Starting phenix.real_space_refine (version: dev) on Sun Apr 17 15:32:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7olc_12976/04_2022/7olc_12976_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.025 sd= 0.534 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "C GLU 542": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C GLU 595": "OE1" <-> "OE2" Residue "LA PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 51": "OD1" <-> "OD2" Residue "LA TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 176": "OD1" <-> "OD2" Residue "LA ASP 208": "OD1" <-> "OD2" Residue "LB ASP 213": "OD1" <-> "OD2" Residue "LB ASP 217": "OD1" <-> "OD2" Residue "LC ASP 13": "OD1" <-> "OD2" Residue "LC ASP 286": "OD1" <-> "OD2" Residue "LE ASP 177": "OD1" <-> "OD2" Residue "LE ASP 193": "OD1" <-> "OD2" Residue "LG ASP 86": "OD1" <-> "OD2" Residue "LG ASP 231": "OD1" <-> "OD2" Residue "LH ASP 162": "OD1" <-> "OD2" Residue "LH ASP 179": "OD1" <-> "OD2" Residue "LI ASP 28": "OD1" <-> "OD2" Residue "LI ASP 45": "OD1" <-> "OD2" Residue "LI GLU 56": "OE1" <-> "OE2" Residue "LI GLU 63": "OE1" <-> "OE2" Residue "LJ ASP 29": "OD1" <-> "OD2" Residue "LL ASP 27": "OD1" <-> "OD2" Residue "LL ASP 52": "OD1" <-> "OD2" Residue "LL TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL ASP 141": "OD1" <-> "OD2" Residue "LM ASP 42": "OD1" <-> "OD2" Residue "LM GLU 86": "OE1" <-> "OE2" Residue "LM ASP 114": "OD1" <-> "OD2" Residue "LM PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 160": "OE1" <-> "OE2" Residue "LO GLU 171": "OE1" <-> "OE2" Residue "LP GLU 31": "OE1" <-> "OE2" Residue "LQ GLU 69": "OE1" <-> "OE2" Residue "LQ GLU 127": "OE1" <-> "OE2" Residue "LR ASP 86": "OD1" <-> "OD2" Residue "LR ASP 160": "OD1" <-> "OD2" Residue "LS ASP 134": "OD1" <-> "OD2" Residue "LT TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 67": "OD1" <-> "OD2" Residue "LV ASP 91": "OD1" <-> "OD2" Residue "LV GLU 123": "OE1" <-> "OE2" Residue "LW ASP 25": "OD1" <-> "OD2" Residue "LW GLU 37": "OE1" <-> "OE2" Residue "LX TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 67": "OE1" <-> "OE2" Residue "LX ASP 117": "OD1" <-> "OD2" Residue "LY GLU 54": "OE1" <-> "OE2" Residue "LY GLU 66": "OE1" <-> "OE2" Residue "LY ASP 111": "OD1" <-> "OD2" Residue "LZ TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ASP 98": "OD1" <-> "OD2" Residue "LZ GLU 118": "OE1" <-> "OE2" Residue "La TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La ASP 76": "OD1" <-> "OD2" Residue "La ASP 103": "OD1" <-> "OD2" Residue "Lb TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc GLU 79": "OE1" <-> "OE2" Residue "Lc ASP 97": "OD1" <-> "OD2" Residue "Lc ASP 102": "OD1" <-> "OD2" Residue "Ld GLU 19": "OE1" <-> "OE2" Residue "Le ASP 108": "OD1" <-> "OD2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lh ASP 51": "OD1" <-> "OD2" Residue "Li GLU 63": "OE1" <-> "OE2" Residue "Li GLU 105": "OE1" <-> "OE2" Residue "Lm ASP 92": "OD1" <-> "OD2" Residue "Lm TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lo ASP 44": "OD1" <-> "OD2" Residue "Lo ASP 96": "OD1" <-> "OD2" Residue "Lp TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq ASP 49": "OD1" <-> "OD2" Residue "Lq GLU 58": "OE1" <-> "OE2" Residue "Lq TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ls ASP 13": "OD1" <-> "OD2" Residue "Ls ASP 31": "OD1" <-> "OD2" Residue "SA TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 183": "OE1" <-> "OE2" Residue "SB ASP 59": "OD1" <-> "OD2" Residue "SB GLU 77": "OE1" <-> "OE2" Residue "SB PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC ASP 86": "OD1" <-> "OD2" Residue "SC GLU 87": "OE1" <-> "OE2" Residue "SC ASP 116": "OD1" <-> "OD2" Residue "SC ASP 203": "OD1" <-> "OD2" Residue "SC GLU 216": "OE1" <-> "OE2" Residue "SD ASP 17": "OD1" <-> "OD2" Residue "SD TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD ASP 50": "OD1" <-> "OD2" Residue "SD TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD ASP 209": "OD1" <-> "OD2" Residue "SE GLU 97": "OE1" <-> "OE2" Residue "SE ASP 158": "OD1" <-> "OD2" Residue "SE ASP 163": "OD1" <-> "OD2" Residue "SF GLU 179": "OE1" <-> "OE2" Residue "SF GLU 184": "OE1" <-> "OE2" Residue "SG ASP 39": "OD1" <-> "OD2" Residue "SG ASP 150": "OD1" <-> "OD2" Residue "SG TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG ASP 228": "OD1" <-> "OD2" Residue "SH ASP 32": "OD1" <-> "OD2" Residue "SH GLU 54": "OE1" <-> "OE2" Residue "SH GLU 168": "OE1" <-> "OE2" Residue "SH ASP 173": "OD1" <-> "OD2" Residue "SI ASP 6": "OD1" <-> "OD2" Residue "SI GLU 189": "OE1" <-> "OE2" Residue "SJ GLU 31": "OE1" <-> "OE2" Residue "SJ GLU 39": "OE1" <-> "OE2" Residue "SJ GLU 86": "OE1" <-> "OE2" Residue "SJ ASP 101": "OD1" <-> "OD2" Residue "SJ ASP 149": "OD1" <-> "OD2" Residue "SJ ASP 155": "OD1" <-> "OD2" Residue "SL ASP 42": "OD1" <-> "OD2" Residue "SL GLU 106": "OE1" <-> "OE2" Residue "SM GLU 70": "OE1" <-> "OE2" Residue "SN GLU 31": "OE1" <-> "OE2" Residue "SN ASP 108": "OD1" <-> "OD2" Residue "SN ASP 110": "OD1" <-> "OD2" Residue "SO GLU 50": "OE1" <-> "OE2" Residue "SP ASP 39": "OD1" <-> "OD2" Residue "SQ TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 82": "OD1" <-> "OD2" Residue "SR ASP 118": "OD1" <-> "OD2" Residue "SS ASP 51": "OD1" <-> "OD2" Residue "ST TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU ASP 89": "OD1" <-> "OD2" Residue "SV GLU 64": "OE1" <-> "OE2" Residue "SV ASP 67": "OD1" <-> "OD2" Residue "SW GLU 115": "OE1" <-> "OE2" Residue "SX ASP 90": "OD1" <-> "OD2" Residue "SY GLU 83": "OE1" <-> "OE2" Residue "SZ ASP 37": "OD1" <-> "OD2" Residue "Sa TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sb ASP 6": "OD1" <-> "OD2" Residue "Sb PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sc GLU 61": "OE1" <-> "OE2" Residue "Sd GLU 45": "OE1" <-> "OE2" Residue "Sd ASP 49": "OD1" <-> "OD2" Residue "Sf ASP 111": "OD1" <-> "OD2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 207344 Number of models: 1 Model: "" Number of chains: 127 Chain: "1" Number of atoms: 68242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3191, 68242 Classifications: {'RNA': 3191} Modifications used: {'rna3p_pyr': 1231, 'rna2p_pur': 325, 'rna3p_pur': 1419, 'rna2p_pyr': 215, 'rna3p': 1} Link IDs: {'rna3p': 2650, 'rna2p': 540} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "2" Number of atoms: 37645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1765, 37645 Classifications: {'RNA': 1765} Modifications used: {'rna3p_pyr': 700, 'rna2p_pur': 147, 'rna3p_pur': 785, 'rna2p_pyr': 132, 'rna3p': 1} Link IDs: {'rna3p': 1486, 'rna2p': 278} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "3" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2535 Classifications: {'RNA': 119} Modifications used: {'rna3p_pyr': 53, 'rna2p_pur': 7, 'rna3p_pur': 54, 'rna2p_pyr': 5} Link IDs: {'rna3p': 106, 'rna2p': 12} Chain: "4" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3319 Classifications: {'RNA': 156} Modifications used: {'rna3p_pyr': 64, 'rna2p_pur': 16, 'rna3p_pur': 64, 'rna2p_pyr': 12} Link IDs: {'rna3p': 128, 'rna2p': 27} Chain: "A" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2438 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "B" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "LA" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1925 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 236, 'PCIS': 1} Chain: "LB" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3088 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 15, 'TRANS': 371} Chain: "LC" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2758 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 24, 'TRANS': 338} Chain: "LD" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2440 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain: "LE" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1518 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "LF" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2017 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain: "LG" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1900 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 222, 'PCIS': 1} Chain: "LH" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1505 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "LI" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1760 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "LJ" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1367 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "LK" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 762 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 174 Chain: "LL" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1666 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "LM" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1125 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "LN" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1703 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "LO" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1613 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 10, 'TRANS': 192} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "LP" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1472 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain: "LQ" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1481 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "LR" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1506 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "LS" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1425 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain: "LT" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1266 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "LU" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 819 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "LV" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 994 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "LW" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1075 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "LX" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "LZ" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "La" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1180 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "Lb" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 508 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Lc" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 722 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Ld" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "Le" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1001 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Lf" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 853 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Lg" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 836 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Lj" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 82, 'PCIS': 1} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "Ll" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 435 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 418 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "Ln" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 224 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "Lo" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "Lp" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 697 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Lq" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1083 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "Lr" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 224 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "Ls" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1449 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain: "SA" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1641 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 14, 'TRANS': 193} Chain: "SB" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1871 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "SC" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1672 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "SD" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1688 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "SE" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2072 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain: "SF" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1557 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "SG" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1875 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 14, 'TRANS': 217} Chain: "SH" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1562 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "SI" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1621 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "SJ" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1466 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "SK" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 742 