdb=" O ILE3C 220 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL3C 170 " --> pdb=" O TYR3C 195 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL3C 197 " --> pdb=" O VAL3C 170 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR3C 172 " --> pdb=" O VAL3C 197 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS3C 169 " --> pdb=" O CYS3C 239 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE3C 241 " --> pdb=" O LYS3C 169 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU3C 171 " --> pdb=" O PHE3C 241 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL3C 240 " --> pdb=" O VAL3C 268 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER3C 270 " --> pdb=" O VAL3C 240 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA3C 242 " --> pdb=" O SER3C 270 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS3C 272 " --> pdb=" O ALA3C 242 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS3C 313 " --> pdb=" O THR3C 305 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR3C 305 " --> pdb=" O HIS3C 313 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE3C 315 " --> pdb=" O GLN3C 303 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLN3C 303 " --> pdb=" O ILE3C 315 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL3C 317 " --> pdb=" O LEU3C 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3D' and resid 13 through 14 removed outlier: 6.434A pdb=" N GLN3D 24 " --> pdb=" O LEU3D 50 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU3D 50 " --> pdb=" O GLN3D 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3D' and resid 97 through 99 removed outlier: 5.308A pdb=" N LEU3D 98 " --> pdb=" O ILE3D 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '3E' and resid 4 through 6 removed outlier: 3.827A pdb=" N ALA3E 13 " --> pdb=" O THR3E 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3E' and resid 86 through 88 removed outlier: 5.908A pdb=" N LEU3E 87 " --> pdb=" O VAL3E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3F' and resid 146 through 151 removed outlier: 6.668A pdb=" N ARG3F 538 " --> pdb=" O VAL3F 526 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL3F 526 " --> pdb=" O ARG3F 538 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU3F 540 " --> pdb=" O ILE3F 524 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE3F 524 " --> pdb=" O LEU3F 540 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER3F 542 " --> pdb=" O THR3F 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3F' and resid 157 through 163 removed outlier: 3.752A pdb=" N CYS3F 159 " --> pdb=" O VAL3F 190 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL3F 190 " --> pdb=" O CYS3F 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE3F 186 " --> pdb=" O PHE3F 163 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN3F 195 " --> pdb=" O SER3F 191 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP3F 200 " --> pdb=" O LYS3F 210 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS3F 210 " --> pdb=" O ASP3F 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3F' and resid 239 through 244 removed outlier: 4.268A pdb=" N GLY3F 255 " --> pdb=" O LYS3F 259 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS3F 259 " --> pdb=" O GLY3F 255 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER3F 264 " --> pdb=" O PRO3F 270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3F' and resid 283 through 288 removed outlier: 3.870A pdb=" N SER3F 285 " --> pdb=" O SER3F 298 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE3F 304 " --> pdb=" O ILE3F 317 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE3F 317 " --> pdb=" O ILE3F 304 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR3F 306 " --> pdb=" O LEU3F 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER3F 313 " --> pdb=" O SER3F 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3F' and resid 328 through 330 Processing sheet with id=AB5, first strand: chain '3F' and resid 404 through 409 removed outlier: 3.642A pdb=" N VAL3F 408 " --> pdb=" O HIS3F 412 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS3F 412 " --> pdb=" O VAL3F 408 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3F' and resid 477 through 480 removed outlier: 6.257A pdb=" N LEU3F 496 " --> pdb=" O GLU3F 513 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU3F 513 " --> pdb=" O LEU3F 496 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL3F 498 " --> pdb=" O LEU3F 511 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3G' and resid 33 through 35 removed outlier: 6.604A pdb=" N ALA3G 100 " --> pdb=" O ILE3G 52 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE3G 52 " --> pdb=" O ALA3G 100 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE3G 102 " --> pdb=" O GLU3G 50 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N VAL3G 79 " --> pdb=" O GLU3G 50 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE3G 52 " --> pdb=" O VAL3G 79 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL3G 81 " --> pdb=" O ILE3G 52 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET3G 54 " --> pdb=" O VAL3G 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3H' and resid 33 through 35 removed outlier: 6.601A pdb=" N ALA3H 100 " --> pdb=" O ILE3H 52 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE3H 52 " --> pdb=" O ALA3H 100 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE3H 102 " --> pdb=" O GLU3H 50 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N VAL3H 79 " --> pdb=" O GLU3H 50 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE3H 52 " --> pdb=" O VAL3H 79 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL3H 81 " --> pdb=" O ILE3H 52 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET3H 54 " --> pdb=" O VAL3H 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'AA' and resid 13 through 18 removed outlier: 7.324A pdb=" N UNKAA 28 " --> pdb=" O UNKAA 14 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N UNKAA 16 " --> pdb=" O UNKAA 26 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N UNKAA 26 " --> pdb=" O UNKAA 16 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'AA' and resid 56 through 57 removed outlier: 3.777A pdb=" N UNKAA 56 " --> pdb=" O UNKAA 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'AA' and resid 95 through 100 Processing sheet with id=AC3, first strand: chain 'AA' and resid 140 through 141 removed outlier: 3.817A pdb=" N UNKAA 140 " --> pdb=" O UNKAA 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AA' and resid 157 through 161 removed outlier: 5.984A pdb=" N UNKAA 157 " --> pdb=" O UNKAA 169 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N UNKAA 169 " --> pdb=" O UNKAA 157 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N UNKAA 159 " --> pdb=" O UNKAA 167 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N UNKAA 165 " --> pdb=" O UNKAA 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'AA' and resid 180 through 182 Processing sheet with id=AC6, first strand: chain 'AA' and resid 198 through 202 removed outlier: 6.035A pdb=" N UNKAA 198 " --> pdb=" O UNKAA 210 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N UNKAA 210 " --> pdb=" O UNKAA 198 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N UNKAA 200 " --> pdb=" O UNKAA 208 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N UNKAA 206 " --> pdb=" O UNKAA 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'AA' and resid 220 through 223 removed outlier: 3.859A pdb=" N UNKAA 234 " --> pdb=" O UNKAA 238 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N UNKAA 238 " --> pdb=" O UNKAA 234 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'AA' and resid 259 through 264 removed outlier: 4.022A pdb=" N UNKAA 261 " --> pdb=" O UNKAA 274 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N UNKAA 263 " --> pdb=" O UNKAA 272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'AA' and resid 310 through 313 Processing sheet with id=AD1, first strand: chain 'AA' and resid 351 through 355 removed outlier: 3.573A pdb=" N UNKAA 359 " --> pdb=" O UNKAA 355 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'AA' and resid 382 through 383 Processing sheet with id=AD3, first strand: chain 'AA' and resid 432 through 436 removed outlier: 6.350A pdb=" N UNKAA 446 " --> pdb=" O UNKAA 451 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N UNKAA 451 " --> pdb=" O UNKAA 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'AA' and resid 483 through 485 Processing sheet with id=AD5, first strand: chain 'AA' and resid 506 through 508 Processing sheet with id=AD6, first strand: chain 'AA' and resid 546 through 548 Processing sheet with id=AD7, first strand: chain 'AB' and resid 4 through 7 removed outlier: 6.495A pdb=" N UNKAB 283 " --> pdb=" O UNKAB 5 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N UNKAB 7 " --> pdb=" O UNKAB 281 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N UNKAB 281 " --> pdb=" O UNKAB 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'AB' and resid 25 through 29 removed outlier: 6.451A pdb=" N UNKAB 39 " --> pdb=" O UNKAB 44 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N UNKAB 44 " --> pdb=" O UNKAB 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'AB' and resid 59 through 60 Processing sheet with id=AE1, first strand: chain 'AB' and resid 99 through 101 removed outlier: 3.587A pdb=" N UNKAB 100 " --> pdb=" O UNKAB 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AB' and resid 137 through 142 removed outlier: 3.816A pdb=" N UNKAB 139 " --> pdb=" O UNKAB 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'AB' and resid 178 through 181 Processing sheet with id=AE4, first strand: chain 'AB' and resid 201 through 202 Processing sheet with id=AE5, first strand: chain 'AB' and resid 230 through 234 removed outlier: 6.627A pdb=" N UNKAB 240 " --> pdb=" O UNKAB 252 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N UNKAB 252 " --> pdb=" O UNKAB 240 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N UNKAB 242 " --> pdb=" O UNKAB 250 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N UNKAB 248 " --> pdb=" O UNKAB 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'AC' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'AC' and resid 16 through 19 removed outlier: 3.650A pdb=" N UNKAC 16 " --> pdb=" O UNKAC 29 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N UNKAC 30 " --> pdb=" O UNKAC 34 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N UNKAC 34 " --> pdb=" O UNKAC 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'AC' and resid 55 through 60 removed outlier: 3.858A pdb=" N UNKAC 57 " --> pdb=" O UNKAC 70 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N UNKAC 80 " --> pdb=" O UNKAC 85 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N UNKAC 85 " --> pdb=" O UNKAC 80 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AC' and resid 96 through 101 removed outlier: 3.537A pdb=" N UNKAC 100 " --> pdb=" O UNKAC 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNKAC 109 " --> pdb=" O UNKAC 100 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N UNKAC 128 " --> pdb=" O UNKAC 119 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'AC' and resid 137 through 141 removed outlier: 6.514A pdb=" N UNKAC 152 " --> pdb=" O UNKAC 138 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N UNKAC 140 " --> pdb=" O UNKAC 150 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N UNKAC 150 " --> pdb=" O UNKAC 140 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNKAC 157 " --> pdb=" O UNKAC 153 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AC' and resid 180 through 181 removed outlier: 4.031A pdb=" N UNKAC 180 " --> pdb=" O UNKAC 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N UNKAC 194 " --> pdb=" O UNKAC 198 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N UNKAC 198 " --> pdb=" O UNKAC 194 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'AC' and resid 222 through 224 Processing sheet with id=AF4, first strand: chain 'AF' and resid 14 through 18 removed outlier: 3.873A pdb=" N UNKAF 18 " --> pdb=" O UNKAF 27 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N UNKAF 27 " --> pdb=" O UNKAF 18 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N UNKAF 39 " --> pdb=" O UNKAF 44 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N UNKAF 44 " --> pdb=" O UNKAF 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'AF' and resid 55 through 60 removed outlier: 4.185A pdb=" N UNKAF 57 " --> pdb=" O UNKAF 70 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N UNKAF 70 " --> pdb=" O UNKAF 57 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N UNKAF 80 " --> pdb=" O UNKAF 85 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N UNKAF 85 " --> pdb=" O UNKAF 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AF' and resid 96 through 101 removed outlier: 3.645A pdb=" N UNKAF 100 " --> pdb=" O UNKAF 109 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N UNKAF 121 " --> pdb=" O UNKAF 126 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N UNKAF 126 " --> pdb=" O UNKAF 121 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'AF' and resid 139 through 142 removed outlier: 3.593A pdb=" N UNKAF 139 " --> pdb=" O UNKAF 152 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N UNKAF 141 " --> pdb=" O UNKAF 150 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N UNKAF 162 " --> pdb=" O UNKAF 167 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N UNKAF 167 " --> pdb=" O UNKAF 162 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'AF' and resid 178 through 183 removed outlier: 3.706A pdb=" N UNKAF 182 " --> pdb=" O UNKAF 191 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'AF' and resid 219 through 224 removed outlier: 3.661A pdb=" N UNKAF 223 " --> pdb=" O UNKAF 232 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N UNKAF 239 " --> pdb=" O UNKAF 235 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'AF' and resid 260 through 265 removed outlier: 6.317A pdb=" N UNKAF 275 " --> pdb=" O UNKAF 261 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N UNKAF 263 " --> pdb=" O UNKAF 273 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N UNKAF 273 " --> pdb=" O UNKAF 263 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'AG' and resid 19 through 20 removed outlier: 3.865A pdb=" N UNKAG 19 " --> pdb=" O UNKAG 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNKAG 28 " --> pdb=" O UNKAG 19 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N UNKAG 36 " --> pdb=" O UNKAG 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N UNKAG 48 " --> pdb=" O UNKAG 36 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N UNKAG 38 " --> pdb=" O UNKAG 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'AG' and resid 56 through 59 Processing sheet with id=AG4, first strand: chain 'AG' and resid 97 through 102 removed outlier: 6.802A pdb=" N UNKAG 118 " --> pdb=" O UNKAG 130 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N UNKAG 130 " --> pdb=" O UNKAG 118 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N UNKAG 120 " --> pdb=" O UNKAG 128 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'AG' and resid 140 through 143 removed outlier: 3.975A pdb=" N UNKAG 158 " --> pdb=" O UNKAG 154 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'AG' and resid 181 through 184 removed outlier: 3.832A pdb=" N UNKAG 181 " --> pdb=" O UNKAG 194 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N UNKAG 194 " --> pdb=" O UNKAG 181 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N UNKAG 183 " --> pdb=" O UNKAG 192 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'AG' and resid 224 through 225 Processing sheet with id=AG8, first strand: chain 'AG' and resid 261 through 266 Processing sheet with id=AG9, first strand: chain 'AG' and resid 284 through 285 Processing sheet with id=AH1, first strand: chain 'AG' and resid 300 through 304 removed outlier: 3.728A pdb=" N UNKAG 332 " --> pdb=" O UNKAG 323 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N UNKAG 325 " --> pdb=" O UNKAG 330 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N UNKAG 330 " --> pdb=" O UNKAG 325 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'AG' and resid 343 through 346 removed outlier: 3.643A pdb=" N UNKAG 343 " --> pdb=" O UNKAG 356 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'AG' and resid 361 through 364 Processing sheet with id=AH4, first strand: chain 'AG' and resid 393 through 394 Processing sheet with id=AH5, first strand: chain 'AG' and resid 434 through 438 removed outlier: 6.686A pdb=" N UNKAG 444 " --> pdb=" O UNKAG 456 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNKAG 456 " --> pdb=" O UNKAG 444 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N UNKAG 446 " --> pdb=" O UNKAG 454 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N UNKAG 452 " --> pdb=" O UNKAG 448 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'AG' and resid 464 through 469 removed outlier: 3.607A pdb=" N UNKAG 468 " --> pdb=" O UNKAG 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNKAG 480 " --> pdb=" O UNKAG 484 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N UNKAG 484 " --> pdb=" O UNKAG 480 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N UNKAG 489 " --> pdb=" O UNKAG 494 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N UNKAG 494 " --> pdb=" O UNKAG 489 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'AG' and resid 507 through 510 removed outlier: 6.208A pdb=" N UNKAG 526 " --> pdb=" O UNKAG 538 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N UNKAG 538 " --> pdb=" O UNKAG 526 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N UNKAG 528 " --> pdb=" O UNKAG 536 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'AG' and resid 546 through 551 removed outlier: 3.535A pdb=" N UNKAG 566 " --> pdb=" O UNKAG 562 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B1' and resid 85 through 86 removed outlier: 3.633A pdb=" N VALB1 51 " --> pdb=" O THRB1 95 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEUB1 118 " --> pdb=" O ILEB1 50 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALAB1 52 " --> pdb=" O LEUB1 118 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEUB1 120 " --> pdb=" O ALAB1 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VALB1 54 " --> pdb=" O LEUB1 120 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLYB1 148 " --> pdb=" O PHEB1 184 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B1' and resid 273 through 276 removed outlier: 3.569A pdb=" N HISB1 268 " --> pdb=" O GLYB1 813 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEUB1 224 " --> pdb=" O TYRB1 253 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYRB1 253 " --> pdb=" O LEUB1 224 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYRB1 251 " --> pdb=" O ASPB1 226 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHEB1 228 " --> pdb=" O ALAB1 249 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALAB1 249 " --> pdb=" O PHEB1 228 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASPB1 230 " --> pdb=" O LYSB1 247 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYSB1 247 " --> pdb=" O ASPB1 230 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLYB1 252 " --> pdb=" O VALB1 789 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLNB1 279 " --> pdb=" O VALB1 792 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B1' and resid 852 through 856 removed outlier: 3.716A pdb=" N CYSB1 897 " --> pdb=" O SERB1 848 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLNB1 900 " --> pdb=" O ILEB1 913 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILEB1 913 " --> pdb=" O GLNB1 900 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLYB1 917 " --> pdb=" O ARGB1 830 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ARGB1 830 " --> pdb=" O GLYB1 917 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VALB1 919 " --> pdb=" O ARGB1 828 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARGB1 828 " --> pdb=" O VALB1 919 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THRB1 862 " --> pdb=" O ARGB1 870 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARGB1 870 " --> pdb=" O THRB1 862 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B1' and resid 839 through 840 removed outlier: 4.464A pdb=" N LEUB1 839 " --> pdb=" O THRB1 875 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'BA' and resid 21 through 22 Processing sheet with id=AI5, first strand: chain 'BA' and resid 78 through 80 Processing sheet with id=AI6, first strand: chain 'BA' and resid 99 through 104 removed outlier: 4.055A pdb=" N ALABA 101 " --> pdb=" O ALABA 114 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SERBA 115 " --> pdb=" O PHEBA 118 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEUBA 119 " --> pdb=" O VALBA 141 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VALBA 141 " --> pdb=" O LEUBA 119 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILEBA 121 " --> pdb=" O HISBA 139 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VALBA 137 " --> pdb=" O LYSBA 123 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'BA' and resid 152 through 154 Processing sheet with id=AI8, first strand: chain 'BA' and resid 194 through 199 removed outlier: 3.577A pdb=" N GLYBA 196 " --> pdb=" O VALBA 209 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'BA' and resid 263 through 268 removed outlier: 3.607A pdb=" N CYSBA 265 " --> pdb=" O GLYBA 278 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHEBA 279 " --> pdb=" O GLUBA 283 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLUBA 283 " --> pdb=" O PHEBA 279 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLNBA 296 " --> pdb=" O LEUBA 286 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASPBA 288 " --> pdb=" O LEUBA 294 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEUBA 294 " --> pdb=" O ASPBA 288 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'BA' and resid 305 through 310 removed outlier: 3.511A pdb=" N ALABA 318 " --> pdb=" O SERBA 309 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHEBA 319 " --> pdb=" O TYRBA 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYRBA 330 " --> pdb=" O PHEBA 319 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'BA' and resid 348 through 353 removed outlier: 6.563A pdb=" N ALABA 363 " --> pdb=" O ASNBA 349 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEUBA 351 " --> pdb=" O VALBA 361 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VALBA 361 " --> pdb=" O LEUBA 351 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALABA 381 " --> pdb=" O VALBA 371 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASPBA 373 " --> pdb=" O CYSBA 379 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYSBA 379 " --> pdb=" O ASPBA 373 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'BA' and resid 390 through 395 removed outlier: 3.591A pdb=" N GLNBA 394 " --> pdb=" O PHEBA 403 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'BA' and resid 435 through 438 removed outlier: 3.606A pdb=" N CYSBA 435 " --> pdb=" O GLYBA 448 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILEBA 455 " --> pdb=" O LEUBA 469 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEUBA 469 " --> pdb=" O ILEBA 455 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'BA' and resid 476 through 481 removed outlier: 4.320A pdb=" N THRBA 496 " --> pdb=" O SERBA 492 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'BA' and resid 520 through 523 removed outlier: 4.524A pdb=" N ALABA 520 " --> pdb=" O SERBA 533 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VALBA 550 " --> pdb=" O ILEBA 541 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASNBA 543 " --> pdb=" O LYSBA 548 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYSBA 548 " --> pdb=" O ASNBA 543 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'BA' and resid 582 through 585 removed outlier: 4.155A pdb=" N LEUBA 612 " --> pdb=" O LEUBA 603 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASPBA 605 " --> pdb=" O VALBA 610 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VALBA 610 " --> pdb=" O ASPBA 605 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'BA' and resid 683 through 686 removed outlier: 3.735A pdb=" N SERBA 683 " --> pdb=" O ALABA 696 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLNBA 685 " --> pdb=" O ALABA 694 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'BB' and resid 34 through 36 removed outlier: 3.508A pdb=" N VALBB 49 " --> pdb=" O LEUBB 63 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SERBB 61 " --> pdb=" O ILEBB 51 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'BB' and resid 65 through 66 removed outlier: 4.164A pdb=" N ALABB 74 " --> pdb=" O GLYBB 66 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'BB' and resid 84 through 87 removed outlier: 3.832A pdb=" N TYRBB 84 " --> pdb=" O GLYBB 97 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLYBB 97 " --> pdb=" O TYRBB 84 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLUBB 86 " --> pdb=" O ALABB 95 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALABB 95 " --> pdb=" O GLUBB 86 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILEBB 103 " --> pdb=" O ASNBB 116 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASNBB 116 " --> pdb=" O ILEBB 103 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VALBB 105 " --> pdb=" O LEUBB 114 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'BB' and resid 124 through 128 removed outlier: 4.407A pdb=" N ASNBB 144 " --> pdb=" O SERBB 140 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'BB' and resid 166 through 168 removed outlier: 6.112A pdb=" N THRBB 180 " --> pdb=" O THRBB 167 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLUBB 198 " --> pdb=" O LEUBB 188 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'BB' and resid 210 through 212 removed outlier: 3.971A pdb=" N ALABB 211 " --> pdb=" O ILEBB 218 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'BB' and resid 249 through 254 removed outlier: 3.672A pdb=" N GLNBB 251 " --> pdb=" O ASNBB 264 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHEBB 261 " --> pdb=" O TYRBB 273 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'BB' and resid 341 through 346 removed outlier: 6.669A pdb=" N THRBB 356 " --> pdb=" O SERBB 342 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THRBB 344 " --> pdb=" O VALBB 354 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VALBB 354 " --> pdb=" O THRBB 344 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'BB' and resid 397 through 398 Processing sheet with id=AK9, first strand: chain 'BB' and resid 414 through 417 removed outlier: 4.205A pdb=" N CYSBB 424 " --> pdb=" O ILEBB 416 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'BB' and resid 435 through 438 removed outlier: 3.944A pdb=" N THRBB 435 " --> pdb=" O GLYBB 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLYBB 448 " --> pdb=" O THRBB 435 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEUBB 454 " --> pdb=" O ILEBB 468 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASPBB 466 " --> pdb=" O LEUBB 456 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASPBB 458 " --> pdb=" O LEUBB 464 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEUBB 464 " --> pdb=" O ASPBB 458 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'BB' and resid 479 through 481 Processing sheet with id=AL3, first strand: chain 'BB' and resid 497 through 498 Processing sheet with id=AL4, first strand: chain 'BB' and resid 537 through 539 removed outlier: 3.506A pdb=" N PHEBB 558 " --> pdb=" O LEUBB 546 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILEBB 548 " --> pdb=" O LYSBB 556 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYSBB 556 " --> pdb=" O ILEBB 548 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VALBB 555 " --> pdb=" O SERBB 568 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SERBB 568 " --> pdb=" O VALBB 555 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VALBB 557 " --> pdb=" O TYRBB 566 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'BB' and resid 576 through 581 removed outlier: 7.052A pdb=" N SERBB 591 " --> pdb=" O LEUBB 577 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILEBB 579 " --> pdb=" O ILEBB 589 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILEBB 589 " --> pdb=" O ILEBB 579 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SERBB 592 " --> pdb=" O ASNBB 596 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASNBB 596 " --> pdb=" O SERBB 592 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'BB' and resid 618 through 623 removed outlier: 4.065A pdb=" N GLNBB 651 " --> pdb=" O TYRBB 641 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASPBB 643 " --> pdb=" O CYSBB 649 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYSBB 649 " --> pdb=" O ASPBB 643 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'BB' and resid 660 through 664 Processing sheet with id=AL8, first strand: chain 'BC' and resid 32 through 33 removed outlier: 3.790A pdb=" N THRBC 46 " --> pdb=" O LEUBC 32 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HISBC 54 " --> pdb=" O LEUBC 45 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'BC' and resid 67 through 69 removed outlier: 4.359A pdb=" N LYSBC 68 " --> pdb=" O THRBC 77 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THRBC 77 " --> pdb=" O LYSBC 68 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEUBC 76 " --> pdb=" O PHEBC 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYRBC 78 " --> pdb=" O LYSBC 86 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYSBC 86 " --> pdb=" O TYRBC 78 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEUBC 85 " --> pdb=" O SERBC 98 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SERBC 98 " --> pdb=" O LEUBC 85 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILEBC 87 " --> pdb=" O VALBC 96 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'BC' and resid 106 through 110 removed outlier: 4.043A pdb=" N ALABC 110 " --> pdb=" O VALBC 119 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VALBC 119 " --> pdb=" O ALABC 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASPBC 130 " --> pdb=" O ALABC 118 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'BC' and resid 172 through 173 Processing sheet with id=AM3, first strand: chain 'BC' and resid 211 through 213 removed outlier: 3.579A pdb=" N SERBC 213 " --> pdb=" O ASNBC 221 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASNBC 221 " --> pdb=" O SERBC 213 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILEBC 220 " --> pdb=" O THRBC 236 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THRBC 236 " --> pdb=" O ILEBC 220 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEUBC 222 " --> pdb=" O LEUBC 234 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'BC' and resid 245 through 246 removed outlier: 3.912A pdb=" N ILEBC 266 " --> pdb=" O GLYBC 262 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHEBC 267 " --> pdb=" O ARGBC 280 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARGBC 280 " --> pdb=" O PHEBC 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEUBC 269 " --> pdb=" O LEUBC 278 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'BC' and resid 304 through 307 removed outlier: 3.548A pdb=" N GLNBC 312 " --> pdb=" O VALBC 305 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SERBC 307 " --> pdb=" O THRBC 310 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THRBC 310 " --> pdb=" O SERBC 307 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'BC' and resid 342 through 345 removed outlier: 3.856A pdb=" N ASPBC 342 " --> pdb=" O ALABC 356 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'BC' and resid 391 through 396 removed outlier: 6.863A pdb=" N ALABC 406 " --> pdb=" O ASNBC 392 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEUBC 394 " --> pdb=" O ALABC 404 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALABC 404 " --> pdb=" O LEUBC 394 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALABC 396 " --> pdb=" O TRPBC 402 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TRPBC 402 " --> pdb=" O ALABC 396 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILEBC 413 " --> pdb=" O THRBC 405 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SERBC 407 " --> pdb=" O THRBC 411 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THRBC 411 " --> pdb=" O SERBC 407 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALABC 412 " --> pdb=" O LYSBC 429 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYSBC 429 " --> pdb=" O ALABC 412 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VALBC 414 " --> pdb=" O TYRBC 427 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'BC' and resid 439 through 441 removed outlier: 3.648A pdb=" N ALABC 439 " --> pdb=" O ALABC 457 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILEBC 463 " --> pdb=" O ARGBC 487 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARGBC 487 " --> pdb=" O ILEBC 463 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'BC' and resid 494 through 499 removed outlier: 7.042A pdb=" N ALABC 509 " --> pdb=" O ASNBC 495 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEUBC 497 " --> pdb=" O ALABC 507 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALABC 507 " --> pdb=" O LEUBC 497 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VALBC 499 " --> pdb=" O ILEBC 505 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILEBC 505 " --> pdb=" O VALBC 499 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THRBC 514 " --> pdb=" O SERBC 510 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASNBC 519 " --> pdb=" O LEUBC 525 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEUBC 525 " --> pdb=" O ASNBC 519 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'BC' and resid 536 through 541 removed outlier: 4.203A pdb=" N ASPBC 538 " --> pdb=" O SERBC 551 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SERBC 552 " --> pdb=" O THRBC 556 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THRBC 556 " --> pdb=" O SERBC 552 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SERBC 561 " --> pdb=" O VALBC 567 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VALBC 567 " --> pdb=" O SERBC 561 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'BC' and resid 578 through 583 removed outlier: 3.548A pdb=" N LYSBC 600 " --> pdb=" O SERBC 592 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'BC' and resid 623 through 625 removed outlier: 3.664A pdb=" N VALBC 633 " --> pdb=" O SERBC 624 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'BD' and resid 254 through 256 removed outlier: 5.814A pdb=" N HISBD 276 " --> pdb=" O LEUBD 284 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEUBD 284 " --> pdb=" O HISBD 276 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'BD' and resid 358 through 360 Processing sheet with id=AN6, first strand: chain 'BD' and resid 410 through 413 removed outlier: 4.535A pdb=" N ASPBD 410 " --> pdb=" O ALABD 425 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'BD' and resid 483 through 485 Processing sheet with id=AN8, first strand: chain 'BD' and resid 529 through 533 Processing sheet with id=AN9, first strand: chain 'BD' and resid 565 through 570 Processing sheet with id=AO1, first strand: chain 'BE' and resid 24 through 30 removed outlier: 6.274A pdb=" N THRBE 655 " --> pdb=" O PROBE 26 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'BE' and resid 40 through 44 removed outlier: 6.726A pdb=" N ASPBE 62 " --> pdb=" O LEUBE 68 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEUBE 68 " --> pdb=" O ASPBE 62 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'BE' and resid 83 through 85 removed outlier: 6.611A pdb=" N VALBE 98 " --> pdb=" O LEUBE 109 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEUBE 109 " --> pdb=" O VALBE 98 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILEBE 100 " --> pdb=" O GLUBE 107 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'BE' and resid 118 through 122 removed outlier: 6.892A pdb=" N SERBE 131 " --> pdb=" O GLUBE 119 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEUBE 121 " --> pdb=" O CYSBE 129 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYSBE 129 " --> pdb=" O LEUBE 121 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SERBE 136 " --> pdb=" O THRBE 132 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILEBE 137 " --> pdb=" O LYSBE 156 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYSBE 156 " --> pdb=" O ILEBE 137 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILEBE 139 " --> pdb=" O TYRBE 154 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'BE' and resid 167 through 171 removed outlier: 7.181A pdb=" N VALBE 183 " --> pdb=" O VALBE 168 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEUBE 170 " --> pdb=" O THRBE 181 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THRBE 181 " --> pdb=" O LEUBE 170 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASNBE 192 " --> pdb=" O LEUBE 198 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEUBE 198 " --> pdb=" O ASNBE 192 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'BE' and resid 209 through 214 removed outlier: 6.552A pdb=" N GLYBE 224 " --> pdb=" O THRBE 210 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALABE 212 " --> pdb=" O ALABE 222 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALABE 222 " --> pdb=" O ALABE 212 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILEBE 220 " --> pdb=" O PROBE 214 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLUBE 229 " --> pdb=" O THRBE 225 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLYBE 228 " --> pdb=" O ILEBE 246 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARGBE 242 " --> pdb=" O METBE 232 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASNBE 234 " --> pdb=" O ARGBE 240 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARGBE 240 " --> pdb=" O ASNBE 234 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'BE' and resid 263 through 267 removed outlier: 5.402A pdb=" N LEUBE 273 " --> pdb=" O VALBE 286 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VALBE 286 " --> pdb=" O LEUBE 273 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHEBE 275 " --> pdb=" O ILEBE 284 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'BE' and resid 298 through 303 removed outlier: 4.065A pdb=" N GLYBE 314 " --> pdb=" O SERBE 318 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SERBE 318 " --> pdb=" O GLYBE 314 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARGBE 344 " --> pdb=" O GLUBE 321 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VALBE 323 " --> pdb=" O TYRBE 342 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYRBE 342 " --> pdb=" O VALBE 323 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'BE' and resid 353 through 358 removed outlier: 6.860A pdb=" N ALABE 369 " --> pdb=" O SERBE 354 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILEBE 356 " --> pdb=" O LEUBE 367 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEUBE 367 " --> pdb=" O ILEBE 356 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHEBE 358 " --> pdb=" O PHEBE 365 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHEBE 365 " --> pdb=" O PHEBE 358 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'BE' and resid 417 through 419 removed outlier: 6.206A pdb=" N ALABE 440 " --> pdb=" O TRPBE 453 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRPBE 453 " --> pdb=" O ALABE 440 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THRBE 442 " --> pdb=" O GLYBE 451 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'BE' and resid 463 through 468 removed outlier: 5.813A pdb=" N ASNBE 488 " --> pdb=" O LEUBE 494 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEUBE 494 " --> pdb=" O ASNBE 488 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'BE' and resid 505 through 510 removed outlier: 3.758A pdb=" N GLYBE 507 " --> pdb=" O CYSBE 520 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILEBE 525 " --> pdb=" O GLYBE 521 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'BE' and resid 546 through 552 removed outlier: 6.875A pdb=" N ALABE 561 " --> pdb=" O THRBE 547 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N METBE 549 " --> pdb=" O ALABE 559 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALABE 559 " --> pdb=" O METBE 549 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYRBE 551 " --> pdb=" O LEUBE 557 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEUBE 557 " --> pdb=" O TYRBE 551 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASPBE 571 " --> pdb=" O VALBE 577 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VALBE 577 " --> pdb=" O ASPBE 571 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'BE' and resid 588 through 593 removed outlier: 6.910A pdb=" N ALABE 603 " --> pdb=" O THRBE 589 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHEBE 591 " --> pdb=" O VALBE 601 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VALBE 601 " --> pdb=" O PHEBE 591 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHEBE 593 " --> pdb=" O TRPBE 599 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TRPBE 599 " --> pdb=" O PHEBE 593 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THRBE 608 " --> pdb=" O SERBE 604 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASPBE 621 " --> pdb=" O THRBE 611 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASPBE 613 " --> pdb=" O CYSBE 619 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N CYSBE 619 " --> pdb=" O ASPBE 613 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'CA' and resid 14 through 19 Processing sheet with id=AP7, first strand: chain 'CA' and resid 52 through 56 Processing sheet with id=AP8, first strand: chain 'CB' and resid 182 through 186 removed outlier: 3.855A pdb=" N ASPCB 204 " --> pdb=" O ILECB 186 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SERCB 201 " --> pdb=" O SERCB 291 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASNCB 293 " --> pdb=" O SERCB 201 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILECB 203 " --> pdb=" O ASNCB 293 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEUCB 295 " --> pdb=" O ILECB 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THRCB 205 " --> pdb=" O LEUCB 295 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLYCB 297 " --> pdb=" O THRCB 205 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEUCB 207 " --> pdb=" O GLYCB 297 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N PHECB 290 " --> pdb=" O CYSCB 272 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N CYSCB 272 " --> pdb=" O PHECB 290 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILECB 296 " --> pdb=" O PROCB 266 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'CB' and resid 456 through 458 removed outlier: 6.165A pdb=" N LEUCB 440 " --> pdb=" O PHECB 468 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'CB' and resid 578 through 586 removed outlier: 6.477A pdb=" N ILECB 618 " --> pdb=" O LYSCB 579 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILECB 581 " --> pdb=" O LYSCB 616 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYSCB 616 " --> pdb=" O ILECB 581 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILECB 583 " --> pdb=" O ARGCB 614 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARGCB 614 " --> pdb=" O ILECB 583 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N METCB 585 " --> pdb=" O PHECB 612 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHECB 612 " --> pdb=" O METCB 585 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'CB' and resid 628 through 633 removed outlier: 5.455A pdb=" N HISCB 665 " --> pdb=" O GLYCB 631 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALACB 633 " --> pdb=" O ILECB 663 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILECB 663 " --> pdb=" O ALACB 633 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'CB' and resid 750 through 755 removed outlier: 4.183A pdb=" N PHECB 786 " --> pdb=" O LEUCB 855 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VALCB 854 " --> pdb=" O VALCB 838 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VALCB 838 " --> pdb=" O VALCB 854 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'CB' and resid 975 through 976 removed outlier: 6.252A pdb=" N LEUCB 975 " --> pdb=" O ALACB1042 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ4 Processing sheet with id=AQ5, first strand: chain 'CB' and resid 1161 through 1165 removed outlier: 3.663A pdb=" N ASNCB1233 " --> pdb=" O ASPCB1101 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARGCB1103 " --> pdb=" O VALCB1231 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VALCB1231 " --> pdb=" O ARGCB1103 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'CB' and resid 1194 through 1195 Processing sheet with id=AQ7, first strand: chain 'E1' and resid 149 through 150 removed outlier: 4.429A pdb=" N LEUE1 121 " --> pdb=" O ILEE1 163 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VALE1 112 " --> pdb=" O VALE1 124 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N METE1 41 " --> pdb=" O GLNE1 111 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYRE1 113 " --> pdb=" O METE1 41 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VALE1 43 " --> pdb=" O TYRE1 113 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLNE1 115 " --> pdb=" O VALE1 43 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEUE1 45 " --> pdb=" O GLNE1 115 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARGE1 176 " --> pdb=" O CYSE1 203 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHEE1 205 " --> pdb=" O ARGE1 176 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VALE1 178 " --> pdb=" O PHEE1 205 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLYE1 207 " --> pdb=" O VALE1 178 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N LEUE1 180 " --> pdb=" O GLYE1 207 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'E1' and resid 52 through 53 Processing sheet with id=AQ9, first strand: chain 'E2' and resid 149 through 151 removed outlier: 6.516A pdb=" N ILEE2 150 " --> pdb=" O LEUE2 159 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEUE2 121 " --> pdb=" O ILEE2 163 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VALE2 112 " --> pdb=" O VALE2 124 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLNE2 111 " --> pdb=" O ILEE2 42 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VALE2 44 " --> pdb=" O GLNE2 111 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYRE2 113 " --> pdb=" O VALE2 44 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALAE2 46 " --> pdb=" O TYRE2 113 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLNE2 115 " --> pdb=" O ALAE2 46 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILEE2 42 " --> pdb=" O VALE2 204 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VALE2 206 " --> pdb=" O ILEE2 42 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VALE2 44 " --> pdb=" O VALE2 206 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARGE2 176 " --> pdb=" O CYSE2 203 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHEE2 205 " --> pdb=" O ARGE2 176 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VALE2 178 " --> pdb=" O PHEE2 205 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLYE2 207 " --> pdb=" O VALE2 178 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N LEUE2 180 " --> pdb=" O GLYE2 207 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLUE2 223 " --> pdb=" O CYSE2 175 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYSE2 177 " --> pdb=" O GLUE2 223 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VALE2 225 " --> pdb=" O LYSE2 177 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THRE2 179 " --> pdb=" O VALE2 225 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'E2' and resid 52 through 53 Processing sheet with id=AR2, first strand: chain 'E4' and resid 4 through 6 removed outlier: 3.593A pdb=" N UNKE4 6 " --> pdb=" O UNKE4 283 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNKE4 282 " --> pdb=" O UNKE4 274 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N UNKE4 273 " --> pdb=" O UNKE4 263 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N UNKE4 263 " --> pdb=" O UNKE4 273 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N UNKE4 275 " --> pdb=" O UNKE4 261 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'E4' and resid 16 through 19 Processing sheet with id=AR4, first strand: chain 'E4' and resid 55 through 60 removed outlier: 3.544A pdb=" N UNKE4 59 " --> pdb=" O UNKE4 68 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNKE4 76 " --> pdb=" O UNKE4 89 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'E4' and resid 98 through 99 removed outlier: 3.586A pdb=" N UNKE4 98 " --> pdb=" O UNKE4 111 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'E4' and resid 141 through 142 Processing sheet with id=AR7, first strand: chain 'E4' and resid 178 through 183 removed outlier: 3.659A pdb=" N UNKE4 180 " --> pdb=" O UNKE4 193 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'E4' and resid 219 through 221 removed outlier: 3.507A pdb=" N UNKE4 239 " --> pdb=" O UNKE4 235 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'K1' and resid 40 through 44 Processing sheet with id=AS1, first strand: chain 'K1' and resid 122 through 127 Processing sheet with id=AS2, first strand: chain 'MA' and resid 141 through 142 removed outlier: 3.527A pdb=" N ASNMA 141 " --> pdb=" O VALMA 138 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VALMA 138 " --> pdb=" O ASNMA 141 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'MB' and resid 114 through 116 removed outlier: 6.460A pdb=" N ILEMB 89 " --> pdb=" O VALMB 140 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEUMB 142 " --> pdb=" O ILEMB 89 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THRMB 91 " --> pdb=" O LEUMB 142 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THRMB 162 " --> pdb=" O ARGMB 262 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLUMB 260 " --> pdb=" O GLNMB 164 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SERMB 166 " --> pdb=" O LEUMB 258 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEUMB 258 " --> pdb=" O SERMB 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHEMB 254 " --> pdb=" O VALMB 233 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HISMB 188 " --> pdb=" O ILEMB 222 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHEMB 224 " --> pdb=" O HISMB 188 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILEMB 190 " --> pdb=" O PHEMB 224 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASNMB 226 " --> pdb=" O ILEMB 190 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASPMB 192 " --> pdb=" O ASNMB 226 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'MB' and resid 239 through 240 Processing sheet with id=AS5, first strand: chain 'P1' and resid 97 through 100 removed outlier: 3.753A pdb=" N ILEP1 99 " --> pdb=" O VALP1 137 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'P1' and resid 180 through 186 Processing sheet with id=AS7, first strand: chain 'R1' and resid 9 through 12 removed outlier: 5.889A pdb=" N THRR1 9 " --> pdb=" O LYSR1 32 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLUR1 34 " --> pdb=" O THRR1 9 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHER1 11 " --> pdb=" O GLUR1 34 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'R1' and resid 60 through 61 Processing sheet with id=AS9, first strand: chain 'R1' and resid 85 through 89 removed outlier: 3.548A pdb=" N PHER1 114 " --> pdb=" O VALR1 170 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLUR1 165 " --> pdb=" O LEUR1 154 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'R1' and resid 181 through 182 Processing sheet with id=AT2, first strand: chain 'R1' and resid 223 through 230 removed outlier: 6.803A pdb=" N ILER1 191 " --> pdb=" O ASNR1 224 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THRR1 226 " --> pdb=" O ILER1 191 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLYR1 193 " --> pdb=" O THRR1 226 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASPR1 228 " --> pdb=" O GLYR1 193 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALAR1 195 " --> pdb=" O ASPR1 228 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TRPR1 230 " --> pdb=" O ALAR1 195 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SERR1 197 " --> pdb=" O TRPR1 230 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRPR1 241 " --> pdb=" O GLYR1 262 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'S1' and resid 117 through 119 removed outlier: 3.984A pdb=" N UNKS1 118 " --> pdb=" O UNKS1 127 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N UNKS1 127 " --> pdb=" O UNKS1 118 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N UNKS1 135 " --> pdb=" O UNKS1 147 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N UNKS1 147 " --> pdb=" O UNKS1 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N UNKS1 137 " --> pdb=" O UNKS1 145 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'S1' and resid 155 through 159 removed outlier: 3.655A pdb=" N UNKS1 157 " --> pdb=" O UNKS1 170 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'S1' and resid 207 through 211 removed outlier: 7.297A pdb=" N UNKS1 217 " --> pdb=" O UNKS1 229 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N UNKS1 229 " --> pdb=" O UNKS1 217 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N UNKS1 219 " --> pdb=" O UNKS1 227 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'S1' and resid 237 through 242 removed outlier: 3.609A pdb=" N UNKS1 252 " --> pdb=" O UNKS1 239 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N UNKS1 257 " --> pdb=" O UNKS1 253 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'S1' and resid 278 through 283 Processing sheet with id=AT8, first strand: chain 'S1' and resid 331 through 333 removed outlier: 3.812A pdb=" N UNKS1 340 " --> pdb=" O UNKS1 353 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'S1' and resid 362 through 364 Processing sheet with id=AU1, first strand: chain 'SC' and resid 29 through 33 removed outlier: 3.652A pdb=" N PHESC 30 " --> pdb=" O THRSC 46 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLYSC 44 " --> pdb=" O ILESC 32 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'SC' and resid 67 through 69 removed outlier: 5.920A pdb=" N ARGSC 87 " --> pdb=" O PHESC 100 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHESC 100 " --> pdb=" O ARGSC 87 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASPSC 89 " --> pdb=" O THRSC 98 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THRSC 98 " --> pdb=" O ASPSC 89 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VALSC 91 " --> pdb=" O LEUSC 96 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEUSC 96 " --> pdb=" O VALSC 91 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N HISSC 101 " --> pdb=" O LEUSC 217 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEUSC 217 " --> pdb=" O HISSC 101 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYSSC 214 " --> pdb=" O PHESC 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILESC 137 " --> pdb=" O VALSC 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALSC 125 " --> pdb=" O ILESC 137 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'SF' and resid 42 through 43 removed outlier: 3.523A pdb=" N ALASF 84 " --> pdb=" O LEUSF 42 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'SF' and resid 70 through 72 removed outlier: 4.149A pdb=" N HISSF 112 " --> pdb=" O ARGSF 100 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VALSF 102 " --> pdb=" O ALASF 110 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'SF' and resid 146 through 148 removed outlier: 7.208A pdb=" N TYRSF 138 " --> pdb=" O VALSF 129 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VALSF 129 " --> pdb=" O TYRSF 138 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VALSF 140 " --> pdb=" O LYSSF 127 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYSSF 122 " --> pdb=" O ILESF 162 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'SF' and resid 207 through 211 removed outlier: 3.679A pdb=" N THRSF 220 " --> pdb=" O VALSF 208 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'SG' and resid 145 through 149 Processing sheet with id=AU8, first strand: chain 'SI' and resid 49 through 50 Processing sheet with id=AU9, first strand: chain 'SI' and resid 60 through 61 removed outlier: 5.817A pdb=" N ILESI 60 " --> pdb=" O LEUSI 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU9 Processing sheet with id=AV1, first strand: chain 'SI' and resid 181 through 184 removed outlier: 3.691A pdb=" N ILESI 149 " --> pdb=" O ARGSI 141 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARGSI 141 " --> pdb=" O ILESI 149 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLYSI 137 " --> pdb=" O LEUSI 153 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYSSI 138 " --> pdb=" O ASPSX 54 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHESX 50 " --> pdb=" O TYRSI 142 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYSSX 60 " --> pdb=" O ILESX 53 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'SJ' and resid 3 through 4 removed outlier: 3.952A pdb=" N ILESJ 3 " --> pdb=" O GLYSJ 30 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'SJ' and resid 42 through 48 removed outlier: 3.524A pdb=" N VALSJ 46 " --> pdb=" O LYSSJ 54 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYSSJ 54 " --> pdb=" O VALSJ 46 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THRSJ 48 " --> pdb=" O ASNSJ 52 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASNSJ 52 " --> pdb=" O THRSJ 48 " (cutoff:3.500A) Processing sheet with id=AV4, first strand: chain 'SJ' and resid 72 through 77 removed outlier: 8.850A pdb=" N GLYSJ 181 " --> pdb=" O THRSJ 62 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASNSJ 64 " --> pdb=" O GLYSJ 181 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILESJ 183 " --> pdb=" O ASNSJ 64 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SERSJ 66 " --> pdb=" O ILESJ 183 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILESJ 101 " --> pdb=" O VALSJ 82 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLYSJ 80 " --> pdb=" O GLNSJ 103 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'SM' and resid 70 through 80 removed outlier: 17.772A pdb=" N ILESM 70 " --> pdb=" O LEUSM 91 " (cutoff:3.500A) removed outlier: 15.058A pdb=" N LEUSM 91 " --> pdb=" O ILESM 70 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N THRSM 72 " --> pdb=" O ALASM 89 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALASM 89 " --> pdb=" O THRSM 72 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VALSM 85 " --> pdb=" O VALSM 76 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THRSM 78 " --> pdb=" O THRSM 83 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THRSM 83 " --> pdb=" O THRSM 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARGSM 99 " --> pdb=" O ILESM 94 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N PHESM 137 " --> pdb=" O ASNSM 106 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VALSM 139 " --> pdb=" O PROSM 108 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N HISSM 110 " --> pdb=" O VALSM 139 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N LYSSM 141 " --> pdb=" O HISSM 110 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VALSM 139 " --> pdb=" O GLYSM 126 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLYSM 126 " --> pdb=" O VALSM 139 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'SP' and resid 30 through 31 removed outlier: 3.580A pdb=" N VALSP 30 " --> pdb=" O ILESP 39 " (cutoff:3.500A) Processing sheet with id=AV7, first strand: chain 'SP' and resid 78 through 79 Processing sheet with id=AV8, first strand: chain 'SP' and resid 82 through 83 Processing sheet with id=AV9, first strand: chain 'SR' and resid 6 through 12 removed outlier: 3.584A pdb=" N VALSR 19 " --> pdb=" O ARGSR 68 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARGSR 66 " --> pdb=" O HISSR 21 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYSSR 30 " --> pdb=" O VALSR 67 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VALSR 69 " --> pdb=" O LYSSR 30 " (cutoff:3.500A) Processing sheet with id=AW1, first strand: chain 'SX' and resid 72 through 74 removed outlier: 5.307A pdb=" N ILESX 125 " --> pdb=" O THRSX 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THRSX 105 " --> pdb=" O ILESX 125 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'SY' and resid 82 through 85 removed outlier: 6.777A pdb=" N ARGSY 73 " --> pdb=" O LEUSY 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALASY 49 " --> pdb=" O LEUSY 104 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLUSY 101 " --> pdb=" O VALSY 127 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VALSY 127 " --> pdb=" O GLUSY 101 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUSY 103 " --> pdb=" O VALSY 125 " (cutoff:3.500A) Processing sheet with id=AW3, first strand: chain 'SZ' and resid 7 through 15 removed outlier: 4.034A pdb=" N VALSZ 12 " --> pdb=" O GLNSZ 22 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLNSZ 22 " --> pdb=" O VALSZ 12 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SERSZ 14 " --> pdb=" O ARGSZ 20 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARGSZ 20 " --> pdb=" O SERSZ 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VALSZ 75 " --> pdb=" O LYSSZ 21 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHESZ 23 " --> pdb=" O GLYSZ 73 