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "SL" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1222 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SM" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 923 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "SN" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1182 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "SO" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1002 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "SP" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "SQ" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1081 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "SR" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1045 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SS" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 2, 'TRANS': 134} Chain: "ST" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1117 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "SU" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 819 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "SV" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 664 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "SW" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "SX" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1099 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "SY" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1061 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "SZ" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "Sa" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 839 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "Sb" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 611 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 6, 'TRANS': 74} Chain: "Sc" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 484 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "Sd" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 419 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "Se" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 322 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "Sf" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 604 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "1" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 415 Unusual residues: {' MG': 415} Classifications: {'undetermined': 415} Link IDs: {None: 414} Chain: "2" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Unusual residues: {' MG': 121} Classifications: {'undetermined': 121} Link IDs: {None: 120} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "4" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "LA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "LP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Sa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 748 Classifications: {'water': 748} Link IDs: {None: 747} Chain: "2" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "4" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "LB" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "LC" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "LD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "LN" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "LO" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "LP" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "LT" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "LW" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Lb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Ld" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Le" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "SL" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "SN" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Sa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A1AZH SG CYSLg 45 148.107 199.818 54.107 1.00100.37 S ATOM A1AZZ SG CYSLg 48 150.546 197.747 55.609 1.00103.07 S ATOM A1B77 SG CYSLg 82 151.616 199.123 52.194 1.00102.33 S ATOM A1B7P SG CYSLg 85 149.663 196.216 51.878 1.00103.36 S ATOM A1CX6 SG CYSLj 19 107.457 220.019 92.942 1.00 85.96 S ATOM A1CXY SG CYSLj 22 105.959 220.598 96.126 1.00 88.32 S ATOM A1D0O SG CYSLj 34 106.801 216.906 95.479 1.00 83.36 S ATOM A1D15 SG CYSLj 37 103.955 218.335 93.482 1.00 85.31 S ATOM A1EAG SG CYSLm 96 137.651 162.930 193.043 1.00 93.70 S ATOM A1EB6 SG CYSLm 99 138.616 166.356 192.347 1.00 93.91 S ATOM A1EDL SG CYSLm 110 137.979 166.100 195.820 1.00 96.95 S ATOM A1EEV SG CYSLm 115 135.277 166.719 193.646 1.00 95.65 S ATOM A1EQJ SG CYSLo 12 48.670 145.641 121.968 1.00110.20 S ATOM A1ERJ SG CYSLo 17 44.940 143.960 120.866 1.00119.07 S ATOM A1F4B SG CYSLo 74 48.947 142.459 119.975 1.00111.23 S ATOM A1F4U SG CYSLo 77 47.305 145.276 118.594 1.00115.16 S ATOM A1FJB SG CYSLp 39 153.661 180.247 59.468 1.00 95.04 S ATOM A1FJZ SG CYSLp 42 156.743 182.089 58.493 1.00 98.76 S ATOM A1FN4 SG CYSLp 57 154.800 183.646 61.555 1.00 96.65 S ATOM A1FNP SG CYSLp 60 153.330 183.798 58.394 1.00100.76 S ATOM A279C SG CYSSa 23 139.422 119.836 78.610 1.00 99.18 S ATOM A279W SG CYSSa 26 139.193 120.579 82.264 1.00100.35 S ATOM A27KM SG CYSSa 74 142.152 118.867 80.872 1.00 98.74 S ATOM A27L5 SG CYSSa 77 139.325 117.001 82.290 1.00100.28 S ATOM A27ZV SG CYSSb 40 172.564 146.123 15.243 1.00182.86 S ATOM A283T SG CYSSb 59 169.605 146.352 17.363 1.00180.75 S ATOM A28Q2 SG CYSSd 21 151.007 59.655 130.538 1.00193.25 S ATOM A28QQ SG CYSSd 24 154.571 62.892 130.607 1.00196.30 S ATOM A28UP SG CYSSd 42 152.786 62.109 127.634 1.00179.95 S Time building chain proxies: 75.89, per 1000 atoms: 0.37 Number of scatterers: 207344 At special positions: 0 Unit cell: (302.5, 290.4, 271.