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VALSZ 25 " --> pdb=" O GLYSZ 71 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYSSZ 68 " --> pdb=" O THRSZ 62 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THRSZ 62 " --> pdb=" O LYSSZ 68 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VALSZ 70 " --> pdb=" O PHESZ 60 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHESZ 60 " --> pdb=" O VALSZ 70 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'Sc' and resid 45 through 47 removed outlier: 3.629A pdb=" N LEUSc 33 " --> pdb=" O VALSc 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARGSc 80 " --> pdb=" O ASPSc 34 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'Sc' and resid 64 through 65 Processing sheet with id=AW6, first strand: chain 'Sd' and resid 40 through 43 removed outlier: 3.726A pdb=" N ARGSd 42 " --> pdb=" O VALSd 28 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VALSd 28 " --> pdb=" O ARGSd 42 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VALSd 25 " --> pdb=" O ARGSd 18 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ARGSd 18 " --> pdb=" O VALSd 25 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLNSd 27 " --> pdb=" O LEUSd 16 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYSSd 14 " --> pdb=" O ARGSd 29 " (cutoff:3.500A) Processing sheet with id=AW7, first strand: chain 'U1' and resid 17 through 18 removed outlier: 3.837A pdb=" N UNKU1 18 " --> pdb=" O UNKU1 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N UNKU1 27 " --> pdb=" O UNKU1 18 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N UNKU1 28 " --> pdb=" O UNKU1 36 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N UNKU1 46 " --> pdb=" O UNKU1 37 " (cutoff:3.500A) Processing sheet with id=AW8, first strand: chain 'U1' and resid 77 through 78 Processing sheet with id=AW9, first strand: chain 'U1' and resid 100 through 101 removed outlier: 3.904A pdb=" N UNKU1 120 " --> pdb=" O UNKU1 108 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNKU1 110 " --> pdb=" O UNKU1 118 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N UNKU1 118 " --> pdb=" O UNKU1 110 " (cutoff:3.500A) Processing sheet with id=AX1, first strand: chain 'U1' and resid 199 through 200 Processing sheet with id=AX2, first strand: chain 'U1' and resid 233 through 235 removed outlier: 3.525A pdb=" N UNKU1 233 " --> pdb=" O UNKU1 241 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N UNKU1 241 " --> pdb=" O UNKU1 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N UNKU1 235 " --> pdb=" O UNKU1 239 " (cutoff:3.500A) Processing sheet with id=AX3, first strand: chain 'U1' and resid 263 through 265 removed outlier: 3.653A pdb=" N UNKU1 264 " --> pdb=" O UNKU1 273 " (cutoff:3.500A) Processing sheet with id=AX4, first strand: chain 'U4' and resid 126 through 127 removed outlier: 3.724A pdb=" N LYSU4 126 " --> pdb=" O PROU4 96 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILEU4 98 " --> pdb=" O LYSU4 126 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'U5' and resid 198 through 203 removed outlier: 3.829A pdb=" N VALU5 199 " --> pdb=" O ILEU5 38 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILEU5 36 " --> pdb=" O VALU5 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSU5 245 " --> pdb=" O HISU5 37 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SERU5 241 " --> pdb=" O ASNU5 41 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILEU5 242 " --> pdb=" O ILEU5 254 " (cutoff:3.500A) Processing sheet with id=AX6, first strand: chain 'U5' and resid 55 through 58 Processing sheet with id=AX7, first strand: chain 'U5' and resid 126 through 127 4616 hydrogen bonds defined for protein. 12954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1039 hydrogen bonds 1730 hydrogen bond angles 0 basepair planarities 425 basepair parallelities 805 stacking parallelities Total time for adding SS restraints: 128.45 Time building geometry restraints manager: 54.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 21760 1.30 - 1.43: 49099 1.43 - 1.57: 81864 1.57 - 1.70: 3211 1.70 - 1.83: 502 Bond restraints: 156436 Sorted by residual: bond pdb=" N UNKUC 249 " pdb=" CA UNKUC 249 " ideal model delta sigma weight residual 1.458 1.569 -0.111 1.90e-02 2.77e+03 3.39e+01 bond pdb=" C ALAAE 112 " pdb=" N PROAE 113 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.23e-02 6.61e+03 2.58e+01 bond pdb=" C2 USA 493 " pdb=" N3 USA 493 " ideal model delta sigma weight residual 1.373 1.273 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C UNKUC 233 " pdb=" O UNKUC 233 " ideal model delta sigma weight residual 1.232 1.321 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C SERSI 31 " pdb=" N PROSI 32 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.20e-02 6.94e+03 1.54e+01 ... (remaining 156431 not shown) Histogram of bond angle deviations from ideal: 98.03 - 107.77: 16658 107.77 - 117.52: 111483 117.52 - 127.26: 87664 127.26 - 137.01: 4458 137.01 - 146.75: 4 Bond angle restraints: 220267 Sorted by residual: angle pdb=" C GLUSR 40 " pdb=" N PROSR 41 " pdb=" CA PROSR 41 " ideal model delta sigma weight residual 119.82 134.54 -14.72 9.80e-01 1.04e+00 2.26e+02 angle pdb=" N PROSR 41 " pdb=" CA PROSR 41 " pdb=" C PROSR 41 " ideal model delta sigma weight residual 113.98 125.71 -11.73 1.29e+00 6.01e-01 8.27e+01 angle pdb=" C PHEB1 808 " pdb=" N PROB1 809 " pdb=" CA PROB1 809 " ideal model delta sigma weight residual 119.93 129.17 -9.24 1.07e+00 8.73e-01 7.45e+01 angle pdb=" C ASNBC 133 " pdb=" N GLYBC 134 " pdb=" CA GLYBC 134 " ideal model delta sigma weight residual 121.70 136.12 -14.42 1.80e+00 3.09e-01 6.42e+01 angle pdb=" C PHEMB 111 " pdb=" N PROMB 112 " pdb=" CA PROMB 112 " ideal model delta sigma weight residual 127.00 144.66 -17.66 2.40e+00 1.74e-01 5.42e+01 ... (remaining 220262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 91824 36.00 - 71.99: 3962 71.99 - 107.99: 427 107.99 - 143.98: 18 143.98 - 179.98: 44 Dihedral angle restraints: 96275 sinusoidal: 47825 harmonic: 48450 Sorted by residual: dihedral pdb=" CA GLUSR 40 " pdb=" C GLUSR 40 " pdb=" N PROSR 41 " pdb=" CA PROSR 41 " ideal model delta harmonic sigma weight residual 180.00 54.89 125.11 0 5.00e+00 4.00e-02 6.26e+02 dihedral pdb=" CA ALABB 796 " pdb=" C ALABB 796 " pdb=" N VALBB 797 " pdb=" CA VALBB 797 " ideal model delta harmonic sigma weight residual 180.00 118.58 61.42 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PHESI 131 " pdb=" C PHESI 131 " pdb=" N PROSI 132 " pdb=" CA PROSI 132 " ideal model delta harmonic sigma weight residual -180.00 -120.01 -59.99 0 5.00e+00 4.00e-02 1.44e+02 ... (remaining 96272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 26282 0.111 - 0.222: 1130 0.222 - 0.333: 63 0.333 - 0.444: 10 0.444 - 0.555: 3 Chirality restraints: 27488 Sorted by residual: chirality pdb=" CB ILEBA 703 " pdb=" CA ILEBA 703 " pdb=" CG1 ILEBA 703 " pdb=" CG2 ILEBA 703 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CB ILEBC 136 " pdb=" CA ILEBC 136 " pdb=" CG1 ILEBC 136 " pdb=" CG2 ILEBC 136 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" CB ILE3B 220 " pdb=" CA ILE3B 220 " pdb=" CG1 ILE3B 220 " pdb=" CG2 ILE3B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 27485 not shown) Planarity restraints: 22428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' USA 493 " -0.000 2.00e-02 2.50e+03 7.92e-02 1.41e+02 pdb=" N1 USA 493 " 0.011 2.00e-02 2.50e+03 pdb=" C2 USA 493 " 0.113 2.00e-02 2.50e+03 pdb=" O2 USA 493 " -0.009 2.00e-02 2.50e+03 pdb=" N3 USA 493 " -0.155 2.00e-02 2.50e+03 pdb=" C4 USA 493 " -0.084 2.00e-02 2.50e+03 pdb=" O4 USA 493 " 0.111 2.00e-02 2.50e+03 pdb=" C5 USA 493 " 0.007 2.00e-02 2.50e+03 pdb=" C6 USA 493 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNKUC 233 " -0.044 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" C UNKUC 233 " 0.147 2.00e-02 2.50e+03 pdb=" O UNKUC 233 " -0.053 2.00e-02 2.50e+03 pdb=" N UNKUC 234 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GSA 487 " -0.004 2.00e-02 2.50e+03 3.77e-02 4.27e+01 pdb=" N9 GSA 487 " 0.004 2.00e-02 2.50e+03 pdb=" C8 GSA 487 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GSA 487 " -0.003 2.00e-02 2.50e+03 pdb=" C5 GSA 487 " 0.035 2.00e-02 2.50e+03 pdb=" C6 GSA 487 " -0.111 2.00e-02 2.50e+03 pdb=" O6 GSA 487 " 0.056 2.00e-02 2.50e+03 pdb=" N1 GSA 487 " 0.004 2.00e-02 2.50e+03 pdb=" C2 GSA 487 " 0.016 2.00e-02 2.50e+03 pdb=" N2 GSA 487 " -0.003 2.00e-02 2.50e+03 pdb=" N3 GSA 487 " -0.004 2.00e-02 2.50e+03 pdb=" C4 GSA 487 " 0.009 2.00e-02 2.50e+03 ... (remaining 22425 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 30 1.84 - 2.61: 2109 2.61 - 3.37: 184963 3.37 - 4.14: 376613 4.14 - 4.90: 602680 Nonbonded interactions: 1166395 Sorted by model distance: nonbonded pdb=" CB LEUSK 28 " pdb=" NH1 ARGSf 43 " model vdw 1.079 3.520 nonbonded pdb=" CG LEUSK 28 " pdb=" NH1 ARGSf 43 " model vdw 1.193 3.550 nonbonded pdb=" CG LEUSK 28 " pdb=" CZ ARGSf 43 " model vdw 1.281 3.700 nonbonded pdb=" OP1 A5A 124 " pdb=" N UNKUB 106 " model vdw 1.297 2.520 nonbonded pdb=" N3 USA 558 " pdb=" O UNKUC 234 " model vdw 1.304 2.520 ... (remaining 1166390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '3B' selection = chain '3C' } ncs_group { reference = chain '3G' selection = chain '3H' } ncs_group { reference = (chain 'AA' and resid 15 through 569) selection = (chain 'AG' and resid 59 through 848) selection = chain 'UB' selection = (chain 'UC' and resid 178 through 1033) } ncs_group { reference = (chain 'AB' and resid 28 through 553) selection = (chain 'AC' and resid 97 through 688) selection = chain 'AF' } ncs_group { reference = (chain 'E1' and (resid 28 through 69 or resid 71 through 79 or (resid 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 251 or (re \ sid 252 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)))) selection = (chain 'E2' and (resid 28 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 77 or (resid 78 through 80 and (n \ ame N or name CA or name C or name O or name CB )) or resid 81 through 85 or (re \ sid 86 through 87 and (name N or name CA or name C or name O or name CB )) or re \ sid 88 through 252)) } ncs_group { reference = chain 'E4' selection = chain 'S1' selection = chain 'U1' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 19.370 Check model and map are aligned: 1.610 Set scattering table: 1.020 Process input model: 386.540 Find NCS groups from input model: 5.990 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 423.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 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 : 0.005 0.114 156436 Z= 0.336 Angle : 1.066 19.702 220267 Z= 0.577 Chirality : 0.051 0.555 27488 Planarity : 0.006 0.100 22428 Dihedral : 17.924 179.978 64515 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.51 % Favored : 91.22 % Rotamer: Outliers : 0.28 % Allowed : 3.73 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.15 % Twisted Proline : 1.36 % Twisted General : 0.51 % 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: -4.11 (0.06), residues: 11351 helix: -3.36 (0.06), residues: 3228 sheet: -1.35 (0.10), residues: 2192 loop : -2.93 (0.07), residues: 5931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP3B 144 HIS 0.020 0.003 HISCB 238 PHE 0.048 0.004 PHESG 20 TYR 0.033 0.003 TYR3B 230 ARG 0.016 0.001 ARGB1 870 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3093 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 3065 time to evaluate : 9.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 232 MET cc_start: 0.7551 (mtm) cc_final: 0.7323 (mtm) REVERT: 3B 233 LEU cc_start: 0.7699 (mm) cc_final: 0.7497 (mm) REVERT: 3C 182 SER cc_start: 0.8570 (p) cc_final: 0.8267 (t) REVERT: 3D 21 LYS cc_start: 0.5172 (mttt) cc_final: 0.4944 (mttt) REVERT: 3D 37 GLN cc_start: 0.5071 (mm-40) cc_final: 0.4597 (mm-40) REVERT: 3E 209 ILE cc_start: 0.8825 (mt) cc_final: 0.8593 (tp) REVERT: 3E 330 LEU cc_start: 0.8488 (mt) cc_final: 0.8276 (mm) REVERT: 3E 333 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7184 (tptt) REVERT: 3E 388 LEU cc_start: 0.7534 (tp) cc_final: 0.7051 (tp) REVERT: 3G 98 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6592 (mp) REVERT: 3H 29 ASN cc_start: 0.8553 (m-40) cc_final: 0.8340 (m-40) REVERT: 3H 75 ASN cc_start: 0.7618 (t0) cc_final: 0.7365 (t0) REVERT: 3H 79 VAL cc_start: 0.8638 (t) cc_final: 0.8355 (t) REVERT: AE 81 LEU cc_start: 0.7318 (tp) cc_final: 0.7058 (pp) REVERT: AE 101 TYR cc_start: 0.7882 (t80) cc_final: 0.7362 (t80) REVERT: AE 152 LEU cc_start: 0.8910 (mt) cc_final: 0.8494 (tp) REVERT: AE 418 CYS cc_start: 0.7635 (m) cc_final: 0.7378 (t) REVERT: B1 889 LEU cc_start: 0.8175 (tp) cc_final: 0.7854 (tt) REVERT: BA 338 ILE cc_start: 0.8314 (tt) cc_final: 0.8105 (mt) REVERT: BA 345 PHE cc_start: 0.4538 (m-80) cc_final: 0.3648 (m-80) REVERT: BA 376 SER cc_start: 0.8603 (t) cc_final: 0.8361 (m) REVERT: BA 434 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7751 (t0) REVERT: BA 539 ILE cc_start: 0.7556 (pp) cc_final: 0.7301 (mt) REVERT: BA 614 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7413 (ttm170) REVERT: BA 684 VAL cc_start: 0.9210 (t) cc_final: 0.8424 (p) REVERT: BA 727 VAL cc_start: 0.7927 (t) cc_final: 0.7368 (t) REVERT: BA 821 MET cc_start: 0.7559 (ttp) cc_final: 0.6627 (tmm) REVERT: BB 231 LEU cc_start: 0.7148 (mt) cc_final: 0.6691 (tp) REVERT: BB 539 VAL cc_start: 0.6448 (t) cc_final: 0.6214 (m) REVERT: BB 555 VAL cc_start: 0.7363 (m) cc_final: 0.7076 (p) REVERT: BB 587 MET cc_start: 0.5946 (pmt) cc_final: 0.5673 (pmt) REVERT: BB 597 ILE cc_start: 0.6615 (mp) cc_final: 0.6278 (pt) REVERT: BD 262 LEU cc_start: 0.7001 (mt) cc_final: 0.6560 (mp) REVERT: BD 274 ILE cc_start: 0.7927 (tt) cc_final: 0.7720 (tt) REVERT: BD 385 ASN cc_start: 0.7476 (m-40) cc_final: 0.6735 (m-40) REVERT: BD 500 MET cc_start: 0.0542 (ttm) cc_final: 0.0015 (mtm) REVERT: BD 522 GLN cc_start: 0.0656 (tt0) cc_final: 0.0050 (mp10) REVERT: BD 588 LEU cc_start: 0.8544 (mm) cc_final: 0.8313 (mp) REVERT: BE 32 ASN cc_start: 0.7734 (m-40) cc_final: 0.7189 (m110) REVERT: BE 134 ASP cc_start: 0.7098 (p0) cc_final: 0.6712 (p0) REVERT: BE 235 MET cc_start: 0.7574 (mmm) cc_final: 0.7298 (tpt) REVERT: BE 358 PHE cc_start: 0.9078 (m-80) cc_final: 0.8705 (m-10) REVERT: BE 365 PHE cc_start: 0.7721 (m-80) cc_final: 0.7511 (m-10) REVERT: BE 424 ILE cc_start: 0.8992 (tt) cc_final: 0.8651 (pt) REVERT: BE 439 PHE cc_start: 0.8413 (p90) cc_final: 0.7276 (p90) REVERT: BE 459 ASP cc_start: 0.7924 (p0) cc_final: 0.6507 (t0) REVERT: BE 460 ASP cc_start: 0.7930 (t70) cc_final: 0.7046 (t0) REVERT: BE 465 SER cc_start: 0.9535 (p) cc_final: 0.9308 (t) REVERT: BE 510 LEU cc_start: 0.8305 (tp) cc_final: 0.7926 (tp) REVERT: BE 513 MET cc_start: 0.7428 (mmm) cc_final: 0.6821 (tpp) REVERT: BE 639 ASP cc_start: 0.8527 (p0) cc_final: 0.7985 (p0) REVERT: BE 652 CYS cc_start: 0.8377 (m) cc_final: 0.7651 (m) REVERT: BE 925 LEU cc_start: 0.7831 (mp) cc_final: 0.7505 (mp) REVERT: CA 188 MET cc_start: 0.4896 (mmp) cc_final: 0.4681 (mmm) REVERT: CB 230 VAL cc_start: 0.8310 (t) cc_final: 0.8014 (t) REVERT: CB 519 ASP cc_start: 0.3677 (m-30) cc_final: 0.3178 (m-30) REVERT: CB 644 VAL cc_start: 0.6586 (t) cc_final: 0.5605 (m) REVERT: CB 664 THR cc_start: 0.6575 (m) cc_final: 0.6044 (p) REVERT: CB 734 PHE cc_start: 0.6694 (t80) cc_final: 0.6421 (t80) REVERT: CB 859 ASP cc_start: 0.6240 (m-30) cc_final: 0.5644 (m-30) REVERT: CB 1030 SER cc_start: 0.6563 (p) cc_final: 0.6216 (t) REVERT: CB 1136 LEU cc_start: 0.6752 (mt) cc_final: 0.6438 (mp) REVERT: CB 1152 TYR cc_start: 0.5222 (m-80) cc_final: 0.5005 (m-10) REVERT: E1 250 ASN cc_start: 0.6340 (m-40) cc_final: 0.6065 (t0) REVERT: E2 246 GLU cc_start: 0.6188 (mt-10) cc_final: 0.5848 (mt-10) REVERT: K1 107 SER cc_start: 0.9064 (m) cc_final: 0.8630 (m) REVERT: K1 203 LEU cc_start: 0.8713 (mt) cc_final: 0.8286 (mt) REVERT: MA 43 ASP cc_start: 0.8348 (m-30) cc_final: 0.8029 (m-30) REVERT: MA 46 LYS cc_start: 0.8297 (mttt) cc_final: 0.8097 (mtpt) REVERT: MA 48 ASN cc_start: 0.9095 (t160) cc_final: 0.8631 (t0) REVERT: MA 85 MET cc_start: 0.8522 (mmm) cc_final: 0.8266 (tpp) REVERT: MA 114 ILE cc_start: 0.8981 (mm) cc_final: 0.8739 (mm) REVERT: MA 133 GLN cc_start: 0.7150 (pt0) cc_final: 0.6826 (mt0) REVERT: MA 144 ASN cc_start: 0.8990 (p0) cc_final: 0.8735 (p0) REVERT: MA 152 ARG cc_start: 0.4817 (ttp-170) cc_final: 0.4393 (ttp80) REVERT: MA 154 MET cc_start: 0.7229 (mmt) cc_final: 0.6986 (tpp) REVERT: MB 84 MET cc_start: 0.8338 (mmm) cc_final: 0.7912 (mmm) REVERT: MB 132 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7834 (tttp) REVERT: MB 172 MET cc_start: 0.0465 (mmm) cc_final: -0.3105 (mtt) REVERT: MB 258 LEU cc_start: 0.7600 (tp) cc_final: 0.7289 (tp) REVERT: R1 76 TYR cc_start: 0.7628 (t80) cc_final: 0.7246 (t80) REVERT: R1 138 MET cc_start: 0.7170 (mtt) cc_final: 0.6566 (mmm) REVERT: R1 194 VAL cc_start: 0.8372 (t) cc_final: 0.8133 (p) REVERT: R1 261 ILE cc_start: 0.7388 (pt) cc_final: 0.6537 (mp) REVERT: SC 172 LEU cc_start: 0.6868 (mt) cc_final: 0.6656 (mt) REVERT: SF 210 ILE cc_start: 0.4752 (mm) cc_final: 0.4492 (mm) REVERT: SF 235 TYR cc_start: 0.4739 (m-10) cc_final: 0.2734 (m-80) REVERT: SG 82 PHE cc_start: 0.7625 (m-80) cc_final: 0.6958 (m-80) REVERT: SG 95 ASN cc_start: 0.9076 (m-40) cc_final: 0.8357 (m-40) REVERT: SI 131 PHE cc_start: 0.6701 (t80) cc_final: 0.6144 (t80) REVERT: SI 174 ASN cc_start: 0.6065 (t0) cc_final: 0.5844 (t0) REVERT: SJ 156 VAL cc_start: 0.7973 (t) cc_final: 0.7173 (p) REVERT: SK 30 LEU cc_start: 0.8165 (mt) cc_final: 0.7153 (mt) REVERT: SK 88 GLU cc_start: 0.8148 (pp20) cc_final: 0.7821 (tm-30) REVERT: SM 91 LEU cc_start: 0.7204 (mt) cc_final: 0.6791 (pp) REVERT: SO 14 SER cc_start: 0.9125 (m) cc_final: 0.8754 (p) REVERT: SP 46 MET cc_start: 0.6584 (mtp) cc_final: 0.6216 (mtp) REVERT: SP 83 ILE cc_start: 0.7924 (tp) cc_final: 0.7553 (tt) REVERT: SP 92 LYS cc_start: 0.8699 (mppt) cc_final: 0.8430 (mtmm) REVERT: SR 58 ASP cc_start: 0.7731 (p0) cc_final: 0.7511 (p0) REVERT: SR 85 ILE cc_start: 0.8022 (mt) cc_final: 0.7788 (mm) REVERT: SR 89 LEU cc_start: 0.9018 (tp) cc_final: 0.8798 (tp) REVERT: SX 26 LEU cc_start: 0.8478 (tt) cc_final: 0.8086 (tt) REVERT: SX 65 LEU cc_start: 0.8576 (pt) cc_final: 0.7505 (tp) REVERT: SX 101 TYR cc_start: 0.8511 (m-80) cc_final: 0.7987 (m-80) REVERT: SY 96 VAL cc_start: 0.7056 (m) cc_final: 0.6696 (m) REVERT: Sc 25 VAL cc_start: 0.9051 (t) cc_final: 0.8835 (t) REVERT: Sc 43 ILE cc_start: 0.7634 (pt) cc_final: 0.7366 (pt) REVERT: Sc 44 THR cc_start: 0.6291 (p) cc_final: 0.6050 (m) REVERT: U4 67 ILE cc_start: 0.9279 (mt) cc_final: 0.9073 (mm) REVERT: U4 75 SER cc_start: 0.9417 (m) cc_final: 0.9217 (p) REVERT: U4 94 CYS cc_start: 0.7509 (m) cc_final: 0.7028 (m) REVERT: U4 118 LYS cc_start: 0.8621 (pttt) cc_final: 0.8087 (tptp) REVERT: U4 149 LYS cc_start: 0.7337 (mttp) cc_final: 0.6802 (mmtm) REVERT: U4 164 ILE cc_start: 0.8905 (mt) cc_final: 0.8682 (tp) REVERT: U5 179 GLN cc_start: 0.4455 (tt0) cc_final: 0.3234 (tt0) outliers start: 28 outliers final: 7 residues processed: 3087 average time/residue: 1.3395 time to fit residues: 7186.0895 Evaluate side-chains 1622 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1613 time to evaluate : 9.