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 290 16.00 P 5231 15.00 Mg 571 11.99 O 53835 8.00 N 38171 7.00 C 109238 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: 68.36 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNLg 200 " pdb="ZN ZNLg 200 " - pdb=" SG CYSLg 48 " pdb="ZN ZNLg 200 " - pdb=" SG CYSLg 85 " pdb="ZN ZNLg 200 " - pdb=" SG CYSLg 82 " pdb="ZN ZNLg 200 " - pdb=" SG CYSLg 45 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 74 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 17 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb=" ZNSa 201 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 23 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 74 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 77 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 26 " pdb=" ZNSb 101 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 59 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 40 " pdb=" ZNSd 101 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 42 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 21 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 24 " Number of angles added : 36 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22054 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 384 helices and 116 sheets defined 40.1% alpha, 14.0% beta 835 base pairs and 2953 stacking pairs defined. Time for finding SS restraints: 70.68 Creating SS restraints... Processing helix chain 'C' and resid 536 through 560 removed outlier: 3.523A pdb=" N GLN C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 568 removed outlier: 4.466A pdb=" N LYS C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS C 568 " --> pdb=" O SER C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 589 removed outlier: 3.838A pdb=" N LYS C 574 " --> pdb=" O GLY C 570 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 585 " --> pdb=" O GLU C 581 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 613 removed outlier: 3.603A pdb=" N LEU C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 610 " --> pdb=" O LEU C 606 " (cutoff:3.500A) Processing helix chain 'LA' and resid 5 through 13 removed outlier: 3.685A pdb=" N ARGLA 9 " --> pdb=" O ILELA 5 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYSLA 10 " --> pdb=" O ARGLA 6 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLYLA 11 " --> pdb=" O ASNLA 7 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARGLA 12 " --> pdb=" O GLNLA 8 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLYLA 13 " --> pdb=" O ARGLA 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 5 through 13' Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 181 through 193 removed outlier: 4.158A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.970A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASNLA 205 " --> pdb=" O GLYLA 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 200 through 205' Processing helix chain 'LB' and resid 111 through 120 removed outlier: 3.919A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 3.951A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALALB 138 " --> pdb=" O ALALB 134 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLULB 139 " --> pdb=" O LYSLB 135 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASNLB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 142 through 155 removed outlier: 3.598A pdb=" N LYSLB 154 " --> pdb=" O GLULB 150 " (cutoff:3.500A) Processing helix chain 'LB' and resid 166 through 171 removed outlier: 4.708A pdb=" N THRLB 170 " --> pdb=" O GLNLB 166 " (cutoff:3.500A) Proline residue: LB 171 - end of helix No H-bonds generated for 'chain 'LB' and resid 166 through 171' Processing helix chain 'LB' and resid 188 through 200 removed outlier: 3.865A pdb=" N LEULB 199 " --> pdb=" O PHELB 195 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHELB 200 " --> pdb=" O GLYLB 196 " (cutoff:3.500A) Processing helix chain 'LB' and resid 205 through 210 removed outlier: 3.970A pdb=" N ILELB 209 " --> pdb=" O THRLB 205 " (cutoff:3.500A) Processing helix chain 'LB' and resid 229 through 234 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 6.131A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLULB 353 " --> pdb=" O ARGLB 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 348 through 353' Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LC' and resid 32 through 46 removed outlier: 3.823A pdb=" N GLYLC 42 " --> pdb=" O HISLC 38 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.962A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 removed outlier: 3.707A pdb=" N GLYLC 140 " --> pdb=" O LEULC 136 " (cutoff:3.500A) Processing helix chain 'LC' and resid 165 through 177 removed outlier: 3.509A pdb=" N ILELC 176 " --> pdb=" O LEULC 172 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLYLC 177 " --> pdb=" O LEULC 173 " (cutoff:3.500A) Processing helix chain 'LC' and resid 178 through 189 removed outlier: 3.700A pdb=" N VALLC 185 " --> pdb=" O ASPLC 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYSLC 186 " --> pdb=" O VALLC 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERLC 188 " --> pdb=" O LYSLC 184 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 195 through 200 removed outlier: 3.981A pdb=" N ARGLC 199 " --> pdb=" O LYSLC 195 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLYLC 200 " --> pdb=" O GLYLC 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 195 through 200' Processing helix chain 'LC' and resid 221 through 228 removed outlier: 4.077A pdb=" N GLYLC 225 " --> pdb=" O GLULC 221 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHELC 226 " --> pdb=" O LEULC 222 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASNLC 228 " --> pdb=" O LYSLC 224 " (cutoff:3.500A) Processing helix chain 'LC' and resid 241 through 247 Proline residue: LC 247 - end of helix Processing helix chain 'LC' and resid 258 through 272 removed outlier: 3.583A pdb=" N LYSLC 263 " --> pdb=" O SERLC 259 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VALLC 268 " --> pdb=" O GLNLC 264 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYRLC 269 " --> pdb=" O LEULC 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLULC 270 " --> pdb=" O ASPLC 266 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SERLC 271 " --> pdb=" O ALALC 267 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYSLC 272 " --> pdb=" O VALLC 268 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 removed outlier: 3.765A pdb=" N LEULC 290 " --> pdb=" O ASPLC 286 " (cutoff:3.500A) Processing helix chain 'LC' and resid 294 through 300 removed outlier: 4.191A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 322 through 330 removed outlier: 3.521A pdb=" N ARGLC 328 " --> pdb=" O GLNLC 324 " (cutoff:3.500A) Processing helix chain 'LC' and resid 332 through 340 Processing helix chain 'LC' and resid 355 through 364 removed outlier: 6.521A pdb=" N LYSLC 359 " --> pdb=" O PROLC 355 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLULC 360 " --> pdb=" O ALALC 356 " (cutoff:3.500A) Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 26 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 4.211A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 4.464A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYRLD 86 " --> pdb=" O GLULD 82 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLYLD 87 " --> pdb=" O LEULD 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 79 through 87' Processing helix chain 'LD' and resid 94 through 114 removed outlier: 3.510A pdb=" N ALALD 98 " --> pdb=" O ASNLD 94 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYSLD 112 " --> pdb=" O ARGLD 108 " (cutoff:3.500A) Processing helix chain 'LD' and resid 115 through 120 removed outlier: 4.529A pdb=" N PHELD 119 " --> pdb=" O LEULD 115 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THRLD 120 " --> pdb=" O ASPLD 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 115 through 120' Processing helix chain 'LD' and resid 160 through 173 removed outlier: 3.966A pdb=" N GLYLD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLYLD 173 " --> pdb=" O ALALD 169 " (cutoff:3.500A) Processing helix chain 'LD' and resid 194 through 204 removed outlier: 6.576A pdb=" N LEULD 198 " --> pdb=" O ASPLD 194 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYSLD 199 " --> pdb=" O THRLD 195 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYRLD 203 " --> pdb=" O LYSLD 199 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLYLD 204 " --> pdb=" O LYSLD 200 " (cutoff:3.500A) Processing helix chain 'LD' and resid 205 through 218 removed outlier: 3.596A pdb=" N GLULD 212 " --> pdb=" O ALALD 208 " (cutoff:3.500A) Processing helix chain 'LD' and resid 219 through 227 Processing helix chain 'LD' and resid 228 through 233 removed outlier: 3.517A pdb=" N ASPLD 232 " --> pdb=" O LYSLD 228 " (cutoff:3.500A) Processing helix chain 'LD' and resid 235 through 253 removed outlier: 3.543A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSLD 248 " --> pdb=" O ALALD 244 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 279 removed outlier: 3.805A pdb=" N LYSLD 271 " --> pdb=" O LYSLD 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYSLD 276 " --> pdb=" O ALALD 272 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYRLD 277 " --> pdb=" O GLULD 273 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYSLD 278 " --> pdb=" O SERLD 274 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYSLD 279 " --> pdb=" O LEULD 275 " (cutoff:3.500A) Processing helix chain 'LD' and resid 283 through 302 removed outlier: 3.854A pdb=" N VALLD 291 " --> pdb=" O ARGLD 287 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLULD 292 " --> pdb=" O LYSLD 288 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLNLD 302 " --> pdb=" O LEULD 298 " (cutoff:3.500A) Processing helix chain 'LE' and resid 98 through 103 removed outlier: 4.458A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 98 through 103' Processing helix chain 'LE' and resid 115 through 124 removed outlier: 6.512A pdb=" N ILELE 119 " --> pdb=" O ASPLE 115 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASPLE 120 " --> pdb=" O GLNLE 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLULE 121 " --> pdb=" O ALALE 117 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLNLE 124 " --> pdb=" O ASPLE 120 " (cutoff:3.500A) Processing helix chain 'LE' and resid 131 through 146 removed outlier: 3.579A pdb=" N GLULE 139 " --> pdb=" O GLULE 135 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHELE 142 " --> pdb=" O SERLE 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLNLE 145 " --> pdb=" O ALALE 141 " (cutoff:3.500A) Processing helix chain 'LE' and resid 155 through 174 removed outlier: 3.615A pdb=" N LYSLE 163 " --> pdb=" O ALALE 159 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALALE 171 " --> pdb=" O LYSLE 167 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.348A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 removed outlier: 3.556A pdb=" N ILELF 12 " --> pdb=" O THRLF 8 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALLF 14 " --> pdb=" O ASNLF 10 " (cutoff:3.500A) Processing helix chain 'LF' and resid 15 through 30 removed outlier: 3.573A pdb=" N SERLF 24 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARGLF 29 " --> pdb=" O GLNLF 25 " (cutoff:3.500A) Processing helix chain 'LF' and resid 33 through 79 removed outlier: 3.635A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYSLF 68 " --> pdb=" O GLNLF 64 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 3.754A pdb=" N GLULF 131 " --> pdb=" O LYSLF 127 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VALLF 136 " --> pdb=" O METLF 132 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLULF 137 " --> pdb=" O ILELF 133 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 157 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.120A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASNLF 178 " --> pdb=" O ILELF 174 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 197 removed outlier: 3.531A pdb=" N LEULF 190 " --> pdb=" O CYSLF 186 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VALLF 197 " --> pdb=" O GLULF 193 " (cutoff:3.500A) Processing helix chain 'LF' and resid 200 through 209 removed outlier: 3.603A pdb=" N LEULF 208 " --> pdb=" O ALALF 204 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 4.020A pdb=" N LEULF 244 " --> pdb=" O HISLF 240 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALALF 247 " --> pdb=" O ALALF 243 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 removed outlier: 4.193A pdb=" N LYSLG 66 " --> pdb=" O GLNLG 62 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILELG 67 " --> pdb=" O ARGLG 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGLG 69 " --> pdb=" O LYSLG 65 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N METLG 70 " --> pdb=" O LYSLG 66 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEULG 72 " --> pdb=" O LEULG 68 " (cutoff:3.500A) Processing helix chain 'LG' and resid 75 through 83 removed outlier: 5.038A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 3.552A pdb=" N LEULG 96 " --> pdb=" O GLNLG 92 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGLG 101 " --> pdb=" O LEULG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 122 removed outlier: 3.860A pdb=" N LYSLG 109 " --> pdb=" O LYSLG 105 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLULG 110 " --> pdb=" O GLNLG 106 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARGLG 111 " --> pdb=" O GLULG 107 " (cutoff:3.500A) Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 168 through 177 Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.541A pdb=" N LEULG 189 " --> pdb=" O GLYLG 185 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEULG 192 " --> pdb=" O ARGLG 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VALLG 193 " --> pdb=" O LEULG 189 " (cutoff:3.500A) Processing helix chain 'LG' and resid 210 through 235 removed outlier: 4.695A pdb=" N LEULG 214 " --> pdb=" O ASPLG 210 