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1508 optimal weight: 2.9990 chunk 1354 optimal weight: 0.9990 chunk 751 optimal weight: 10.0000 chunk 462 optimal weight: 30.0000 chunk 913 optimal weight: 10.0000 chunk 723 optimal weight: 7.9990 chunk 1400 optimal weight: 7.9990 chunk 542 optimal weight: 0.0980 chunk 851 optimal weight: 2.9990 chunk 1042 optimal weight: 8.9990 chunk 1622 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 91 HIS 3B 183 HIS ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 151 GLN 3D 156 HIS 3D 170 ASN 3D 230 ASN 3E 55 ASN 3E 256 ASN 3E 302 HIS 3E 334 HIS 3E 355 ASN 3G 29 ASN AE 227 ASN AE 258 HIS B1 91 HIS ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 842 ASN ** B1 878 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 893 ASN B1 909 ASN B1 986 HIS B11016 ASN BA 28 GLN ** BA 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 147 GLN BA 156 GLN ** BA 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 303 ASN BA 306 ASN ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 456 HIS BA 485 ASN ** BA 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 598 ASN BB 88 HIS ** BB 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 360 ASN BB 403 ASN BB 455 GLN BB 514 ASN BB 608 HIS BB 628 HIS ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 903 GLN BC 28 ASN BC 54 HIS BC 184 HIS ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 337 HIS ** BC 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 585 ASN ** BC 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 747 ASN BC 757 GLN BC 766 HIS BD 245 HIS ** BD 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 520 ASN ** BD 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 67 HIS BE 86 HIS BE 171 GLN BE 391 GLN BE 473 ASN BE 627 ASN BE 659 GLN ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 381 HIS CB 414 HIS ** CB 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 441 GLN CB 443 HIS CB 445 ASN CB 500 ASN ** CB 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 560 ASN CB 582 GLN CB 634 HIS ** CB 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 729 ASN ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 895 HIS CB1029 ASN CB1073 ASN ** CB1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1159 ASN E1 105 ASN E2 73 HIS E2 243 HIS K1 143 GLN ** K1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 156 HIS MB 168 HIS MB 211 ASN MB 226 ASN P1 232 HIS ** R1 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1 317 GLN ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 79 HIS SC 118 GLN ** SC 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 98 ASN ** SF 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 209 HIS SF 224 ASN SG 34 GLN SG 104 ASN SG 200 ASN SI 42 GLN SJ 9 HIS ** SJ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 105 ASN SR 74 HIS SR 77 GLN SX 44 HIS SX 92 ASN ** SZ 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 77 ASN ** Sd 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U4 148 HIS U4 178 HIS ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 105 ASN U5 165 GLN U5 192 ASN ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 217 GLN Total number of N/Q/H flips: 99 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 156436 Z= 0.196 Angle : 0.713 12.264 220267 Z= 0.362 Chirality : 0.040 0.485 27488 Planarity : 0.005 0.155 22428 Dihedral : 20.060 178.928 42191 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.47 % Favored : 92.32 % Rotamer: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 1.13 % Twisted General : 0.27 % 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: -2.90 (0.07), residues: 11351 helix: -1.45 (0.08), residues: 3339 sheet: -0.97 (0.11), residues: 2227 loop : -2.66 (0.07), residues: 5785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPCB 141 HIS 0.016 0.001 HISBD 348 PHE 0.039 0.002 PHESG 43 TYR 0.035 0.002 TYRBA 193 ARG 0.033 0.001 ARGE1 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2119 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2108 time to evaluate : 9.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.8671 (t0) cc_final: 0.8247 (t0) REVERT: 3B 259 MET cc_start: 0.7370 (tpp) cc_final: 0.6962 (tpp) REVERT: 3C 172 TYR cc_start: 0.5464 (t80) cc_final: 0.5256 (t80) REVERT: 3D 37 GLN cc_start: 0.5161 (mm-40) cc_final: 0.4854 (mm-40) REVERT: 3D 79 LYS cc_start: 0.8789 (mttt) cc_final: 0.8433 (mttp) REVERT: 3D 268 MET cc_start: 0.6298 (mmt) cc_final: 0.5336 (mmm) REVERT: 3E 4 VAL cc_start: 0.4058 (t) cc_final: 0.3832 (t) REVERT: 3E 227 LEU cc_start: 0.5846 (mt) cc_final: 0.5618 (mt) REVERT: 3E 271 GLN cc_start: 0.6355 (tm-30) cc_final: 0.6107 (tm-30) REVERT: 3E 330 LEU cc_start: 0.8758 (mt) cc_final: 0.8362 (mm) REVERT: 3E 333 LYS cc_start: 0.7424 (mtmt) cc_final: 0.7219 (tptt) REVERT: 3F 164 GLN cc_start: 0.6342 (tp-100) cc_final: 0.6093 (tp-100) REVERT: 3F 563 ILE cc_start: 0.5723 (mt) cc_final: 0.5498 (mt) REVERT: 3G 16 LEU cc_start: 0.7159 (tp) cc_final: 0.6835 (tt) REVERT: 3G 71 CYS cc_start: 0.7614 (m) cc_final: 0.7290 (m) REVERT: 3H 29 ASN cc_start: 0.8750 (m-40) cc_final: 0.8307 (m-40) REVERT: 3H 67 LEU cc_start: 0.8994 (mt) cc_final: 0.8736 (mt) REVERT: AE 10 GLN cc_start: 0.8254 (pp30) cc_final: 0.7830 (pp30) REVERT: AE 92 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7887 (mtmm) REVERT: AE 101 TYR cc_start: 0.8064 (t80) cc_final: 0.7782 (t80) REVERT: AE 152 LEU cc_start: 0.9152 (mt) cc_final: 0.8695 (tp) REVERT: AE 179 MET cc_start: 0.8941 (mmm) cc_final: 0.8591 (mmm) REVERT: AE 220 VAL cc_start: 0.8210 (t) cc_final: 0.7919 (t) REVERT: AE 366 ILE cc_start: 0.7332 (mp) cc_final: 0.7074 (mt) REVERT: B1 51 VAL cc_start: 0.7251 (t) cc_final: 0.6717 (p) REVERT: B1 119 LEU cc_start: 0.7347 (mm) cc_final: 0.6866 (mm) REVERT: B1 143 MET cc_start: 0.6772 (mtt) cc_final: 0.6276 (mtm) REVERT: B1 214 LEU cc_start: 0.7203 (tp) cc_final: 0.6027 (tt) REVERT: B1 280 ILE cc_start: 0.4500 (pt) cc_final: 0.4157 (pt) REVERT: B1 845 LEU cc_start: 0.9166 (tp) cc_final: 0.8938 (tp) REVERT: B1 889 LEU cc_start: 0.6864 (tp) cc_final: 0.6553 (tt) REVERT: BA 41 ASP cc_start: 0.8460 (p0) cc_final: 0.8172 (t70) REVERT: BA 376 SER cc_start: 0.8475 (t) cc_final: 0.8147 (m) REVERT: BA 602 CYS cc_start: 0.7286 (t) cc_final: 0.6585 (t) REVERT: BA 614 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7453 (mtp180) REVERT: BA 703 ILE cc_start: 0.7006 (pt) cc_final: 0.6562 (pt) REVERT: BB 563 MET cc_start: 0.8223 (ppp) cc_final: 0.6392 (ttt) REVERT: BB 806 MET cc_start: 0.3813 (mmt) cc_final: 0.3335 (mpp) REVERT: BB 888 ARG cc_start: 0.7478 (ptt180) cc_final: 0.7195 (ptp-170) REVERT: BB 895 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6254 (tm-30) REVERT: BC 169 ASN cc_start: 0.8285 (p0) cc_final: 0.7890 (p0) REVERT: BC 320 LEU cc_start: 0.4678 (mt) cc_final: 0.4265 (mp) REVERT: BC 559 ILE cc_start: 0.6570 (mt) cc_final: 0.6071 (mt) REVERT: BD 262 LEU cc_start: 0.6992 (mt) cc_final: 0.6530 (mp) REVERT: BD 446 ARG cc_start: 0.7009 (ptp-170) cc_final: 0.6640 (ptp-170) REVERT: BD 500 MET cc_start: 0.1189 (ttm) cc_final: 0.0089 (mtm) REVERT: BD 588 LEU cc_start: 0.8572 (mm) cc_final: 0.8345 (mm) REVERT: BE 32 ASN cc_start: 0.8196 (m-40) cc_final: 0.7698 (m-40) REVERT: BE 134 ASP cc_start: 0.6870 (p0) cc_final: 0.6310 (p0) REVERT: BE 310 ILE cc_start: 0.8101 (tt) cc_final: 0.7755 (tt) REVERT: BE 312 THR cc_start: 0.9313 (p) cc_final: 0.9097 (t) REVERT: BE 358 PHE cc_start: 0.8858 (m-80) cc_final: 0.8624 (m-10) REVERT: BE 439 PHE cc_start: 0.8006 (p90) cc_final: 0.7369 (p90) REVERT: BE 459 ASP cc_start: 0.8163 (p0) cc_final: 0.6980 (t0) REVERT: BE 481 ASN cc_start: 0.6613 (m-40) cc_final: 0.6243 (m110) REVERT: BE 489 MET cc_start: 0.8557 (tpt) cc_final: 0.8282 (mmm) REVERT: BE 506 THR cc_start: 0.9376 (p) cc_final: 0.9068 (t) REVERT: BE 549 MET cc_start: 0.9421 (ttm) cc_final: 0.9011 (ttp) REVERT: BE 639 ASP cc_start: 0.8697 (p0) cc_final: 0.7915 (p0) REVERT: BE 644 THR cc_start: 0.8393 (p) cc_final: 0.7956 (p) REVERT: BE 652 CYS cc_start: 0.8449 (m) cc_final: 0.8134 (m) REVERT: BE 924 ASP cc_start: 0.7212 (p0) cc_final: 0.6641 (p0) REVERT: CA 14 ILE cc_start: 0.2339 (mt) cc_final: 0.2054 (mt) REVERT: CB 99 LYS cc_start: 0.0956 (tppt) cc_final: 0.0561 (ttmt) REVERT: CB 209 MET cc_start: -0.0352 (ttp) cc_final: -0.0667 (ttt) REVERT: CB 638 MET cc_start: 0.2154 (mmm) cc_final: 0.1895 (mmm) REVERT: CB 1030 SER cc_start: 0.6909 (p) cc_final: 0.6443 (t) REVERT: CB 1136 LEU cc_start: 0.6940 (mt) cc_final: 0.6580 (mp) REVERT: E1 49 SER cc_start: 0.6849 (p) cc_final: 0.6617 (p) REVERT: E1 92 THR cc_start: 0.6109 (p) cc_final: 0.5726 (p) REVERT: E1 111 GLN cc_start: 0.5577 (tt0) cc_final: 0.5363 (tt0) REVERT: E1 130 ILE cc_start: 0.8000 (mm) cc_final: 0.7771 (mm) REVERT: E1 133 THR cc_start: 0.6757 (p) cc_final: 0.6181 (m) REVERT: E2 124 VAL cc_start: 0.9252 (t) cc_final: 0.8944 (t) REVERT: E2 143 GLN cc_start: 0.7450 (mm110) cc_final: 0.7195 (tp40) REVERT: E2 203 CYS cc_start: 0.7399 (t) cc_final: 0.7022 (t) REVERT: MA 46 LYS cc_start: 0.8366 (mttt) cc_final: 0.8102 (mtpt) REVERT: MA 51 CYS cc_start: 0.8356 (m) cc_final: 0.7870 (t) REVERT: MA 94 ILE cc_start: 0.8995 (mm) cc_final: 0.8176 (mm) REVERT: MA 120 MET cc_start: 0.7761 (mtm) cc_final: 0.7425 (mtm) REVERT: MA 133 GLN cc_start: 0.7400 (pt0) cc_final: 0.7182 (mt0) REVERT: MA 144 ASN cc_start: 0.8895 (p0) cc_final: 0.8280 (p0) REVERT: MB 84 MET cc_start: 0.8131 (mmm) cc_final: 0.7777 (mmm) REVERT: MB 258 LEU cc_start: 0.7886 (tp) cc_final: 0.7543 (tp) REVERT: MC 430 LEU cc_start: 0.8529 (mm) cc_final: 0.8234 (mm) REVERT: P1 116 ILE cc_start: 0.5523 (tp) cc_final: 0.5296 (tp) REVERT: P1 262 ASN cc_start: 0.7482 (p0) cc_final: 0.7192 (p0) REVERT: R1 76 TYR cc_start: 0.7546 (t80) cc_final: 0.7181 (t80) REVERT: R1 111 LYS cc_start: 0.7332 (mtpt) cc_final: 0.7041 (mptt) REVERT: R1 138 MET cc_start: 0.7646 (mtt) cc_final: 0.6823 (mpp) REVERT: R1 170 VAL cc_start: 0.4558 (m) cc_final: 0.4313 (m) REVERT: SC 81 PHE cc_start: 0.8189 (p90) cc_final: 0.7980 (p90) REVERT: SC 88 VAL cc_start: 0.7110 (t) cc_final: 0.6826 (t) REVERT: SC 122 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5811 (mm-30) REVERT: SC 172 LEU cc_start: 0.6558 (mt) cc_final: 0.6338 (mt) REVERT: SF 235 TYR cc_start: 0.4610 (m-10) cc_final: 0.3068 (m-80) REVERT: SK 16 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8386 (mtmt) REVERT: SK 34 PHE cc_start: 0.8034 (m-80) cc_final: 0.7038 (m-80) REVERT: SK 39 LYS cc_start: 0.7029 (ptpp) cc_final: 0.4525 (mmtp) REVERT: SK 52 ILE cc_start: 0.9131 (pt) cc_final: 0.8823 (mm) REVERT: SK 88 GLU cc_start: 0.8043 (pp20) cc_final: 0.7821 (tm-30) REVERT: SK 106 GLU cc_start: 0.7480 (pt0) cc_final: 0.7122 (pt0) REVERT: SO 14 SER cc_start: 0.9125 (m) cc_final: 0.8865 (p) REVERT: SP 46 MET cc_start: 0.5784 (mtp) cc_final: 0.5540 (mtp) REVERT: SP 84 ARG cc_start: 0.5613 (ttt180) cc_final: 0.5187 (ttt180) REVERT: SP 92 LYS cc_start: 0.8942 (mppt) cc_final: 0.8612 (mtmm) REVERT: SP 117 ASP cc_start: 0.7524 (t70) cc_final: 0.7187 (t0) REVERT: SP 118 VAL cc_start: 0.7034 (m) cc_final: 0.6779 (m) REVERT: SR 52 LEU cc_start: 0.8708 (mp) cc_final: 0.8286 (mp) REVERT: SR 58 ASP cc_start: 0.8236 (p0) cc_final: 0.7730 (p0) REVERT: SX 53 ILE cc_start: 0.7337 (pt) cc_final: 0.7087 (pt) REVERT: SY 144 ARG cc_start: 0.5037 (ptp90) cc_final: 0.4674 (ptp-170) REVERT: U4 89 CYS cc_start: 0.6394 (t) cc_final: 0.5997 (t) REVERT: U4 94 CYS cc_start: 0.7502 (m) cc_final: 0.6307 (m) REVERT: U4 118 LYS cc_start: 0.8486 (pttt) cc_final: 0.8282 (tptp) REVERT: U4 149 LYS cc_start: 0.6965 (mttp) cc_final: 0.6412 (mtpt) outliers start: 11 outliers final: 2 residues processed: 2115 average time/residue: 1.2243 time to fit residues: 4574.0025 Evaluate side-chains 1453 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1451 time to evaluate : 9.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 901 optimal weight: 1.9990 chunk 503 optimal weight: 20.0000 chunk 1350 optimal weight: 2.9990 chunk 1105 optimal weight: 50.0000 chunk 447 optimal weight: 20.0000 chunk 1625 optimal weight: 6.9990 chunk 1756 optimal weight: 9.9990 chunk 1447 optimal weight: 9.9990 chunk 1612 optimal weight: 10.0000 chunk 554 optimal weight: 6.9990 chunk 1304 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 258 HIS ** 3C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 39 ASN ** 3D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 67 ASN 3D 398 ASN ** 3E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 203 ASN AE 233 GLN B1 136 ASN ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 218 ASN B11016 ASN ** BA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 54 HIS ** BA 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 139 HIS BA 145 HIS BA 306 ASN ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 485 ASN BA 597 ASN BA 598 ASN BA 691 ASN ** BA 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 746 ASN BA 791 HIS BA 813 HIS ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 388 GLN BB 626 GLN ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 13 ASN ** BC 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 618 ASN ** BD 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 498 ASN BD 520 ASN ** BD 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 101 ASN ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 197 GLN ** CB 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 378 ASN ** CB 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1023 ASN ** CB1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1154 ASN CB1159 ASN E1 105 ASN E1 143 GLN E2 73 HIS E2 243 HIS ** K1 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 48 ASN MB 211 ASN P1 111 ASN P1 123 HIS R1 126 ASN ** R1 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1 317 GLN ** R1 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 74 GLN ** SC 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 118 GLN ** SF 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 224 ASN SG 79 ASN SG 104 ASN ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 200 ASN SI 29 ASN ** SJ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 176 ASN SR 94 GLN ** SX 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 44 HIS SZ 34 ASN SZ 63 GLN ** U4 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 105 ASN U5 133 HIS ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 156436 Z= 0.348 Angle : 0.893 13.971 220267 Z= 0.446 Chirality : 0.046 0.426 27488 Planarity : 0.006 0.092 22428 Dihedral : 20.197 179.192 42191 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.74 % Favored : 89.09 % Rotamer: Outliers : 0.33 % Allowed : 5.72 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 1.13 % Twisted General : 0.30 % 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: -2.65 (0.07), residues: 11351 helix: -0.86 (0.08), residues: 3353 sheet: -1.02 (0.11), residues: 2163 loop : -2.66 (0.07), residues: 5835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRPCB 141 HIS 0.020 0.002 HISBA 91 PHE 0.041 0.003 PHESK 34 TYR 0.033 0.003 TYRB1 253 ARG 0.022 0.001 ARGCB 853 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1751 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1718 time to evaluate : 9.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 253 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8733 (mm) REVERT: 3B 261 LEU cc_start: 0.8907 (tp) cc_final: 0.8590 (tp) REVERT: 3C 252 ILE cc_start: 0.7760 (mm) cc_final: 0.7509 (mt) REVERT: 3C 316 VAL cc_start: 0.8559 (t) cc_final: 0.8298 (t) REVERT: 3D 21 LYS cc_start: 0.5446 (mttt) cc_final: 0.5116 (mmtt) REVERT: 3D 39 ASN cc_start: 0.8068 (m-40) cc_final: 0.7715 (p0) REVERT: 3D 268 MET cc_start: 0.6383 (mmt) cc_final: 0.5815 (mmt) REVERT: 3E 57 LEU cc_start: 0.6663 (pp) cc_final: 0.5969 (mm) REVERT: 3E 94 LEU cc_start: 0.8368 (mt) cc_final: 0.7796 (tp) REVERT: 3E 124 LEU cc_start: 0.4399 (mt) cc_final: 0.4015 (mt) REVERT: 3E 139 MET cc_start: 0.0915 (ppp) cc_final: 0.0699 (ppp) REVERT: 3E 230 GLU cc_start: 0.7395 (mp0) cc_final: 0.6395 (tm-30) REVERT: 3E 330 LEU cc_start: 0.8489 (mt) cc_final: 0.8250 (mm) REVERT: 3F 333 MET cc_start: 0.6109 (tpp) cc_final: 0.5225 (mmt) REVERT: 3G 16 LEU cc_start: 0.7160 (tp) cc_final: 0.6823 (tt) REVERT: 3H 29 ASN cc_start: 0.8812 (m-40) cc_final: 0.8520 (m-40) REVERT: 3H 67 LEU cc_start: 0.9179 (mt) cc_final: 0.8926 (mt) REVERT: AE 101 TYR cc_start: 0.8070 (t80) cc_final: 0.7735 (t80) REVERT: AE 179 MET cc_start: 0.9019 (mmm) cc_final: 0.8692 (mmm) REVERT: AE 212 PHE cc_start: 0.8502 (t80) cc_final: 0.8171 (t80) REVERT: AE 249 LYS cc_start: 0.7171 (mtmt) cc_final: 0.6449 (mmtp) REVERT: AE 279 MET cc_start: 0.8230 (ttm) cc_final: 0.7711 (ttp) REVERT: AE 300 CYS cc_start: 0.7424 (m) cc_final: 0.5881 (m) REVERT: B1 845 LEU cc_start: 0.8982 (tp) cc_final: 0.8716 (tp) REVERT: BA 41 ASP cc_start: 0.8000 (p0) cc_final: 0.7796 (p0) REVERT: BA 176 ASP cc_start: 0.8336 (m-30) cc_final: 0.6780 (m-30) REVERT: BA 180 LYS cc_start: 0.7583 (mtpt) cc_final: 0.6766 (mtmt) REVERT: BA 190 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.3241 (m-70) REVERT: BA 331 GLU cc_start: 0.7744 (tp30) cc_final: 0.7366 (tp30) REVERT: BA 435 CYS cc_start: 0.8275 (t) cc_final: 0.8059 (t) REVERT: BA 473 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6849 (mm-30) REVERT: BA 539 ILE cc_start: 0.7720 (pt) cc_final: 0.7501 (mt) REVERT: BA 602 CYS cc_start: 0.7191 (t) cc_final: 0.6768 (t) REVERT: BA 608 ASN cc_start: 0.8237 (m110) cc_final: 0.7865 (m-40) REVERT: BA 701 LEU cc_start: 0.5615 (mt) cc_final: 0.5053 (mt) REVERT: BB 238 MET cc_start: 0.5688 (tpt) cc_final: 0.5256 (mmm) REVERT: BB 563 MET cc_start: 0.7881 (ppp) cc_final: 0.5174 (mtp) REVERT: BB 895 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6559 (tm-30) REVERT: BC 169 ASN cc_start: 0.8615 (p0) cc_final: 0.8321 (p0) REVERT: BC 692 MET cc_start: 0.8034 (mmt) cc_final: 0.7675 (mpp) REVERT: BC 782 VAL cc_start: 0.7305 (m) cc_final: 0.7033 (p) REVERT: BC 791 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8427 (mtm-85) REVERT: BD 262 LEU cc_start: 0.7239 (mt) cc_final: 0.6663 (mp) REVERT: BD 274 ILE cc_start: 0.7712 (tt) cc_final: 0.7322 (tt) REVERT: BD 317 ARG cc_start: 0.5368 (mmp-170) cc_final: 0.5005 (mmp80) REVERT: BD 354 SER cc_start: 0.7198 (m) cc_final: 0.5681 (m) REVERT: BD 385 ASN cc_start: 0.7667 (m110) cc_final: 0.7198 (m-40) REVERT: BD 500 MET cc_start: 0.1430 (ttm) cc_final: 0.0739 (mtt) REVERT: BE 61 TYR cc_start: 0.6875 (m-10) cc_final: 0.6123 (m-80) REVERT: BE 134 ASP cc_start: 0.7304 (p0) cc_final: 0.6947 (p0) REVERT: BE 323 VAL cc_start: 0.8273 (t) cc_final: 0.7787 (t) REVERT: BE 343 LEU cc_start: 0.8112 (tp) cc_final: 0.7744 (tt) REVERT: BE 439 PHE cc_start: 0.8609 (p90) cc_final: 0.8304 (p90) REVERT: BE 489 MET cc_start: 0.8914 (tpt) cc_final: 0.8329 (tmm) REVERT: BE 523 ASP cc_start: 0.9173 (p0) cc_final: 0.8277 (p0) REVERT: BE 549 MET cc_start: 0.9338 (ttm) cc_final: 0.9133 (ttp) REVERT: BE 639 ASP cc_start: 0.8934 (p0) cc_final: 0.8580 (p0) REVERT: BE 920 ASP cc_start: 0.7482 (m-30) cc_final: 0.7084 (t0) REVERT: BE 925 LEU cc_start: 0.8312 (mp) cc_final: 0.7789 (mp) REVERT: CB 141 TRP cc_start: 0.3011 (t60) cc_final: 0.2244 (t60) REVERT: CB 644 VAL cc_start: 0.6170 (t) cc_final: 0.4869 (m) REVERT: CB 756 VAL cc_start: 0.7616 (m) cc_final: 0.6735 (p) REVERT: CB 1030 SER cc_start: 0.7028 (p) cc_final: 0.6641 (p) REVERT: E1 106 LYS cc_start: 0.7281 (mmtt) cc_final: 0.7058 (mttt) REVERT: E1 133 THR cc_start: 0.6701 (p) cc_final: 0.5754 (m) REVERT: E2 124 VAL cc_start: 0.9256 (t) cc_final: 0.9048 (t) REVERT: E2 143 GLN cc_start: 0.7692 (mm110) cc_final: 0.7451 (tp40) REVERT: E2 203 CYS cc_start: 0.7338 (t) cc_final: 0.7086 (t) REVERT: K1 121 MET cc_start: 0.8146 (ttm) cc_final: 0.7568 (ttm) REVERT: MA 46 LYS cc_start: 0.8530 (mttt) cc_final: 0.8299 (mtpt) REVERT: MA 94 ILE cc_start: 0.9039 (mm) cc_final: 0.8020 (mm) REVERT: MB 207 LYS cc_start: 0.8353 (mttt) cc_final: 0.8081 (tmtt) REVERT: MB 259 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.4418 (t80) REVERT: R1 322 PHE cc_start: 0.5187 (t80) cc_final: 0.4966 (t80) REVERT: SC 88 VAL cc_start: 0.7487 (t) cc_final: 0.7224 (t) REVERT: SC 113 MET cc_start: 0.7453 (ttm) cc_final: 0.6387 (ttm) REVERT: SC 121 ILE cc_start: 0.8541 (pt) cc_final: 0.8162 (pt) REVERT: SC 224 ASP cc_start: 0.8427 (m-30) cc_final: 0.7776 (m-30) REVERT: SJ 189 LEU cc_start: 0.6627 (mt) cc_final: 0.6392 (mt) REVERT: SK 52 ILE cc_start: 0.9194 (pt) cc_final: 0.8635 (mm) REVERT: SM 90 TYR cc_start: 0.4336 (t80) cc_final: 0.3998 (t80) REVERT: SM 100 TYR cc_start: 0.6167 (m-10) cc_final: 0.5441 (m-10) REVERT: SM 116 ARG cc_start: 0.2945 (mpp80) cc_final: 0.0823 (mmm160) REVERT: SO 98 VAL cc_start: 0.8565 (t) cc_final: 0.8228 (p) REVERT: SO 117 LEU cc_start: 0.7611 (mt) cc_final: 0.7339 (mm) REVERT: SP 46 MET cc_start: 0.6290 (mtp) cc_final: 0.5985 (mtp) REVERT: SP 92 LYS cc_start: 0.8967 (mppt) cc_final: 0.8685 (mtmm) REVERT: SY 95 PHE cc_start: 0.8137 (m-80) cc_final: 0.7789 (m-80) REVERT: Sd 51 ASN cc_start: 0.8864 (m110) cc_final: 0.7687 (m110) REVERT: U4 150 CYS cc_start: 0.8658 (p) cc_final: 0.7624 (t) REVERT: U5 189 TYR cc_start: 0.5359 (m-80) cc_final: 0.4274 (m-80) outliers start: 33 outliers final: 9 residues processed: 1748 average time/residue: 1.2165 time to fit residues: 3768.8140 Evaluate side-chains 1280 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1267 time to evaluate : 9.