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASPLG 231 " --> pdb=" O GLULG 227 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THRLG 232 " --> pdb=" O LYSLG 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARGLG 233 " --> pdb=" O VALLG 229 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYSLG 234 " --> pdb=" O GLULG 230 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) Processing helix chain 'LG' and resid 242 through 257 removed outlier: 3.536A pdb=" N ARGLG 252 " --> pdb=" O ARGLG 248 " (cutoff:3.500A) Processing helix chain 'LH' and resid 61 through 84 removed outlier: 4.037A pdb=" N ALALH 67 " --> pdb=" O LYSLH 63 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEULH 68 " --> pdb=" O ASPLH 64 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARGLH 69 " --> pdb=" O VALLH 65 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THRLH 70 " --> pdb=" O ALALH 66 " (cutoff:3.500A) Processing helix chain 'LH' and resid 152 through 168 removed outlier: 3.809A pdb=" N CYSLH 167 " --> pdb=" O ILELH 163 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYSLH 168 " --> pdb=" O GLNLH 164 " (cutoff:3.500A) Processing helix chain 'LH' and resid 173 through 178 removed outlier: 4.377A pdb=" N LEULH 178 " --> pdb=" O ILELH 174 " (cutoff:3.500A) Processing helix chain 'LI' and resid 5 through 10 removed outlier: 4.733A pdb=" N TYRLI 9 " --> pdb=" O PROLI 5 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARGLI 10 " --> pdb=" O ALALI 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 5 through 10' Processing helix chain 'LI' and resid 42 through 47 removed outlier: 4.065A pdb=" N PHELI 46 " --> pdb=" O THRLI 42 " (cutoff:3.500A) Proline residue: LI 47 - end of helix No H-bonds generated for 'chain 'LI' and resid 42 through 47' Processing helix chain 'LI' and resid 61 through 80 removed outlier: 3.586A pdb=" N TYRLI 75 " --> pdb=" O CYSLI 71 " (cutoff:3.500A) Processing helix chain 'LI' and resid 144 through 160 removed outlier: 3.685A pdb=" N GLNLI 156 " --> pdb=" O LEULI 152 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYRLI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYSLI 158 " --> pdb=" O ARGLI 154 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHELI 159 " --> pdb=" O CYSLI 155 " (cutoff:3.500A) Proline residue: LI 160 - end of helix Processing helix chain 'LI' and resid 177 through 188 removed outlier: 3.589A pdb=" N GLYLI 188 " --> pdb=" O LYSLI 184 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 214 removed outlier: 3.952A pdb=" N ASNLI 209 " --> pdb=" O ASNLI 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N METLI 210 " --> pdb=" O LEULI 206 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARGLI 211 " --> pdb=" O GLULI 207 " (cutoff:3.500A) Proline residue: LI 214 - end of helix Processing helix chain 'LI' and resid 101 through 107 removed outlier: 3.960A pdb=" N ALALI 106 " --> pdb=" O LYSLI 101 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLYLI 107 " --> pdb=" O METLI 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 101 through 107' Processing helix chain 'LJ' and resid 28 through 43 removed outlier: 3.528A pdb=" N GLULJ 39 " --> pdb=" O ALALJ 35 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLNLJ 40 " --> pdb=" O LYSLJ 36 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEULJ 41 " --> pdb=" O VALLJ 37 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SERLJ 42 " --> pdb=" O LEULJ 38 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 74 through 89 removed outlier: 3.527A pdb=" N VALLJ 87 " --> pdb=" O ARGLJ 83 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 137 through 142 removed outlier: 4.312A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 156 through 168 removed outlier: 3.556A pdb=" N THRLJ 160 " --> pdb=" O THRLJ 156 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILELJ 161 " --> pdb=" O ARGLJ 157 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 93 through 98 removed outlier: 3.625A pdb=" N PHELJ 97 " --> pdb=" O ARGLJ 94 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SERLJ 98 " --> pdb=" O ARGLJ 95 " (cutoff:3.500A) Processing helix chain 'LK' and resid 29 through 37 Proline residue: LK 34 - end of helix removed outlier: 4.082A pdb=" N LEULK 37 " --> pdb=" O GLYLK 33 " (cutoff:3.500A) Processing helix chain 'LK' and resid 39 through 52 removed outlier: 3.819A pdb=" N GLYLK 43 " --> pdb=" O PROLK 39 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THRLK 50 " --> pdb=" O ILELK 46 " (cutoff:3.500A) Processing helix chain 'LK' and resid 77 through 86 removed outlier: 4.673A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 107 through 118 removed outlier: 3.624A pdb=" N GLULK 111 " --> pdb=" O ASPLK 107 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THRLK 115 " --> pdb=" O GLULK 111 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N METLK 116 " --> pdb=" O ILELK 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARGLK 117 " --> pdb=" O ALALK 113 " (cutoff:3.500A) Processing helix chain 'LK' and resid 125 through 137 removed outlier: 3.773A pdb=" N VALLK 129 " --> pdb=" O LEULK 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLULK 131 " --> pdb=" O GLYLK 127 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHELK 137 " --> pdb=" O LEULK 133 " (cutoff:3.500A) Processing helix chain 'LK' and resid 147 through 155 removed outlier: 4.967A pdb=" N ILELK 155 " --> pdb=" O ILELK 151 " (cutoff:3.500A) Processing helix chain 'LK' and resid 92 through 97 removed outlier: 5.522A pdb=" N GLULK 95 " --> pdb=" O ARGLK 92 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYSLK 96 " --> pdb=" O LYSLK 93 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASNLK 97 " --> pdb=" O LYSLK 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 92 through 97' Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.343A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VALLL 22 " --> pdb=" O TRPLL 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 22' Processing helix chain 'LL' and resid 27 through 47 removed outlier: 3.920A pdb=" N ALALL 47 " --> pdb=" O ALALL 43 " (cutoff:3.500A) Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 94 Proline residue: LL 91 - end of helix removed outlier: 4.056A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 4.320A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYRLL 119 " --> pdb=" O ARGLL 115 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALALL 121 " --> pdb=" O LYSLL 117 " (cutoff:3.500A) Processing helix chain 'LL' and resid 150 through 156 removed outlier: 6.175A pdb=" N SERLL 154 " --> pdb=" O SERLL 150 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHELL 155 " --> pdb=" O LEULL 151 " (cutoff:3.500A) Processing helix chain 'LL' and resid 180 through 195 removed outlier: 3.781A pdb=" N ALALL 192 " --> pdb=" O ALALL 188 " (cutoff:3.500A) Processing helix chain 'LL' and resid 196 through 210 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 4.290A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 58 through 63' Processing helix chain 'LM' and resid 77 through 89 removed outlier: 3.514A pdb=" N ALALM 84 " --> pdb=" O ALALM 80 " (cutoff:3.500A) Processing helix chain 'LM' and resid 90 through 98 removed outlier: 3.857A pdb=" N GLULM 96 " --> pdb=" O ALALM 92 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THRLM 97 " --> pdb=" O LYSLM 93 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 4.036A pdb=" N ARGLM 109 " --> pdb=" O GLNLM 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SERLM 111 " --> pdb=" O GLULM 107 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 140 removed outlier: 3.737A pdb=" N GLULM 130 " --> pdb=" O GLNLM 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSLM 133 " --> pdb=" O PHELM 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALALM 134 " --> pdb=" O GLULM 130 " (cutoff:3.500A) Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.119A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYSLN 12 " --> pdb=" O GLULN 8 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.271A pdb=" N ARGLN 31 " --> pdb=" O CYSLN 27 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLNLN 32 " --> pdb=" O TRPLN 28 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEULN 33 " --> pdb=" O GLULN 29 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASNLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 removed outlier: 3.535A pdb=" N LEULN 51 " --> pdb=" O LYSLN 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLYLN 52 " --> pdb=" O ALALN 48 " (cutoff:3.500A) Processing helix chain 'LN' and resid 83 through 88 removed outlier: 4.011A pdb=" N GLNLN 87 " --> pdb=" O LYSLN 83 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLYLN 88 " --> pdb=" O PROLN 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 83 through 88' Processing helix chain 'LN' and resid 97 through 111 removed outlier: 3.528A pdb=" N THRLN 101 " --> pdb=" O SERLN 97 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SERLN 111 " --> pdb=" O GLYLN 107 " (cutoff:3.500A) Processing helix chain 'LN' and resid 139 through 146 removed outlier: 4.184A pdb=" N ASPLN 145 " --> pdb=" O ALALN 141 " (cutoff:3.500A) Proline residue: LN 146 - end of helix Processing helix chain 'LN' and resid 148 through 153 removed outlier: 4.737A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASNLN 153 " --> pdb=" O ASNLN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 148 through 153' Processing helix chain 'LN' and resid 158 through 163 removed outlier: 3.985A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLYLN 163 " --> pdb=" O ARGLN 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 158 through 163' Processing helix chain 'LN' and resid 165 through 173 removed outlier: 4.584A pdb=" N GLYLN 173 " --> pdb=" O LYSLN 169 " (cutoff:3.500A) Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 removed outlier: 3.608A pdb=" N ILELO 23 " --> pdb=" O ARGLO 19 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEULO 29 " --> pdb=" O ALALO 25 " (cutoff:3.500A) Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.591A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.937A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILELO 90 " --> pdb=" O VALLO 86 " (cutoff:3.500A) Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 3.539A pdb=" N GLULO 102 " --> pdb=" O ALALO 98 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 111 through 116 removed outlier: 5.661A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 removed outlier: 3.640A pdb=" N GLULO 146 " --> pdb=" O ARGLO 142 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALLO 147 " --> pdb=" O LEULO 143 " (cutoff:3.500A) Processing helix chain 'LO' and resid 153 through 188 removed outlier: 3.732A pdb=" N ALALO 168 " --> pdb=" O ALALO 164 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLULO 182 " --> pdb=" O ARGLO 178 " (cutoff:3.500A) Processing helix chain 'LO' and resid 194 through 203 removed outlier: 3.595A pdb=" N ALALO 198 " --> pdb=" O LYSLO 194 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYRLO 202 " --> pdb=" O ALALO 198 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 removed outlier: 3.627A pdb=" N GLULP 31 " --> pdb=" O LYSLP 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALALP 35 " --> pdb=" O GLULP 31 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILELP 36 " --> pdb=" O THRLP 32 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASNLP 37 " --> pdb=" O ALALP 33 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 54 removed outlier: 3.513A pdb=" N ILELP 52 " --> pdb=" O LEULP 48 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 removed outlier: 3.667A pdb=" N PHELP 90 " --> pdb=" O LYSLP 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALALP 104 " --> pdb=" O ALALP 100 " (cutoff:3.500A) Processing helix chain 'LP' and resid 172 through 187 Processing helix chain 'LP' and resid 70 through 76 removed outlier: 3.801A pdb=" N GLYLP 73 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYSLP 74 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNLP 75 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 51 through 68 removed outlier: 3.516A pdb=" N ARGLQ 66 " --> pdb=" O ARGLQ 62 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 4.339A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VALLQ 75 " --> pdb=" O PROLQ 71 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHELQ 81 " --> pdb=" O LEULQ 77 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N METLQ 82 " --> pdb=" O ARGLQ 78 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.652A pdb=" N ASNLQ 98 " --> pdb=" O ARGLQ 94 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYSLQ 100 " --> pdb=" O ALALQ 96 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 134 through 145 removed outlier: 3.644A pdb=" N GLYLQ 145 " --> pdb=" O ILELQ 141 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LQ' and resid 174 through 181 removed outlier: 3.905A pdb=" N LYSLQ 178 " --> pdb=" O ARGLQ 174 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HISLQ 179 " --> pdb=" O GLULQ 175 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHELQ 180 " --> pdb=" O ALALQ 176 