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1606 optimal weight: 0.2980 chunk 1222 optimal weight: 9.9990 chunk 843 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 775 optimal weight: 9.9990 chunk 1091 optimal weight: 0.9980 chunk 1631 optimal weight: 7.9990 chunk 1727 optimal weight: 9.9990 chunk 852 optimal weight: 2.9990 chunk 1546 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 264 GLN 3C 303 GLN ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 38 ASN ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B11016 ASN BA 45 ASN BA 92 HIS BA 132 GLN BA 145 HIS BA 190 HIS BA 306 ASN ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 485 ASN BA 598 ASN BA 724 HIS BA 734 GLN ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 13 ASN BC 74 GLN BC 241 GLN ** BC 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 766 HIS ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 289 ASN ** BE 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 447 ASN BE 627 ASN BE 645 HIS ** CA 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 441 GLN ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 895 HIS CB 904 HIS CB 907 GLN CB1083 GLN CB1159 ASN E1 53 HIS E1 105 ASN E2 73 HIS K1 151 ASN ** K1 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 211 ASN MB 235 GLN P1 111 ASN P1 123 HIS R1 152 HIS R1 206 ASN R1 334 ASN ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 118 GLN SC 211 HIS ** SF 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 224 ASN ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 79 ASN ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 89 HIS SK 38 ASN ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 70 ASN ** SY 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 41 ASN ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 156436 Z= 0.200 Angle : 0.681 13.427 220267 Z= 0.343 Chirality : 0.040 0.514 27488 Planarity : 0.004 0.089 22428 Dihedral : 19.911 179.459 42191 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.26 % Favored : 91.60 % Rotamer: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 1.13 % Twisted General : 0.19 % 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: -2.22 (0.07), residues: 11351 helix: -0.29 (0.09), residues: 3373 sheet: -0.83 (0.11), residues: 2152 loop : -2.52 (0.07), residues: 5826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPB1 174 HIS 0.009 0.001 HISBA 584 PHE 0.036 0.002 PHECB 964 TYR 0.028 0.002 TYRU5 203 ARG 0.010 0.001 ARGSZ 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1737 time to evaluate : 9.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.8990 (t0) cc_final: 0.8328 (t0) REVERT: 3B 259 MET cc_start: 0.7207 (tpp) cc_final: 0.6676 (tpp) REVERT: 3B 261 LEU cc_start: 0.8733 (tp) cc_final: 0.8443 (tp) REVERT: 3B 286 PHE cc_start: 0.8242 (m-80) cc_final: 0.7903 (m-80) REVERT: 3B 295 GLU cc_start: 0.7830 (pp20) cc_final: 0.6970 (tm-30) REVERT: 3C 252 ILE cc_start: 0.7650 (mm) cc_final: 0.7324 (mt) REVERT: 3D 88 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7680 (mmmt) REVERT: 3D 268 MET cc_start: 0.6394 (mmt) cc_final: 0.5658 (mmt) REVERT: 3D 272 CYS cc_start: 0.8459 (m) cc_final: 0.8243 (m) REVERT: 3E 57 LEU cc_start: 0.6674 (pp) cc_final: 0.5962 (mm) REVERT: 3E 154 PHE cc_start: 0.5513 (m-80) cc_final: 0.5087 (m-80) REVERT: 3F 333 MET cc_start: 0.5843 (tpp) cc_final: 0.5128 (mmt) REVERT: 3G 16 LEU cc_start: 0.6925 (tp) cc_final: 0.6323 (tt) REVERT: 3G 25 GLN cc_start: 0.7637 (tp40) cc_final: 0.7390 (tp40) REVERT: 3G 71 CYS cc_start: 0.7765 (m) cc_final: 0.7506 (m) REVERT: 3G 80 PHE cc_start: 0.6942 (m-10) cc_final: 0.6037 (m-80) REVERT: 3H 29 ASN cc_start: 0.8801 (m-40) cc_final: 0.8532 (t0) REVERT: 3H 111 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8369 (mtpp) REVERT: AE 101 TYR cc_start: 0.8075 (t80) cc_final: 0.7874 (t80) REVERT: AE 279 MET cc_start: 0.8126 (ttm) cc_final: 0.7835 (ttm) REVERT: AE 300 CYS cc_start: 0.6919 (m) cc_final: 0.5481 (m) REVERT: B1 147 LEU cc_start: 0.6577 (mt) cc_final: 0.6221 (mt) REVERT: BA 331 GLU cc_start: 0.7072 (tp30) cc_final: 0.6715 (tp30) REVERT: BA 338 ILE cc_start: 0.8620 (mt) cc_final: 0.8401 (mt) REVERT: BA 368 LYS cc_start: 0.6976 (pttm) cc_final: 0.6346 (pttm) REVERT: BA 376 SER cc_start: 0.8491 (t) cc_final: 0.8284 (m) REVERT: BA 408 ASP cc_start: 0.7825 (m-30) cc_final: 0.7548 (p0) REVERT: BA 602 CYS cc_start: 0.6811 (t) cc_final: 0.6445 (t) REVERT: BA 682 THR cc_start: 0.8377 (p) cc_final: 0.7907 (m) REVERT: BA 733 LYS cc_start: 0.6512 (ptmt) cc_final: 0.5932 (ptmt) REVERT: BB 238 MET cc_start: 0.5568 (tpt) cc_final: 0.5088 (mmm) REVERT: BB 653 LEU cc_start: 0.4412 (mt) cc_final: 0.4058 (mp) REVERT: BB 753 MET cc_start: 0.4208 (mmm) cc_final: 0.3954 (tpt) REVERT: BB 895 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6161 (tm-30) REVERT: BC 169 ASN cc_start: 0.8905 (p0) cc_final: 0.8415 (p0) REVERT: BC 172 VAL cc_start: 0.6152 (t) cc_final: 0.5930 (t) REVERT: BC 320 LEU cc_start: 0.4479 (mt) cc_final: 0.4197 (mp) REVERT: BC 337 HIS cc_start: 0.5936 (t-90) cc_final: 0.5729 (t-170) REVERT: BC 559 ILE cc_start: 0.6519 (mt) cc_final: 0.6068 (mt) REVERT: BC 740 MET cc_start: 0.9225 (tmm) cc_final: 0.8970 (tmm) REVERT: BC 782 VAL cc_start: 0.6779 (m) cc_final: 0.6376 (m) REVERT: BD 262 LEU cc_start: 0.7167 (mt) cc_final: 0.6616 (mp) REVERT: BD 274 ILE cc_start: 0.7555 (tt) cc_final: 0.6952 (tt) REVERT: BD 317 ARG cc_start: 0.5456 (mmp-170) cc_final: 0.5030 (mmp80) REVERT: BD 354 SER cc_start: 0.7062 (m) cc_final: 0.5601 (m) REVERT: BD 433 TRP cc_start: 0.6867 (t-100) cc_final: 0.6237 (t-100) REVERT: BD 446 ARG cc_start: 0.6845 (ptp-170) cc_final: 0.6621 (ptp90) REVERT: BD 500 MET cc_start: 0.3358 (ttm) cc_final: -0.0097 (mtt) REVERT: BE 134 ASP cc_start: 0.7212 (p0) cc_final: 0.6896 (p0) REVERT: BE 387 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7214 (tm-30) REVERT: BE 439 PHE cc_start: 0.8539 (p90) cc_final: 0.8335 (p90) REVERT: BE 489 MET cc_start: 0.8666 (tpt) cc_final: 0.8197 (mmm) REVERT: BE 510 LEU cc_start: 0.8650 (tp) cc_final: 0.8433 (tp) REVERT: BE 639 ASP cc_start: 0.8729 (p0) cc_final: 0.8217 (p0) REVERT: BE 796 LEU cc_start: 0.5342 (tt) cc_final: 0.5010 (tt) REVERT: CA 206 ILE cc_start: 0.9061 (mm) cc_final: 0.8623 (tp) REVERT: CB 264 LEU cc_start: 0.3599 (mt) cc_final: 0.3367 (pp) REVERT: CB 336 VAL cc_start: 0.5387 (t) cc_final: 0.5114 (p) REVERT: CB 480 MET cc_start: 0.2823 (ppp) cc_final: 0.2623 (ppp) REVERT: CB 644 VAL cc_start: 0.7463 (t) cc_final: 0.7231 (t) REVERT: CB 1030 SER cc_start: 0.6909 (p) cc_final: 0.6270 (t) REVERT: CB 1230 MET cc_start: 0.3399 (mmp) cc_final: 0.2711 (mmp) REVERT: E1 92 THR cc_start: 0.7198 (p) cc_final: 0.6987 (p) REVERT: E1 106 LYS cc_start: 0.7325 (mmtt) cc_final: 0.7029 (mttt) REVERT: E1 133 THR cc_start: 0.6265 (p) cc_final: 0.5964 (t) REVERT: E1 209 MET cc_start: 0.6851 (pmm) cc_final: 0.6623 (pmm) REVERT: E2 42 ILE cc_start: 0.8125 (mp) cc_final: 0.7880 (mp) REVERT: E2 203 CYS cc_start: 0.7316 (t) cc_final: 0.6975 (t) REVERT: K1 151 ASN cc_start: 0.6591 (OUTLIER) cc_final: 0.6390 (t0) REVERT: K1 202 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5838 (mm-30) REVERT: MA 51 CYS cc_start: 0.8528 (m) cc_final: 0.8037 (t) REVERT: MA 67 THR cc_start: 0.8780 (p) cc_final: 0.8560 (p) REVERT: MA 114 ILE cc_start: 0.9196 (mm) cc_final: 0.8978 (mm) REVERT: MA 118 LEU cc_start: 0.8664 (mt) cc_final: 0.8410 (mm) REVERT: MA 132 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7337 (mt-10) REVERT: MA 144 ASN cc_start: 0.8834 (p0) cc_final: 0.8496 (p0) REVERT: MB 132 LYS cc_start: 0.7880 (tttt) cc_final: 0.7558 (tttt) REVERT: MC 436 GLU cc_start: 0.7519 (pp20) cc_final: 0.6904 (pp20) REVERT: R1 111 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7062 (mmtt) REVERT: R1 138 MET cc_start: 0.7690 (mtt) cc_final: 0.6815 (mmp) REVERT: R1 196 TYR cc_start: 0.8100 (p90) cc_final: 0.7534 (p90) REVERT: R1 244 THR cc_start: 0.7402 (m) cc_final: 0.7196 (m) REVERT: SC 88 VAL cc_start: 0.7373 (t) cc_final: 0.7045 (t) REVERT: SC 224 ASP cc_start: 0.7947 (m-30) cc_final: 0.7697 (m-30) REVERT: SK 34 PHE cc_start: 0.7302 (m-10) cc_final: 0.6956 (m-10) REVERT: SK 39 LYS cc_start: 0.6495 (ptpp) cc_final: 0.5372 (mmmm) REVERT: SK 52 ILE cc_start: 0.9082 (pt) cc_final: 0.8748 (mm) REVERT: SK 88 GLU cc_start: 0.8168 (pp20) cc_final: 0.7938 (tm-30) REVERT: SK 106 GLU cc_start: 0.7596 (pt0) cc_final: 0.7323 (pt0) REVERT: SM 80 MET cc_start: 0.6042 (mpp) cc_final: 0.5723 (mtm) REVERT: SM 90 TYR cc_start: 0.4275 (t80) cc_final: 0.3800 (t80) REVERT: SM 100 TYR cc_start: 0.5881 (m-10) cc_final: 0.5558 (m-80) REVERT: SM 116 ARG cc_start: 0.2691 (mpp80) cc_final: 0.0161 (mmm160) REVERT: SO 98 VAL cc_start: 0.8411 (t) cc_final: 0.8104 (p) REVERT: SR 47 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8774 (mmmt) REVERT: SR 52 LEU cc_start: 0.8709 (mp) cc_final: 0.8316 (mp) REVERT: SR 83 GLN cc_start: 0.7996 (tp40) cc_final: 0.7594 (tp40) REVERT: SR 96 TYR cc_start: 0.8416 (m-80) cc_final: 0.8044 (m-80) REVERT: SR 103 ASN cc_start: 0.8385 (m110) cc_final: 0.8016 (m-40) REVERT: SX 70 ASN cc_start: 0.8267 (m-40) cc_final: 0.8029 (m-40) REVERT: SY 95 PHE cc_start: 0.7863 (m-80) cc_final: 0.7652 (m-80) REVERT: U4 150 CYS cc_start: 0.8555 (p) cc_final: 0.7612 (t) REVERT: U5 56 ILE cc_start: 0.7591 (tp) cc_final: 0.7248 (tp) REVERT: U5 189 TYR cc_start: 0.5746 (m-80) cc_final: 0.4457 (m-80) outliers start: 5 outliers final: 0 residues processed: 1742 average time/residue: 1.2208 time to fit residues: 3770.6841 Evaluate side-chains 1290 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1289 time to evaluate : 9.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1438 optimal weight: 4.9990 chunk 980 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 1286 optimal weight: 20.0000 chunk 712 optimal weight: 0.0010 chunk 1473 optimal weight: 5.9990 chunk 1193 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 882 optimal weight: 0.6980 chunk 1550 optimal weight: 20.0000 chunk 435 optimal weight: 0.6980 overall best weight: 2.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 93 HIS ** 3B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 268 HIS B11016 ASN BA 17 GLN BA 28 GLN BA 145 HIS ** BA 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 306 ASN ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 485 ASN ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 584 HIS BA 598 ASN BA 734 GLN ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 13 ASN ** BC 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 204 ASN BC 241 GLN ** BC 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 32 ASN BE 171 GLN BE 285 HIS ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 171 ASN ** CB 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1159 ASN E1 105 ASN ** E1 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 73 HIS E2 143 GLN ** K1 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 211 ASN ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 42 ASN SC 118 GLN SC 211 HIS SF 224 ASN ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 79 ASN ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 89 HIS SI 174 ASN SJ 116 HIS SR 21 HIS ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 34 ASN ** Sc 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 52 ASN U5 105 ASN U5 186 ASN ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 156436 Z= 0.182 Angle : 0.649 11.843 220267 Z= 0.327 Chirality : 0.039 0.503 27488 Planarity : 0.004 0.137 22428 Dihedral : 19.765 179.395 42191 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.92 % Favored : 90.98 % Rotamer: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 1.13 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.08), residues: 11351 helix: 0.00 (0.09), residues: 3377 sheet: -0.72 (0.11), residues: 2172 loop : -2.46 (0.08), residues: 5802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPBD 383 HIS 0.011 0.001 HISBB 162 PHE 0.031 0.002 PHEBA 345 TYR 0.024 0.002 TYRU5 203 ARG 0.017 0.000 ARG3F 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1680 time to evaluate : 9.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.9003 (t0) cc_final: 0.8524 (t0) REVERT: 3B 236 MET cc_start: 0.7111 (mmm) cc_final: 0.6888 (mmm) REVERT: 3B 261 LEU cc_start: 0.8622 (tp) cc_final: 0.8422 (tp) REVERT: 3B 286 PHE cc_start: 0.8441 (m-80) cc_final: 0.8170 (m-80) REVERT: 3B 295 GLU cc_start: 0.7775 (pp20) cc_final: 0.7051 (tm-30) REVERT: 3C 252 ILE cc_start: 0.7566 (mm) cc_final: 0.7348 (mt) REVERT: 3D 88 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7677 (mmmt) REVERT: 3D 268 MET cc_start: 0.6337 (mmt) cc_final: 0.5642 (mmt) REVERT: 3D 272 CYS cc_start: 0.8487 (m) cc_final: 0.8195 (m) REVERT: 3E 57 LEU cc_start: 0.7094 (pp) cc_final: 0.6873 (mm) REVERT: 3E 154 PHE cc_start: 0.5656 (m-80) cc_final: 0.5355 (m-80) REVERT: 3F 333 MET cc_start: 0.5879 (tpp) cc_final: 0.5203 (mmt) REVERT: 3F 563 ILE cc_start: 0.6381 (mt) cc_final: 0.6144 (mt) REVERT: 3G 16 LEU cc_start: 0.6891 (tp) cc_final: 0.6455 (tp) REVERT: 3G 17 THR cc_start: 0.7723 (m) cc_final: 0.7493 (m) REVERT: 3G 54 MET cc_start: 0.6963 (ttt) cc_final: 0.6747 (ttm) REVERT: 3G 71 CYS cc_start: 0.7896 (m) cc_final: 0.7519 (m) REVERT: 3G 80 PHE cc_start: 0.6923 (m-10) cc_final: 0.6108 (m-80) REVERT: 3H 29 ASN cc_start: 0.8893 (m-40) cc_final: 0.8625 (t0) REVERT: AE 101 TYR cc_start: 0.7887 (t80) cc_final: 0.7652 (t80) REVERT: AE 275 ILE cc_start: 0.8290 (mt) cc_final: 0.7994 (tt) REVERT: AE 279 MET cc_start: 0.8187 (ttm) cc_final: 0.7594 (ttm) REVERT: AE 300 CYS cc_start: 0.6972 (m) cc_final: 0.5486 (m) REVERT: AE 367 LEU cc_start: 0.8098 (tt) cc_final: 0.7735 (tp) REVERT: B1 889 LEU cc_start: 0.7723 (tp) cc_final: 0.7291 (tt) REVERT: BA 338 ILE cc_start: 0.8324 (mt) cc_final: 0.8021 (mt) REVERT: BA 376 SER cc_start: 0.8486 (t) cc_final: 0.8220 (m) REVERT: BA 408 ASP cc_start: 0.8241 (m-30) cc_final: 0.7890 (p0) REVERT: BA 478 CYS cc_start: 0.9160 (t) cc_final: 0.8699 (m) REVERT: BA 539 ILE cc_start: 0.6693 (mt) cc_final: 0.6354 (mt) REVERT: BA 602 CYS cc_start: 0.7166 (t) cc_final: 0.6697 (t) REVERT: BA 682 THR cc_start: 0.8458 (p) cc_final: 0.7990 (m) REVERT: BB 217 LEU cc_start: 0.6799 (tp) cc_final: 0.6223 (pp) REVERT: BB 238 MET cc_start: 0.4710 (tpt) cc_final: 0.4509 (mmm) REVERT: BB 519 VAL cc_start: 0.5603 (t) cc_final: 0.5388 (t) REVERT: BB 563 MET cc_start: 0.7886 (ppp) cc_final: 0.5140 (mtp) REVERT: BB 636 ASP cc_start: 0.7666 (p0) cc_final: 0.7075 (p0) REVERT: BB 753 MET cc_start: 0.3907 (mmm) cc_final: 0.3682 (tpt) REVERT: BC 169 ASN cc_start: 0.8969 (p0) cc_final: 0.8471 (p0) REVERT: BC 320 LEU cc_start: 0.4552 (mt) cc_final: 0.4291 (mp) REVERT: BC 559 ILE cc_start: 0.6377 (mt) cc_final: 0.5950 (mt) REVERT: BC 782 VAL cc_start: 0.6988 (m) cc_final: 0.6477 (m) REVERT: BC 803 SER cc_start: 0.8716 (m) cc_final: 0.8497 (m) REVERT: BD 262 LEU cc_start: 0.7157 (mt) cc_final: 0.6535 (mp) REVERT: BD 274 ILE cc_start: 0.7477 (tt) cc_final: 0.6828 (tt) REVERT: BD 433 TRP cc_start: 0.6461 (t-100) cc_final: 0.6074 (t-100) REVERT: BD 446 ARG cc_start: 0.6740 (ptp-170) cc_final: 0.6364 (ptp-170) REVERT: BD 490 PHE cc_start: 0.4248 (t80) cc_final: 0.4004 (t80) REVERT: BD 500 MET cc_start: 0.2289 (ttm) cc_final: -0.1052 (mtt) REVERT: BD 587 ARG cc_start: 0.7318 (mpt-90) cc_final: 0.6560 (mpt-90) REVERT: BE 415 VAL cc_start: 0.8659 (t) cc_final: 0.8182 (p) REVERT: BE 489 MET cc_start: 0.8654 (tpt) cc_final: 0.8125 (mmm) REVERT: BE 510 LEU cc_start: 0.8594 (tp) cc_final: 0.8368 (tp) REVERT: BE 549 MET cc_start: 0.9256 (ttm) cc_final: 0.9029 (ttp) REVERT: BE 614 LEU cc_start: 0.9260 (mp) cc_final: 0.8898 (mt) REVERT: BE 639 ASP cc_start: 0.8656 (p0) cc_final: 0.8042 (p0) REVERT: BE 796 LEU cc_start: 0.5214 (tt) cc_final: 0.4929 (tt) REVERT: CA 206 ILE cc_start: 0.9062 (mm) cc_final: 0.8701 (tp) REVERT: CB 336 VAL cc_start: 0.5306 (t) cc_final: 0.5068 (p) REVERT: CB 364 VAL cc_start: 0.5392 (t) cc_final: 0.5152 (t) REVERT: CB 480 MET cc_start: 0.2739 (ppp) cc_final: 0.1847 (ppp) REVERT: CB 863 TYR cc_start: 0.7008 (m-80) cc_final: 0.5638 (m-10) REVERT: CB 1030 SER cc_start: 0.6997 (p) cc_final: 0.6342 (t) REVERT: CB 1230 MET cc_start: 0.3201 (mmp) cc_final: 0.2333 (mmp) REVERT: E1 106 LYS cc_start: 0.6937 (mmtt) cc_final: 0.6540 (mttt) REVERT: E1 133 THR cc_start: 0.6323 (p) cc_final: 0.6000 (t) REVERT: E2 203 CYS cc_start: 0.7216 (t) cc_final: 0.6917 (t) REVERT: K1 206 LYS cc_start: 0.7987 (mptt) cc_final: 0.7546 (mptt) REVERT: MA 51 CYS cc_start: 0.8467 (m) cc_final: 0.7976 (t) REVERT: MA 132 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7292 (mt-10) REVERT: MA 144 ASN cc_start: 0.8817 (p0) cc_final: 0.8564 (p0) REVERT: P1 245 GLU cc_start: 0.8179 (pm20) cc_final: 0.7838 (pm20) REVERT: SC 81 PHE cc_start: 0.8168 (p90) cc_final: 0.7892 (p90) REVERT: SC 88 VAL cc_start: 0.7158 (t) cc_final: 0.6825 (t) REVERT: SC 224 ASP cc_start: 0.8170 (m-30) cc_final: 0.7900 (m-30) REVERT: SI 78 THR cc_start: 0.5655 (p) cc_final: 0.5428 (p) REVERT: SJ 189 LEU cc_start: 0.6391 (mt) cc_final: 0.6047 (mt) REVERT: SK 39 LYS cc_start: 0.6594 (ptpp) cc_final: 0.4696 (mmmm) REVERT: SK 52 ILE cc_start: 0.9042 (pt) cc_final: 0.8716 (mm) REVERT: SM 80 MET cc_start: 0.5417 (mpp) cc_final: 0.5091 (mtm) REVERT: SM 90 TYR cc_start: 0.4244 (t80) cc_final: 0.3711 (t80) REVERT: SM 100 TYR cc_start: 0.6034 (m-10) cc_final: 0.5704 (m-80) REVERT: SO 98 VAL cc_start: 0.8299 (t) cc_final: 0.8000 (p) REVERT: SP 118 VAL cc_start: 0.8243 (m) cc_final: 0.7817 (p) REVERT: SP 119 THR cc_start: 0.7511 (p) cc_final: 0.7190 (p) REVERT: SR 47 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8688 (mmmm) REVERT: SR 52 LEU cc_start: 0.8541 (mp) cc_final: 0.8277 (mp) REVERT: SR 83 GLN cc_start: 0.8066 (tp40) cc_final: 0.7542 (tp40) REVERT: SX 70 ASN cc_start: 0.7814 (m-40) cc_final: 0.7592 (m-40) REVERT: SY 95 PHE cc_start: 0.7809 (m-80) cc_final: 0.7597 (m-80) REVERT: Sc 26 GLN cc_start: 0.6662 (pt0) cc_final: 0.6435 (pt0) REVERT: Sd 52 ASP cc_start: 0.7841 (p0) cc_final: 0.7633 (p0) REVERT: U4 150 CYS cc_start: 0.8736 (p) cc_final: 0.7942 (t) REVERT: U5 189 TYR cc_start: 0.5448 (m-80) cc_final: 0.4529 (m-80) outliers start: 6 outliers final: 1 residues processed: 1685 average time/residue: 1.1990 time to fit residues: 3590.0810 Evaluate side-chains 1289 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1288 time to evaluate : 9.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 581 optimal weight: 0.7980 chunk 1555 optimal weight: 0.8980 chunk 341 optimal weight: 50.0000 chunk 1014 optimal weight: 6.9990 chunk 426 optimal weight: 8.9990 chunk 1728 optimal weight: 7.9990 chunk 1435 optimal weight: 8.9990 chunk 800 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 571 optimal weight: 2.9990 chunk 907 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 264 GLN ** 3D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 150 HIS 3F 314 GLN 3G 18 GLN ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B11016 ASN BA 145 HIS ** BA 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 598 ASN ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 204 ASN BC 241 GLN ** BC 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 618 ASN ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 385 ASN ** BD 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 171 GLN ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 580 GLN BE 627 ASN ** CA 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 381 HIS ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1045 ASN ** CB1148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1159 ASN E1 105 ASN ** E1 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 73 HIS E2 143 GLN E2 250 ASN ** K1 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 59 ASN ** MB 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 104 HIS R1 334 ASN ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 118 GLN SC 199 ASN SC 232 HIS ** SF 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 79 ASN SG 127 GLN ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 92 ASN U4 70 ASN ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 105 ASN U5 165 GLN ** U5 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 156436 Z= 0.217 Angle : 0.679 11.256 220267 Z= 0.342 Chirality : 0.040 0.557 27488 Planarity : 0.004 0.087 22428 Dihedral : 19.738 179.388 42191 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 1.13 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.08), residues: 11351 helix: 0.09 (0.09), residues: 3369 sheet: -0.73 (0.11), residues: 2187 loop : -2.46 (0.08), residues: 5795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP3D 198 HIS 0.016 0.001 HISBA 269 PHE 0.040 0.002 PHEMB 259 TYR 0.028 0.002 TYR3B 195 ARG 0.014 0.001 ARGSX 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1624 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1622 time to evaluate : 9.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.9063 (t0) cc_final: 0.8642 (t0) REVERT: 3B 260 PHE cc_start: 0.7675 (m-80) cc_final: 0.7192 (m-80) REVERT: 3B 295 GLU cc_start: 0.7928 (pp20) cc_final: 0.7228 (tm-30) REVERT: 3D 13 THR cc_start: 0.8263 (p) cc_final: 0.7994 (p) REVERT: 3D 88 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7776 (mmmt) REVERT: 3D 272 CYS cc_start: 0.8525 (m) cc_final: 0.8172 (m) REVERT: 3E 57 LEU cc_start: 0.7745 (pp) cc_final: 0.6802 (mm) REVERT: 3E 139 MET cc_start: 0.1409 (ppp) cc_final: 0.1135 (ppp) REVERT: 3E 264 GLU cc_start: 0.6430 (pt0) cc_final: 0.5301 (pt0) REVERT: 3F 333 MET cc_start: 0.6090 (tpp) cc_final: 0.5484 (mmt) REVERT: 3F 563 ILE cc_start: 0.6537 (mt) cc_final: 0.6314 (mt) REVERT: 3G 16 LEU cc_start: 0.7181 (tp) cc_final: 0.6844 (tp) REVERT: 3G 71 CYS cc_start: 0.7809 (m) cc_final: 0.7602 (m) REVERT: 3G 80 PHE cc_start: 0.6916 (m-10) cc_final: 0.6183 (m-80) REVERT: 3H 29 ASN cc_start: 0.8814 (m-40) cc_final: 0.8612 (t0) REVERT: AE 179 MET cc_start: 0.8565 (mmm) cc_final: 0.7425 (mmm) REVERT: AE 244 LYS cc_start: 0.8107 (pttm) cc_final: 0.7874 (pttp) REVERT: AE 275 ILE cc_start: 0.8290 (mt) cc_final: 0.8017 (tt) REVERT: AE 279 MET cc_start: 0.7734 (ttm) cc_final: 0.7446 (ttm) REVERT: AE 300 CYS cc_start: 0.7189 (m) cc_final: 0.6183 (m) REVERT: AE 400 LEU cc_start: 0.6819 (mt) cc_final: 0.6579 (tp) REVERT: B1 143 MET cc_start: 0.6002 (mmm) cc_final: 0.5752 (mmm) REVERT: B1 845 LEU cc_start: 0.8490 (mm) cc_final: 0.8203 (mm) REVERT: B1 889 LEU cc_start: 0.7878 (tp) cc_final: 0.7338 (tt) REVERT: BA 176 ASP cc_start: 0.7651 (p0) cc_final: 0.7376 (p0) REVERT: BA 277 VAL cc_start: 0.9269 (t) cc_final: 0.8973 (m) REVERT: BA 408 ASP cc_start: 0.8213 (m-30) cc_final: 0.7859 (p0) REVERT: BA 435 CYS cc_start: 0.7958 (t) cc_final: 0.7360 (t) REVERT: BA 478 CYS cc_start: 0.8994 (t) cc_final: 0.8763 (m) REVERT: BA 539 ILE cc_start: 0.7041 (mt) cc_final: 0.6642 (mt) REVERT: BA 557 LYS cc_start: 0.9492 (mptt) cc_final: 0.9226 (mmtt) REVERT: BA 602 CYS cc_start: 0.7005 (t) cc_final: 0.6537 (t) REVERT: BA 682 THR cc_start: 0.8358 (p) cc_final: 0.7922 (m) REVERT: BB 238 MET cc_start: 0.4975 (tpt) cc_final: 0.4703 (mmm) REVERT: BB 519 VAL cc_start: 0.5773 (t) cc_final: 0.5471 (t) REVERT: BB 563 MET cc_start: 0.7731 (ppp) cc_final: 0.4336 (mtp) REVERT: BB 636 ASP cc_start: 0.7749 (p0) cc_final: 0.7172 (p0) REVERT: BB 753 MET cc_start: 0.3992 (mmm) cc_final: 0.3784 (tpt) REVERT: BC 169 ASN cc_start: 0.9087 (p0) cc_final: 0.8613 (p0) REVERT: BC 172 VAL cc_start: 0.6059 (t) cc_final: 0.5840 (t) REVERT: BC 320 LEU cc_start: 0.4774 (mt) cc_final: 0.4352 (mp) REVERT: BC 559 ILE cc_start: 0.6484 (mt) cc_final: 0.6058 (mt) REVERT: BC 782 VAL cc_start: 0.6846 (m) cc_final: 0.6285 (m) REVERT: BD 262 LEU cc_start: 0.7201 (mt) cc_final: 0.6550 (mp) REVERT: BD 274 ILE cc_start: 0.7515 (tt) cc_final: 0.6786 (tt) REVERT: BD 369 ASN cc_start: 0.7510 (m-40) cc_final: 0.7209 (m-40) REVERT: BD 446 ARG cc_start: 0.6795 (ptp-170) cc_final: 0.6306 (ptp90) REVERT: BD 459 GLN cc_start: 0.6596 (tp-100) cc_final: 0.6258 (tp-100) REVERT: BD 500 MET cc_start: 0.1704 (ttm) cc_final: -0.1668 (mtt) REVERT: BD 587 ARG cc_start: 0.7288 (mpt-90) cc_final: 0.5878 (mpt-90) REVERT: BE 415 VAL cc_start: 0.8782 (t) cc_final: 0.8286 (p) REVERT: BE 471 CYS cc_start: 0.9287 (p) cc_final: 0.8996 (t) REVERT: BE 489 MET cc_start: 0.8732 (tpt) cc_final: 0.8221 (mmm) REVERT: BE 510 LEU cc_start: 0.8644 (tp) cc_final: 0.8395 (tp) REVERT: BE 549 MET cc_start: 0.9241 (ttm) cc_final: 0.8965 (ttp) REVERT: BE 614 LEU cc_start: 0.9157 (mp) cc_final: 0.8833 (mt) REVERT: BE 641 LEU cc_start: 0.8725 (tp) cc_final: 0.8385 (tp) REVERT: BE 796 LEU cc_start: 0.5345 (tt) cc_final: 0.5137 (tt) REVERT: CA 190 ILE cc_start: 0.6988 (tt) cc_final: 0.6648 (mt) REVERT: CA 206 ILE cc_start: 0.9094 (mm) cc_final: 0.8761 (tp) REVERT: CB 480 MET cc_start: 0.3665 (ppp) cc_final: 0.3006 (ppp) REVERT: CB 658 PHE cc_start: 0.6108 (m-80) cc_final: 0.5878 (m-80) REVERT: CB 664 THR cc_start: 0.6170 (m) cc_final: 0.5573 (p) REVERT: CB 860 GLU cc_start: 0.7716 (pm20) cc_final: 0.7504 (pm20) REVERT: CB 901 ASN cc_start: 0.4794 (t0) cc_final: 0.4544 (t0) REVERT: CB 1030 SER cc_start: 0.7047 (p) cc_final: 0.6620 (p) REVERT: CB 1230 MET cc_start: 0.3269 (mmp) cc_final: 0.2303 (mmp) REVERT: E1 133 THR cc_start: 0.6243 (p) cc_final: 0.6041 (t) REVERT: E2 157 GLU cc_start: 0.0120 (mp0) cc_final: -0.0273 (mp0) REVERT: K1 121 MET cc_start: 0.8503 (ptm) cc_final: 0.7728 (ttp) REVERT: MA 51 CYS cc_start: 0.8461 (m) cc_final: 0.8059 (t) REVERT: MA 132 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7190 (mt-10) REVERT: MA 144 ASN cc_start: 0.8950 (p0) cc_final: 0.8670 (p0) REVERT: MC 447 LYS cc_start: 0.8693 (tppt) cc_final: 0.8336 (tppp) REVERT: P1 245 GLU cc_start: 0.8201 (pm20) cc_final: 0.7875 (pm20) REVERT: P1 262 ASN cc_start: 0.6928 (p0) cc_final: 0.6578 (p0) REVERT: R1 138 MET cc_start: 0.7692 (mtt) cc_final: 0.7257 (mmp) REVERT: R1 223 VAL cc_start: 0.6322 (t) cc_final: 0.6032 (p) REVERT: SC 88 VAL cc_start: 0.7193 (t) cc_final: 0.6937 (t) REVERT: SC 122 GLU cc_start: 0.6239 (mm-30) cc_final: 0.4197 (tm-30) REVERT: SC 224 ASP cc_start: 0.8295 (m-30) cc_final: 0.7948 (m-30) REVERT: SG 82 PHE cc_start: 0.7377 (m-10) cc_final: 0.6997 (m-10) REVERT: SJ 189 LEU cc_start: 0.6375 (mt) cc_final: 0.6131 (mt) REVERT: SK 39 LYS cc_start: 0.6675 (ptpp) cc_final: 0.5601 (mmmm) REVERT: SK 52 ILE cc_start: 0.9050 (pt) cc_final: 0.8725 (mm) REVERT: SM 80 MET cc_start: 0.5467 (mpp) cc_final: 0.5202 (mtm) REVERT: SM 90 TYR cc_start: 0.4221 (t80) cc_final: 0.3821 (t80) REVERT: SO 98 VAL cc_start: 0.8294 (t) cc_final: 0.8041 (p) REVERT: SP 23 PHE cc_start: 0.7054 (m-80) cc_final: 0.6809 (m-80) REVERT: SP 118 VAL cc_start: 0.8174 (m) cc_final: 0.7846 (p) REVERT: SP 119 THR cc_start: 0.7444 (p) cc_final: 0.7243 (p) REVERT: SR 52 LEU cc_start: 0.8604 (mp) cc_final: 0.8224 (mp) REVERT: SR 54 LEU cc_start: 0.9168 (mt) cc_final: 0.8675 (mt) REVERT: SR 83 GLN cc_start: 0.8173 (tp40) cc_final: 0.7597 (tp40) REVERT: SY 95 PHE cc_start: 0.7858 (m-80) cc_final: 0.7621 (m-80) REVERT: SZ 63 GLN cc_start: 0.7922 (pt0) cc_final: 0.7719 (pt0) REVERT: U4 88 ASP cc_start: 0.7193 (m-30) cc_final: 0.6977 (m-30) REVERT: U4 94 CYS cc_start: 0.6988 (m) cc_final: 0.6603 (m) REVERT: U5 46 MET cc_start: 0.7444 (mpp) cc_final: 0.7219 (mpp) REVERT: U5 156 MET cc_start: 0.4427 (tpt) cc_final: 0.4036 (tpt) REVERT: U5 189 TYR cc_start: 0.5643 (m-80) cc_final: 0.4665 (m-80) outliers start: 2 outliers final: 0 residues processed: 1622 average time/residue: 1.1827 time to fit residues: 3419.7816 Evaluate side-chains 1256 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1256 time to evaluate : 9.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1666 optimal weight: 40.0000 chunk 194 optimal weight: 10.0000 chunk 985 optimal weight: 20.0000 chunk 1262 optimal weight: 50.0000 chunk 978 optimal weight: 40.0000 chunk 1455 optimal weight: 7.9990 chunk 965 optimal weight: 10.0000 chunk 1722 optimal weight: 10.0000 chunk 1077 optimal weight: 0.0870 chunk 1050 optimal weight: 20.0000 chunk 795 optimal weight: 20.0000 overall best weight: 7.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 91 HIS ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 314 GLN 3G 18 GLN ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 218 ASN ** B11016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 145 HIS BA 188 ASN BA 190 HIS ** BA 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 383 HIS BB 626 GLN ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 58 ASN BC 204 ASN BC 241 GLN ** BC 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 495 ASN ** BC 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 618 ASN ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 335 GLN ** BD 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 117 ASN BE 171 GLN ** BE 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 381 HIS ** CB 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1026 ASN CB1159 ASN CB1203 ASN ** E1 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 73 HIS E2 143 GLN E2 250 ASN ** K1 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 59 ASN MA 116 HIS ** MB 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 118 GLN SF 188 ASN ** SF 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 224 ASN ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 89 HIS ** SK 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SX 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 34 ASN ** U4 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 105 ASN U5 192 ASN ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 156436 Z= 0.419 Angle : 0.945 14.672 220267 Z= 0.471 Chirality : 0.048 0.615 27488 Planarity : 0.006 0.087 22428 Dihedral : 20.197 178.695 42191 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.19 % Favored : 87.65 % Rotamer: Outliers : 0.01 % Allowed : 2.88 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 1.13 % 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: -2.55 (0.07), residues: 11351 helix: -0.57 (0.08), residues: 3346 sheet: -1.00 (0.11), residues: 2167 loop : -2.74 (0.07), residues: 5838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP3D 198 HIS 0.017 0.002 HISBA 190 PHE 0.065 0.003 PHEMB 259 TYR 0.047 0.003 TYRBD 429 ARG 0.035 0.001 ARG3C 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1514 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1513 time to evaluate : 9.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.8991 (t0) cc_final: 0.8743 (t0) REVERT: 3B 261 LEU cc_start: 0.8981 (tp) cc_final: 0.8746 (tp) REVERT: 3B 295 GLU cc_start: 0.7991 (pp20) cc_final: 0.7604 (tm-30) REVERT: 3D 268 MET cc_start: 0.7533 (mmm) cc_final: 0.6215 (mmt) REVERT: 3E 94 LEU cc_start: 0.8054 (mt) cc_final: 0.7661 (tp) REVERT: 3E 264 GLU cc_start: 0.5727 (pt0) cc_final: 0.5303 (pt0) REVERT: 3E 330 LEU cc_start: 0.8571 (mt) cc_final: 0.8320 (mm) REVERT: 3F 540 LEU cc_start: 0.7151 (mm) cc_final: 0.6948 (mm) REVERT: 3G 16 LEU cc_start: 0.7730 (tp) cc_final: 0.7205 (tp) REVERT: AE 24 ARG cc_start: 0.7254 (ttm-80) cc_final: 0.6993 (ttm-80) REVERT: AE 279 MET cc_start: 0.8138 (ttm) cc_final: 0.7860 (ttm) REVERT: AE 300 CYS cc_start: 0.7581 (m) cc_final: 0.6389 (m) REVERT: AE 306 LEU cc_start: 0.8003 (tp) cc_final: 0.7744 (tp) REVERT: BA 176 ASP cc_start: 0.8145 (p0) cc_final: 0.7943 (p0) REVERT: BA 353 TYR cc_start: 0.8455 (m-10) cc_final: 0.8148 (m-10) REVERT: BA 394 GLN cc_start: 0.9117 (pp30) cc_final: 0.8913 (pp30) REVERT: BA 408 ASP cc_start: 0.8088 (m-30) cc_final: 0.7551 (m-30) REVERT: BA 557 LYS cc_start: 0.9546 (mptt) cc_final: 0.9328 (mmtt) REVERT: BA 602 CYS cc_start: 0.7262 (t) cc_final: 0.6665 (t) REVERT: BA 682 THR cc_start: 0.8564 (p) cc_final: 0.8149 (m) REVERT: BA 703 ILE cc_start: 0.7446 (pt) cc_final: 0.7237 (pt) REVERT: BB 238 MET cc_start: 0.5655 (tpt) cc_final: 0.4984 (ttm) REVERT: BB 563 MET cc_start: 0.7589 (ppp) cc_final: 0.7178 (ppp) REVERT: BB 653 LEU cc_start: 0.5101 (mp) cc_final: 0.4815 (mp) REVERT: BB 679 HIS cc_start: 0.5400 (p-80) cc_final: 0.4964 (p-80) REVERT: BB 753 MET cc_start: 0.4309 (mmm) cc_final: 0.4087 (tpt) REVERT: BD 274 ILE cc_start: 0.7657 (tt) cc_final: 0.7000 (tt) REVERT: BD 369 ASN cc_start: 0.7145 (m-40) cc_final: 0.6723 (m-40) REVERT: BD 404 ILE cc_start: 0.6355 (mp) cc_final: 0.6051 (mt) REVERT: BD 433 TRP cc_start: 0.6955 (t-100) cc_final: 0.6201 (t-100) REVERT: BD 446 ARG cc_start: 0.6683 (ptp-170) cc_final: 0.5650 (ptp90) REVERT: BD 500 MET cc_start: 0.1221 (ttm) cc_final: -0.2341 (mtt) REVERT: BE 61 TYR cc_start: 0.7690 (m-10) cc_final: 0.7307 (m-80) REVERT: BE 148 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7745 (mtpp) REVERT: BE 292 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6785 (mmp80) REVERT: BE 415 VAL cc_start: 0.8976 (t) cc_final: 0.8479 (p) REVERT: BE 549 MET cc_start: 0.9297 (ttm) cc_final: 0.9075 (ttp) REVERT: CA 160 TYR cc_start: 0.5915 (m-80) cc_final: 0.5695 (m-80) REVERT: CA 190 ILE cc_start: 0.7131 (tt) cc_final: 0.6815 (mt) REVERT: CA 206 ILE cc_start: 0.9213 (mm) cc_final: 0.8879 (tp) REVERT: CA 208 ASP cc_start: 0.8008 (p0) cc_final: 0.7790 (p0) REVERT: CB 480 MET cc_start: 0.4328 (ppp) cc_final: 0.3946 (ppp) REVERT: CB 536 TYR cc_start: 0.4619 (t80) cc_final: 0.4195 (t80) REVERT: CB 649 TRP cc_start: 0.4431 (m100) cc_final: 0.3664 (m100) REVERT: CB 860 GLU cc_start: 0.7970 (pm20) cc_final: 0.7749 (pm20) REVERT: CB 1230 MET cc_start: 0.3801 (mmp) cc_final: 0.3342 (mmp) REVERT: E1 133 THR cc_start: 0.6662 (p) cc_final: 0.6426 (p) REVERT: E2 94 GLN cc_start: 0.8252 (mp10) cc_final: 0.7837 (mp10) REVERT: E2 157 GLU cc_start: 0.0705 (mp0) cc_final: 0.0484 (mp0) REVERT: K1 121 MET cc_start: 0.8415 (ptm) cc_final: 0.7902 (ttp) REVERT: MA 51 CYS cc_start: 0.8766 (m) cc_final: 0.8472 (t) REVERT: MA 120 MET cc_start: 0.7732 (ttp) cc_final: 0.7530 (ttp) REVERT: MB 206 LEU cc_start: 0.9104 (mt) cc_final: 0.8898 (mt) REVERT: MC 447 LYS cc_start: 0.8627 (tppt) cc_final: 0.8410 (tppp) REVERT: SC 88 VAL cc_start: 0.7382 (t) cc_final: 0.7032 (t) REVERT: SC 103 MET cc_start: 0.7799 (tmm) cc_final: 0.7500 (tmm) REVERT: SC 118 GLN cc_start: 0.7176 (pt0) cc_final: 0.6826 (mt0) REVERT: SC 122 GLU cc_start: 0.6554 (mm-30) cc_final: 0.5516 (mm-30) REVERT: SJ 189 LEU cc_start: 0.6807 (mt) cc_final: 0.6571 (mt) REVERT: SK 39 LYS cc_start: 0.6964 (ptpp) cc_final: 0.6096 (mtmt) REVERT: SK 146 PHE cc_start: 0.7450 (t80) cc_final: 0.7028 (t80) REVERT: SM 90 TYR cc_start: 0.4451 (t80) cc_final: 0.3932 (t80) REVERT: SO 98 VAL cc_start: 0.8350 (t) cc_final: 0.8136 (p) REVERT: SR 54 LEU cc_start: 0.9302 (mt) cc_final: 0.9061 (mt) REVERT: SY 95 PHE cc_start: 0.7601 (m-80) cc_final: 0.7381 (m-80) REVERT: SZ 60 PHE cc_start: 0.5759 (m-10) cc_final: 0.5400 (m-10) REVERT: Sd 50 GLU cc_start: 0.7992 (tt0) cc_final: 0.7749 (tt0) REVERT: Sf 42 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7931 (tpp-160) REVERT: U4 100 ASP cc_start: 0.8192 (m-30) cc_final: 0.7989 (m-30) REVERT: U5 167 MET cc_start: 0.4301 (mmm) cc_final: 0.3998 (mmm) outliers start: 1 outliers final: 0 residues processed: 1513 average time/residue: 1.2321 time to fit residues: 3305.5175 Evaluate side-chains 1154 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1154 time to evaluate : 9.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1065 optimal weight: 6.9990 chunk 687 optimal weight: 20.0000 chunk 1028 optimal weight: 7.9990 chunk 518 optimal weight: 9.9990 chunk 338 optimal weight: 40.0000 chunk 333 optimal weight: 10.0000 chunk 1095 optimal weight: 40.0000 chunk 1173 optimal weight: 30.0000 chunk 851 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 1353 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 264 GLN ** 3C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3G 18 GLN ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 179 GLN B11016 ASN ** BA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 145 HIS ** BA 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 204 ASN BC 241 GLN ** BC 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 522 ASN ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB1148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1159 ASN E1 105 ASN ** E1 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 143 GLN ** K1 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 59 ASN MA 74 HIS ** MB 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 104 HIS P1 123 HIS ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 118 GLN SC 124 ASN ** SF 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 224 ASN ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 200 ASN SI 89 HIS ** SM 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U4 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U5 41 ASN ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 156436 Z= 0.303 Angle : 0.795 12.509 220267 Z= 0.399 Chirality : 0.044 0.482 27488 Planarity : 0.005 0.109 22428 Dihedral : 20.096 178.573 42191 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.70 % Favored : 89.21 % Rotamer: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 0.90 % 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: -2.45 (0.07), residues: 11351 helix: -0.40 (0.09), residues: 3344 sheet: -1.03 (0.11), residues: 2151 loop : -2.69 (0.07), residues: 5856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRPBB 208 HIS 0.020 0.002 HISBA 269 PHE 0.040 0.003 PHEBA 686 TYR 0.032 0.002 TYRBD 429 ARG 0.023 0.001 ARG3C 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1508 time to evaluate : 9.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.8864 (t0) cc_final: 0.8607 (t0) REVERT: 3B 261 LEU cc_start: 0.9003 (tp) cc_final: 0.8709 (tp) REVERT: 3B 295 GLU cc_start: 0.7856 (pp20) cc_final: 0.7437 (tm-30) REVERT: 3D 88 LYS cc_start: 0.8518 (mmpt) cc_final: 0.8171 (mmmt) REVERT: 3D 268 MET cc_start: 0.7575 (mmm) cc_final: 0.6274 (mmt) REVERT: 3E 57 LEU cc_start: 0.7739 (pp) cc_final: 0.7154 (mm) REVERT: 3E 139 MET cc_start: 0.1844 (ppp) cc_final: 0.1305 (ppp) REVERT: 3E 330 LEU cc_start: 0.8487 (mt) cc_final: 0.8195 (mm) REVERT: 3G 16 LEU cc_start: 0.7875 (tp) cc_final: 0.7050 (tp) REVERT: 3G 54 MET cc_start: 0.6322 (ttm) cc_final: 0.6028 (ttm) REVERT: 3G 73 ASP cc_start: 0.7943 (t0) cc_final: 0.7740 (t0) REVERT: 3G 80 PHE cc_start: 0.6964 (m-10) cc_final: 0.6574 (m-80) REVERT: 3H 29 ASN cc_start: 0.8924 (m-40) cc_final: 0.8580 (m-40) REVERT: 3H 54 MET cc_start: 0.7405 (mpp) cc_final: 0.7191 (mpp) REVERT: AE 279 MET cc_start: 0.8037 (ttm) cc_final: 0.7581 (ttm) REVERT: AE 300 CYS cc_start: 0.7505 (m) cc_final: 0.6293 (m) REVERT: AE 400 LEU cc_start: 0.6887 (mt) cc_final: 0.6482 (tp) REVERT: B1 37 MET cc_start: 0.4838 (ttt) cc_final: 0.4267 (ttm) REVERT: B1 923 ASP cc_start: 0.4780 (p0) cc_final: 0.4197 (p0) REVERT: B1 943 LYS cc_start: 0.5937 (tttm) cc_final: 0.5096 (tttm) REVERT: B1 1006 TRP cc_start: 0.5602 (m100) cc_final: 0.3736 (m100) REVERT: BA 353 TYR cc_start: 0.8665 (m-10) cc_final: 0.8436 (m-10) REVERT: BA 394 GLN cc_start: 0.9008 (pp30) cc_final: 0.8795 (pp30) REVERT: BA 557 LYS cc_start: 0.9538 (mptt) cc_final: 0.9331 (mmtt) REVERT: BA 602 CYS cc_start: 0.7113 (t) cc_final: 0.6744 (t) REVERT: BA 682 THR cc_start: 0.8658 (p) cc_final: 0.8262 (m) REVERT: BB 75 ARG cc_start: 0.4447 (tpt170) cc_final: 0.3979 (ttt90) REVERT: BB 238 MET cc_start: 0.3884 (tpt) cc_final: 0.3549 (ttm) REVERT: BB 563 MET cc_start: 0.7569 (ppp) cc_final: 0.6989 (ppp) REVERT: BB 753 MET cc_start: 0.4339 (mmm) cc_final: 0.4093 (tpt) REVERT: BB 884 LYS cc_start: 0.7925 (ttmt) cc_final: 0.6761 (ttmm) REVERT: BC 739 LEU cc_start: 0.8947 (tp) cc_final: 0.8718 (tp) REVERT: BC 778 MET cc_start: 0.5107 (pmm) cc_final: 0.4760 (ptm) REVERT: BD 262 LEU cc_start: 0.7299 (mt) cc_final: 0.6592 (mp) REVERT: BD 274 ILE cc_start: 0.7454 (tt) cc_final: 0.6783 (tt) REVERT: BD 358 PHE cc_start: 0.4220 (p90) cc_final: 0.3921 (p90) REVERT: BD 404 ILE cc_start: 0.6382 (mp) cc_final: 0.5906 (mt) REVERT: BD 500 MET cc_start: 0.1175 (ttm) cc_final: -0.2330 (mtt) REVERT: BE 148 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7684 (mtpp) REVERT: BE 292 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6863 (mmp80) REVERT: BE 415 VAL cc_start: 0.8834 (t) cc_final: 0.8292 (p) REVERT: BE 439 PHE cc_start: 0.8695 (p90) cc_final: 0.8395 (p90) REVERT: BE 489 MET cc_start: 0.8811 (tpt) cc_final: 0.8449 (mmm) REVERT: BE 641 LEU cc_start: 0.8681 (tp) cc_final: 0.8344 (tp) REVERT: CA 42 HIS cc_start: 0.3824 (t-170) cc_final: 0.3580 (t-170) REVERT: CA 188 MET cc_start: 0.4290 (mmm) cc_final: 0.3852 (mmm) REVERT: CA 190 ILE cc_start: 0.7217 (tt) cc_final: 0.6871 (mt) REVERT: CA 206 ILE cc_start: 0.9120 (mm) cc_final: 0.8845 (tp) REVERT: CB 536 TYR cc_start: 0.4790 (t80) cc_final: 0.4504 (t80) REVERT: CB 638 MET cc_start: 0.2379 (mmm) cc_final: 0.1696 (mmm) REVERT: CB 649 TRP cc_start: 0.4528 (m100) cc_final: 0.3733 (m100) REVERT: CB 1077 THR cc_start: 0.6634 (p) cc_final: 0.6361 (p) REVERT: CB 1230 MET cc_start: 0.3593 (mmp) cc_final: 0.3256 (mmp) REVERT: E1 115 GLN cc_start: 0.7321 (tp40) cc_final: 0.6707 (tp-100) REVERT: K1 106 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7678 (ttm110) REVERT: K1 121 MET cc_start: 0.8450 (ptm) cc_final: 0.7946 (ttp) REVERT: K1 206 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7983 (ttmm) REVERT: MA 51 CYS cc_start: 0.8644 (m) cc_final: 0.8116 (t) REVERT: MB 132 LYS cc_start: 0.8017 (tttt) cc_final: 0.7654 (tttt) REVERT: MB 142 LEU cc_start: 0.8879 (tt) cc_final: 0.8660 (tt) REVERT: P1 245 GLU cc_start: 0.8207 (pm20) cc_final: 0.7571 (pm20) REVERT: SC 103 MET cc_start: 0.7925 (tmm) cc_final: 0.7722 (tmm) REVERT: SG 82 PHE cc_start: 0.7295 (m-10) cc_final: 0.7014 (m-10) REVERT: SK 39 LYS cc_start: 0.7165 (ptpp) cc_final: 0.5849 (mtmt) REVERT: SK 87 SER cc_start: 0.8300 (p) cc_final: 0.7841 (p) REVERT: SK 103 ASP cc_start: 0.9093 (p0) cc_final: 0.8304 (p0) REVERT: SM 90 TYR cc_start: 0.4183 (t80) cc_final: 0.3754 (t80) REVERT: SM 93 TYR cc_start: 0.7573 (t80) cc_final: 0.7218 (t80) REVERT: SP 91 THR cc_start: 0.9434 (p) cc_final: 0.9090 (m) REVERT: SR 50 GLU cc_start: 0.8753 (pt0) cc_final: 0.8312 (pt0) REVERT: SR 52 LEU cc_start: 0.8743 (mp) cc_final: 0.8519 (mp) REVERT: SR 103 ASN cc_start: 0.8691 (m-40) cc_final: 0.8412 (m-40) REVERT: SX 97 ARG cc_start: 0.8058 (mpp80) cc_final: 0.7496 (mpp80) REVERT: Sd 50 GLU cc_start: 0.8014 (tt0) cc_final: 0.7786 (tt0) REVERT: Sf 42 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7811 (tpp-160) REVERT: U4 100 ASP cc_start: 0.8196 (m-30) cc_final: 0.7957 (m-30) REVERT: U4 118 LYS cc_start: 0.8843 (pttt) cc_final: 0.8460 (tppt) REVERT: U5 183 ILE cc_start: 0.8692 (mm) cc_final: 0.8330 (tp) outliers start: 3 outliers final: 0 residues processed: 1510 average time/residue: 1.2173 time to fit residues: 3264.3119 Evaluate side-chains 1170 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1170 time to evaluate : 9.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1566 optimal weight: 10.0000 chunk 1650 optimal weight: 10.0000 chunk 1505 optimal weight: 0.0980 chunk 1605 optimal weight: 0.1980 chunk 1649 optimal weight: 10.0000 chunk 966 optimal weight: 0.9990 chunk 699 optimal weight: 8.9990 chunk 1260 optimal weight: 30.0000 chunk 492 optimal weight: 40.0000 chunk 1450 optimal weight: 1.9990 chunk 1518 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 145 ASN 3B 249 GLN ** 3B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 314 GLN 3G 18 GLN ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 136 ASN B11016 ASN BA 45 ASN BA 145 HIS BA 181 ASN ** BA 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 598 ASN ** BB 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 677 HIS ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 204 ASN BC 241 GLN ** BC 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 311 ASN ** BD 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 263 HIS ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 96 HIS ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB1159 ASN E1 105 ASN ** E1 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 59 ASN MA 74 HIS P1 123 HIS ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 124 ASN ** SF 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 224 ASN ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 127 GLN ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 89 HIS SK 155 HIS ** SM 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 94 GLN ** U4 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 156436 Z= 0.175 Angle : 0.677 12.295 220267 Z= 0.341 Chirality : 0.040 0.568 27488 Planarity : 0.004 0.101 22428 Dihedral : 19.851 179.980 42191 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.30 % Favored : 90.58 % Rotamer: Outliers : 0.03 % Allowed : 0.74 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 0.90 % Twisted General : 0.20 % 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: -2.11 (0.08), residues: 11351 helix: -0.02 (0.09), residues: 3361 sheet: -0.89 (0.11), residues: 2152 loop : -2.52 (0.08), residues: 5838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPBB 208 HIS 0.011 0.001 HISBE 263 PHE 0.042 0.002 PHEAE 404 TYR 0.037 0.002 TYRBA 515 ARG 0.021 0.001 ARGBE 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1590 time to evaluate : 9.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 260 PHE cc_start: 0.7882 (m-80) cc_final: 0.7575 (m-80) REVERT: 3B 261 LEU cc_start: 0.8833 (tp) cc_final: 0.8459 (tp) REVERT: 3B 295 GLU cc_start: 0.7636 (pp20) cc_final: 0.7101 (tm-30) REVERT: 3D 57 LYS cc_start: 0.7491 (pptt) cc_final: 0.6878 (mmtp) REVERT: 3D 88 LYS cc_start: 0.8409 (mmpt) cc_final: 0.8170 (mmpt) REVERT: 3D 268 MET cc_start: 0.7546 (mmm) cc_final: 0.5851 (mmt) REVERT: 3E 57 LEU cc_start: 0.7677 (pp) cc_final: 0.7045 (mm) REVERT: 3E 139 MET cc_start: 0.2243 (ppp) cc_final: 0.1737 (ppp) REVERT: 3E 330 LEU cc_start: 0.8513 (mt) cc_final: 0.8229 (mm) REVERT: 3G 16 LEU cc_start: 0.7870 (tp) cc_final: 0.7262 (tp) REVERT: 3G 25 GLN cc_start: 0.7652 (tp40) cc_final: 0.7240 (tp40) REVERT: 3G 80 PHE cc_start: 0.6453 (m-10) cc_final: 0.6193 (m-80) REVERT: 3H 67 LEU cc_start: 0.9155 (mt) cc_final: 0.8921 (mt) REVERT: AE 152 LEU cc_start: 0.9061 (mm) cc_final: 0.8851 (tp) REVERT: AE 279 MET cc_start: 0.8096 (ttm) cc_final: 0.7306 (ttm) REVERT: AE 300 CYS cc_start: 0.7154 (m) cc_final: 0.5581 (m) REVERT: B1 147 LEU cc_start: 0.7511 (mt) cc_final: 0.7217 (mt) REVERT: B1 900 GLN cc_start: 0.8573 (tp40) cc_final: 0.8220 (tm-30) REVERT: B1 923 ASP cc_start: 0.4547 (p0) cc_final: 0.4065 (p0) REVERT: B1 1006 TRP cc_start: 0.5500 (m100) cc_final: 0.4142 (m100) REVERT: BA 176 ASP cc_start: 0.7906 (p0) cc_final: 0.7482 (p0) REVERT: BA 294 LEU cc_start: 0.8253 (tp) cc_final: 0.7810 (tt) REVERT: BA 338 ILE cc_start: 0.8282 (mt) cc_final: 0.8079 (mt) REVERT: BA 435 CYS cc_start: 0.8142 (t) cc_final: 0.7576 (t) REVERT: BA 539 ILE cc_start: 0.7185 (mt) cc_final: 0.6903 (mt) REVERT: BA 602 CYS cc_start: 0.7113 (t) cc_final: 0.6762 (t) REVERT: BA 604 TYR cc_start: 0.8935 (m-80) cc_final: 0.8396 (m-80) REVERT: BB 75 ARG cc_start: 0.4092 (tpt170) cc_final: 0.3668 (ttt90) REVERT: BB 185 MET cc_start: 0.2363 (mtp) cc_final: 0.2019 (mtm) REVERT: BB 217 LEU cc_start: 0.6901 (tp) cc_final: 0.6215 (tt) REVERT: BB 563 MET cc_start: 0.7543 (ppp) cc_final: 0.6997 (ppp) REVERT: BB 679 HIS cc_start: 0.4872 (p-80) cc_final: 0.4326 (p-80) REVERT: BB 840 MET cc_start: 0.7923 (tmm) cc_final: 0.7621 (tmm) REVERT: BC 320 LEU cc_start: 0.4988 (mt) cc_final: 0.4539 (mp) REVERT: BC 559 ILE cc_start: 0.6969 (mt) cc_final: 0.6639 (mt) REVERT: BD 274 ILE cc_start: 0.7975 (tt) cc_final: 0.7115 (tt) REVERT: BD 369 ASN cc_start: 0.7713 (m-40) cc_final: 0.7464 (m-40) REVERT: BD 446 ARG cc_start: 0.6591 (ptp-170) cc_final: 0.5627 (ptp90) REVERT: BD 455 ILE cc_start: 0.7599 (mp) cc_final: 0.7370 (mm) REVERT: BD 490 PHE cc_start: 0.4356 (t80) cc_final: 0.3967 (t80) REVERT: BD 500 MET cc_start: -0.0475 (ttm) cc_final: -0.2854 (mtt) REVERT: BE 148 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7770 (mtpp) REVERT: BE 415 VAL cc_start: 0.8718 (t) cc_final: 0.8199 (p) REVERT: BE 476 PHE cc_start: 0.7340 (m-10) cc_final: 0.6850 (m-10) REVERT: BE 489 MET cc_start: 0.8985 (tpt) cc_final: 0.8419 (tmm) REVERT: CA 42 HIS cc_start: 0.4465 (t-170) cc_final: 0.4223 (t-170) REVERT: CA 188 MET cc_start: 0.4254 (mmm) cc_final: 0.3854 (mmm) REVERT: CA 190 ILE cc_start: 0.7105 (tt) cc_final: 0.6755 (mt) REVERT: CB 209 MET cc_start: -0.1459 (ttt) cc_final: -0.2102 (tpp) REVERT: CB 283 TYR cc_start: 0.2927 (m-80) cc_final: 0.2668 (m-80) REVERT: CB 480 MET cc_start: 0.1146 (ppp) cc_final: 0.0722 (ppp) REVERT: CB 536 TYR cc_start: 0.4478 (t80) cc_final: 0.4274 (t80) REVERT: CB 638 MET cc_start: 0.2494 (mmm) cc_final: 0.2191 (mmm) REVERT: CB 1143 MET cc_start: 0.3344 (tpp) cc_final: 0.3009 (tpp) REVERT: E1 97 LEU cc_start: 0.6883 (mt) cc_final: 0.6612 (mt) REVERT: E1 115 GLN cc_start: 0.7290 (tp40) cc_final: 0.6603 (tp-100) REVERT: E1 133 THR cc_start: 0.6094 (p) cc_final: 0.5628 (m) REVERT: E1 209 MET cc_start: 0.5804 (pmm) cc_final: 0.5434 (pmm) REVERT: E2 77 LEU cc_start: 0.8639 (mt) cc_final: 0.8241 (mm) REVERT: K1 121 MET cc_start: 0.8400 (ptm) cc_final: 0.7842 (ttp) REVERT: MA 51 CYS cc_start: 0.8711 (m) cc_final: 0.8201 (t) REVERT: MA 144 ASN cc_start: 0.8860 (p0) cc_final: 0.8569 (p0) REVERT: MB 172 MET cc_start: 0.1920 (mmp) cc_final: -0.0215 (mtm) REVERT: SC 103 MET cc_start: 0.7952 (tmm) cc_final: 0.7702 (tmm) REVERT: SC 113 MET cc_start: 0.7943 (ttm) cc_final: 0.7636 (ttm) REVERT: SG 169 ASN cc_start: 0.6672 (m110) cc_final: 0.6310 (m-40) REVERT: SI 55 LYS cc_start: 0.3496 (mmtp) cc_final: 0.3048 (mmtm) REVERT: SK 39 LYS cc_start: 0.6802 (ptpp) cc_final: 0.5222 (mmmm) REVERT: SK 52 ILE cc_start: 0.9017 (pt) cc_final: 0.8486 (mm) REVERT: SK 103 ASP cc_start: 0.8936 (p0) cc_final: 0.7819 (p0) REVERT: SO 14 SER cc_start: 0.9226 (m) cc_final: 0.8981 (p) REVERT: SP 83 ILE cc_start: 0.7913 (mp) cc_final: 0.7674 (mp) REVERT: SP 91 THR cc_start: 0.9483 (p) cc_final: 0.9150 (m) REVERT: SP 119 THR cc_start: 0.7226 (p) cc_final: 0.6933 (p) REVERT: SR 52 LEU cc_start: 0.8446 (mp) cc_final: 0.8146 (mt) REVERT: SR 54 LEU cc_start: 0.9251 (mt) cc_final: 0.8712 (mt) REVERT: SR 83 GLN cc_start: 0.8073 (tp40) cc_final: 0.7544 (tp40) REVERT: SR 103 ASN cc_start: 0.8677 (m-40) cc_final: 0.8046 (m-40) REVERT: SX 97 ARG cc_start: 0.7931 (mpp80) cc_final: 0.7585 (mpp80) REVERT: SZ 63 GLN cc_start: 0.7011 (pt0) cc_final: 0.6738 (pt0) REVERT: Sd 50 GLU cc_start: 0.8033 (tt0) cc_final: 0.7825 (tt0) REVERT: Sd 52 ASP cc_start: 0.7850 (p0) cc_final: 0.7632 (p0) REVERT: U4 94 CYS cc_start: 0.6972 (m) cc_final: 0.6545 (m) REVERT: U4 100 ASP cc_start: 0.8167 (m-30) cc_final: 0.7914 (m-30) REVERT: U4 117 LEU cc_start: 0.8734 (tp) cc_final: 0.8343 (tt) REVERT: U4 118 LYS cc_start: 0.8784 (pttt) cc_final: 0.8390 (tppt) REVERT: U4 172 LEU cc_start: 0.8491 (pt) cc_final: 0.8244 (tp) REVERT: U5 183 ILE cc_start: 0.8783 (mm) cc_final: 0.8482 (tp) outliers start: 3 outliers final: 0 residues processed: 1591 average time/residue: 1.2179 time to fit residues: 3459.8376 Evaluate side-chains 1204 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1204 time to evaluate : 8.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 1599 optimal weight: 0.0020 chunk 1053 optimal weight: 20.0000 chunk 1697 optimal weight: 20.0000 chunk 1035 optimal weight: 30.0000 chunk 805 optimal weight: 4.9990 chunk 1179 optimal weight: 0.8980 chunk 1780 optimal weight: 20.0000 chunk 1638 optimal weight: 10.0000 chunk 1417 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 1095 optimal weight: 40.0000 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 264 GLN ** 3B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 314 GLN 3G 18 GLN ** 3G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 144 GLN B11016 ASN ** BA 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BA 259 ASN BA 306 ASN ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 204 ASN BC 241 GLN ** BC 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 146 GLN ** BE 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB1159 ASN E1 105 ASN ** E1 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 59 ASN MA 74 HIS MB 159 HIS ** MB 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 211 ASN ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 124 ASN ** SF 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 127 GLN ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 89 HIS ** SM 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 103 ASN ** SY 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U4 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U5 214 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 156436 Z= 0.219 Angle : 0.704 11.037 220267 Z= 0.354 Chirality : 0.041 0.772 27488 Planarity : 0.005 0.171 22428 Dihedral : 19.837 179.558 42191 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.39 % Favored : 89.51 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 0.90 % Twisted General : 0.17 % 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: -2.06 (0.08), residues: 11351 helix: 0.03 (0.09), residues: 3347 sheet: -0.84 (0.11), residues: 2120 loop : -2.50 (0.08), residues: 5884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRPBB 208 HIS 0.010 0.001 HISP1 104 PHE 0.037 0.002 PHECA 212 TYR 0.029 0.002 TYRBA 193 ARG 0.025 0.001 ARGSG 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22702 Ramachandran restraints generated. 11351 Oldfield, 0 Emsley, 11351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1492 time to evaluate : 9.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3B 216 ASN cc_start: 0.8842 (t0) cc_final: 0.8589 (t0) REVERT: 3B 260 PHE cc_start: 0.7744 (m-80) cc_final: 0.7453 (m-80) REVERT: 3B 295 GLU cc_start: 0.7792 (pp20) cc_final: 0.7202 (tm-30) REVERT: 3D 88 LYS cc_start: 0.8383 (mmpt) cc_final: 0.8125 (mmpt) REVERT: 3D 268 MET cc_start: 0.7313 (mmm) cc_final: 0.6315 (mmt) REVERT: 3D 272 CYS cc_start: 0.8525 (m) cc_final: 0.8284 (m) REVERT: 3E 57 LEU cc_start: 0.7758 (pp) cc_final: 0.7135 (mm) REVERT: 3E 139 MET cc_start: 0.1363 (ppp) cc_final: 0.0981 (ppp) REVERT: 3E 330 LEU cc_start: 0.8486 (mt) cc_final: 0.8174 (mm) REVERT: 3F 333 MET cc_start: 0.6374 (mmm) cc_final: 0.5965 (tmm) REVERT: 3G 16 LEU cc_start: 0.7745 (tp) cc_final: 0.7095 (tp) REVERT: 3G 54 MET cc_start: 0.6817 (ttm) cc_final: 0.6613 (ttm) REVERT: 3G 80 PHE cc_start: 0.6680 (m-10) cc_final: 0.6413 (m-80) REVERT: 3H 67 LEU cc_start: 0.9057 (mt) cc_final: 0.8837 (mt) REVERT: AE 279 MET cc_start: 0.8171 (ttm) cc_final: 0.7581 (ttm) REVERT: AE 300 CYS cc_start: 0.7165 (m) cc_final: 0.5548 (m) REVERT: AE 400 LEU cc_start: 0.7120 (mt) cc_final: 0.5970 (tp) REVERT: B1 845 LEU cc_start: 0.8148 (mm) cc_final: 0.7874 (mm) REVERT: B1 889 LEU cc_start: 0.8000 (mt) cc_final: 0.7360 (tt) REVERT: B1 1006 TRP cc_start: 0.5408 (m100) cc_final: 0.3908 (m100) REVERT: BA 176 ASP cc_start: 0.8130 (p0) cc_final: 0.7838 (p0) REVERT: BA 294 LEU cc_start: 0.8397 (tp) cc_final: 0.7853 (tt) REVERT: BA 338 ILE cc_start: 0.8144 (mt) cc_final: 0.7617 (mt) REVERT: BA 539 ILE cc_start: 0.7262 (mt) cc_final: 0.7043 (mt) REVERT: BA 602 CYS cc_start: 0.6917 (t) cc_final: 0.6586 (t) REVERT: BB 185 MET cc_start: 0.2511 (mtp) cc_final: 0.2264 (mtm) REVERT: BB 217 LEU cc_start: 0.7043 (tp) cc_final: 0.6356 (tt) REVERT: BB 563 MET cc_start: 0.7598 (ppp) cc_final: 0.6982 (ppp) REVERT: BB 679 HIS cc_start: 0.4972 (p-80) cc_final: 0.4409 (p-80) REVERT: BB 753 MET cc_start: 0.3636 (mmm) cc_final: 0.3183 (tpt) REVERT: BB 840 MET cc_start: 0.8004 (tmm) cc_final: 0.7221 (tmm) REVERT: BB 895 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6464 (tm-30) REVERT: BC 320 LEU cc_start: 0.5055 (mt) cc_final: 0.4626 (mp) REVERT: BC 559 ILE cc_start: 0.7038 (mt) cc_final: 0.6753 (mt) REVERT: BC 778 MET cc_start: 0.4206 (ptm) cc_final: 0.3986 (ptp) REVERT: BD 262 LEU cc_start: 0.7118 (mt) cc_final: 0.6475 (mp) REVERT: BD 274 ILE cc_start: 0.7998 (tt) cc_final: 0.7086 (tt) REVERT: BD 369 ASN cc_start: 0.7944 (m-40) cc_final: 0.7224 (m-40) REVERT: BD 446 ARG cc_start: 0.6612 (ptp-170) cc_final: 0.5676 (ptp90) REVERT: BD 455 ILE cc_start: 0.7761 (mp) cc_final: 0.7441 (mm) REVERT: BD 500 MET cc_start: -0.0405 (ttm) cc_final: -0.2809 (mtt) REVERT: BE 148 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7963 (mtpp) REVERT: BE 415 VAL cc_start: 0.8690 (t) cc_final: 0.8258 (p) REVERT: BE 489 MET cc_start: 0.8975 (tpt) cc_final: 0.8539 (tmm) REVERT: BE 641 LEU cc_start: 0.8606 (tp) cc_final: 0.8294 (tp) REVERT: BE 652 CYS cc_start: 0.8520 (m) cc_final: 0.8315 (m) REVERT: CA 42 HIS cc_start: 0.4473 (t-170) cc_final: 0.4218 (t-170) REVERT: CA 188 MET cc_start: 0.4321 (mmm) cc_final: 0.3886 (mmm) REVERT: CA 190 ILE cc_start: 0.7087 (tt) cc_final: 0.6672 (mt) REVERT: CB 209 MET cc_start: -0.1388 (ttt) cc_final: -0.2074 (tpp) REVERT: CB 364 VAL cc_start: 0.5745 (t) cc_final: 0.5541 (t) REVERT: CB 536 TYR cc_start: 0.4842 (t80) cc_final: 0.4530 (t80) REVERT: CB 1022 MET cc_start: 0.8274 (mmm) cc_final: 0.7988 (mmp) REVERT: CB 1143 MET cc_start: 0.3078 (tpp) cc_final: 0.2793 (tpp) REVERT: CB 1230 MET cc_start: 0.3202 (mmp) cc_final: 0.2415 (mmp) REVERT: E1 97 LEU cc_start: 0.6966 (mt) cc_final: 0.6667 (mt) REVERT: E1 115 GLN cc_start: 0.7282 (tp40) cc_final: 0.6683 (tp-100) REVERT: E1 133 THR cc_start: 0.5978 (p) cc_final: 0.5419 (m) REVERT: E1 209 MET cc_start: 0.6075 (pmm) cc_final: 0.5671 (pmm) REVERT: E2 41 MET cc_start: 0.6880 (tpt) cc_final: 0.6679 (tpt) REVERT: E2 47 MET cc_start: 0.6696 (mmm) cc_final: 0.5682 (mmm) REVERT: E2 77 LEU cc_start: 0.8487 (mt) cc_final: 0.8229 (mm) REVERT: E2 143 GLN cc_start: 0.6819 (tp40) cc_final: 0.6477 (tp40) REVERT: K1 121 MET cc_start: 0.8486 (ptm) cc_final: 0.7889 (ttp) REVERT: MA 51 CYS cc_start: 0.8364 (m) cc_final: 0.7948 (t) REVERT: MA 120 MET cc_start: 0.7360 (ttp) cc_final: 0.7073 (ttp) REVERT: MA 144 ASN cc_start: 0.8913 (p0) cc_final: 0.8600 (p0) REVERT: MB 172 MET cc_start: 0.1894 (mmp) cc_final: -0.0229 (ttm) REVERT: MB 231 ILE cc_start: 0.8693 (pt) cc_final: 0.7821 (pt) REVERT: R1 138 MET cc_start: 0.7848 (mpp) cc_final: 0.7600 (mpp) REVERT: SC 82 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6743 (mtm110) REVERT: SC 122 GLU cc_start: 0.6325 (mm-30) cc_final: 0.5857 (mm-30) REVERT: SC 224 ASP cc_start: 0.8428 (m-30) cc_final: 0.8152 (m-30) REVERT: SI 55 LYS cc_start: 0.3747 (mmtp) cc_final: 0.2657 (mmmt) REVERT: SK 39 LYS cc_start: 0.6607 (ptpp) cc_final: 0.5040 (mtmt) REVERT: SK 52 ILE cc_start: 0.9081 (pt) cc_final: 0.8617 (mm) REVERT: SK 103 ASP cc_start: 0.8860 (p0) cc_final: 0.7645 (p0) REVERT: SP 83 ILE cc_start: 0.7704 (mp) cc_final: 0.7469 (mp) REVERT: SP 91 THR cc_start: 0.9415 (p) cc_final: 0.8993 (m) REVERT: SR 52 LEU cc_start: 0.8438 (mp) cc_final: 0.8233 (mp) REVERT: SR 54 LEU cc_start: 0.9184 (mt) cc_final: 0.8703 (mt) REVERT: SR 83 GLN cc_start: 0.8245 (tp40) cc_final: 0.7598 (tp40) REVERT: SX 97 ARG cc_start: 0.7977 (mpp80) cc_final: 0.7617 (mpp80) REVERT: Sd 50 GLU cc_start: 0.8037 (tt0) cc_final: 0.7836 (tt0) REVERT: U4 67 ILE cc_start: 0.9294 (mm) cc_final: 0.9094 (mm) REVERT: U4 100 ASP cc_start: 0.8166 (m-30) cc_final: 0.7964 (m-30) REVERT: U4 173 MET cc_start: 0.7318 (tpp) cc_final: 0.6306 (mmm) REVERT: U5 183 ILE cc_start: 0.8652 (mm) cc_final: 0.8275 (tp) outliers start: 4 outliers final: 1 residues processed: 1494 average time/residue: 1.2378 time to fit residues: 3316.2990 Evaluate side-chains 1158 residues out of total 10080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1157 time to evaluate : 9.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1787 random chunks: chunk 869 optimal weight: 0.7980 chunk 1126 optimal weight: 1.9990 chunk 1510 optimal weight: 1.9990 chunk 434 optimal weight: 0.9990 chunk 1307 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 393 optimal weight: 20.0000 chunk 1419 optimal weight: 20.0000 chunk 594 optimal weight: 0.9980 chunk 1458 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 256 ASN ** 3C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 314 GLN 3G 18 GLN 3G 75 ASN 3H 38 ASN B1 218 ASN BA 145 HIS BA 306 ASN ** BA 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 598 ASN ** BB 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 58 ASN ** BC 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 204 ASN BC 241 GLN ** BC 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 513 GLN BE 208 GLN BE 285 HIS ** BE 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 645 HIS CA 96 HIS ** CB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB1154 ASN CB1159 ASN E1 105 ASN ** E1 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1 118 GLN MA 59 ASN MA 74 HIS P1 123 HIS R1 334 ASN ** R1 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 89 HIS SK 155 HIS ** SM 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SR 32 ASN SR 100 GLN ** SR 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U4 64 GLN ** U4 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U4 73 ASN ** U5 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U5 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.128742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.110437 restraints weight = 725672.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.108856 restraints weight = 1056244.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109913 restraints weight = 884974.986| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 156436 Z= 0.154 Angle : 0.633 13.726 220267 Z= 0.318 Chirality : 0.038 0.643 27488 Planarity : 0.004 0.096 22428 Dihedral : 19.650 179.909 42191 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.18 % Favored : 91.74 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.16 % Twisted Proline : 0.90 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.08), residues: 11351 helix: 0.24 (0.09), residues: 3380 sheet: -0.75 (0.11), residues: 2144 loop : -2.41 (0.08), residues: 5827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP3F 552 HIS 0.021 0.001 HISBA 472 PHE 0.037 0.002 PHEBA 693 TYR 0.041 0.002 TYRSK 43 ARG 0.016 0.001 ARGBD 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49237.86 seconds wall clock time: 854 minutes 2.09 seconds (51242.09 seconds total)