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLYLQ 181 " --> pdb=" O VALLQ 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 174 through 181' Processing helix chain 'LR' and resid 4 through 16 removed outlier: 3.528A pdb=" N SERLR 13 " --> pdb=" O ARGLR 9 " (cutoff:3.500A) Processing helix chain 'LR' and resid 28 through 35 removed outlier: 3.948A pdb=" N ASNLR 34 " --> pdb=" O SERLR 30 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 removed outlier: 3.662A pdb=" N ALALR 46 " --> pdb=" O ARGLR 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASPLR 47 " --> pdb=" O LYSLR 43 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLYLR 48 " --> pdb=" O LEULR 44 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 73 removed outlier: 3.918A pdb=" N ILELR 72 " --> pdb=" O LEULR 68 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLYLR 73 " --> pdb=" O ALALR 69 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 113 Proline residue: LR 90 - end of helix removed outlier: 6.646A pdb=" N VALLR 93 " --> pdb=" O METLR 89 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 130 removed outlier: 3.506A pdb=" N GLULR 122 " --> pdb=" O HISLR 118 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASNLR 130 " --> pdb=" O LEULR 126 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 185 removed outlier: 3.527A pdb=" N GLULR 148 " --> pdb=" O ARGLR 144 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARGLR 170 " --> pdb=" O THRLR 166 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLULR 171 " --> pdb=" O LYSLR 167 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARGLR 172 " --> pdb=" O ALALR 168 " (cutoff:3.500A) Processing helix chain 'LS' and resid 33 through 49 removed outlier: 3.800A pdb=" N SERLS 39 " --> pdb=" O VALLS 35 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLYLS 47 " --> pdb=" O TYRLS 43 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEULS 48 " --> pdb=" O PHELS 44 " (cutoff:3.500A) Processing helix chain 'LS' and resid 98 through 114 removed outlier: 3.989A pdb=" N ALALS 102 " --> pdb=" O SERLS 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VALLS 103 " --> pdb=" O ARGLS 99 " (cutoff:3.500A) Processing helix chain 'LS' and resid 137 through 145 removed outlier: 3.547A pdb=" N LYSLS 141 " --> pdb=" O ARGLS 137 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLNLS 142 " --> pdb=" O PROLS 138 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALLS 144 " --> pdb=" O ILELS 140 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALALS 145 " --> pdb=" O LYSLS 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 137 through 145' Processing helix chain 'LT' and resid 11 through 16 removed outlier: 3.761A pdb=" N PHELT 15 " --> pdb=" O THRLT 11 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SERLT 16 " --> pdb=" O ARGLT 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 11 through 16' Processing helix chain 'LT' and resid 27 through 32 removed outlier: 4.378A pdb=" N LEULT 31 " --> pdb=" O LEULT 27 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARGLT 32 " --> pdb=" O SERLT 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 27 through 32' Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.817A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 102 through 123 removed outlier: 3.598A pdb=" N LYSLT 110 " --> pdb=" O LEULT 106 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALALT 119 " --> pdb=" O LEULT 115 " (cutoff:3.500A) Processing helix chain 'LU' and resid 25 through 32 removed outlier: 3.665A pdb=" N ASPLU 31 " --> pdb=" O GLNLU 27 " (cutoff:3.500A) Processing helix chain 'LU' and resid 35 through 47 removed outlier: 3.566A pdb=" N PHELU 39 " --> pdb=" O ASPLU 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLULU 45 " --> pdb=" O LYSLU 41 " (cutoff:3.500A) Processing helix chain 'LU' and resid 79 through 95 removed outlier: 3.586A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) Processing helix chain 'LV' and resid 68 through 73 removed outlier: 3.713A pdb=" N ARGLV 72 " --> pdb=" O LYSLV 68 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 68 through 73' Processing helix chain 'LV' and resid 121 through 128 removed outlier: 3.557A pdb=" N ALALV 125 " --> pdb=" O GLYLV 121 " (cutoff:3.500A) Processing helix chain 'LV' and resid 129 through 135 Processing helix chain 'LW' and resid 33 through 43 removed outlier: 3.981A pdb=" N GLULW 37 " --> pdb=" O ASNLW 33 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARGLW 43 " --> pdb=" O LEULW 39 " (cutoff:3.500A) Processing helix chain 'LW' and resid 45 through 50 removed outlier: 3.743A pdb=" N ILELW 49 " --> pdb=" O ASNLW 45 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALALW 50 " --> pdb=" O PROLW 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'LW' and resid 45 through 50' Processing helix chain 'LW' and resid 52 through 60 Processing helix chain 'LW' and resid 68 through 75 removed outlier: 3.919A pdb=" N THRLW 72 " --> pdb=" O ALALW 68 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARGLW 73 " --> pdb=" O LYSLW 69 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARGLW 74 " --> pdb=" O LYSLW 70 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THRLW 75 " --> pdb=" O ARGLW 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'LW' and resid 68 through 75' Processing helix chain 'LW' and resid 86 through 96 removed outlier: 3.501A pdb=" N ILELW 90 " --> pdb=" O SERLW 86 " (cutoff:3.500A) Processing helix chain 'LW' and resid 97 through 133 removed outlier: 3.596A pdb=" N ARGLW 101 " --> pdb=" O ARGLW 97 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALALW 128 " --> pdb=" O LYSLW 124 " (cutoff:3.500A) Processing helix chain 'LX' and resid 71 through 77 removed outlier: 3.560A pdb=" N ILELX 76 " --> pdb=" O GLULX 72 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 3.803A pdb=" N LYSLX 87 " --> pdb=" O GLULX 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYSLX 88 " --> pdb=" O GLYLX 84 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILELX 89 " --> pdb=" O ALALX 85 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLULX 90 " --> pdb=" O LEULX 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLULX 91 " --> pdb=" O LYSLX 87 " (cutoff:3.500A) Processing helix chain 'LX' and resid 104 through 116 Processing helix chain 'LX' and resid 144 through 153 removed outlier: 4.041A pdb=" N ILELX 148 " --> pdb=" O ASPLX 144 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEULX 153 " --> pdb=" O ALALX 149 " (cutoff:3.500A) Processing helix chain 'LY' and resid 10 through 21 removed outlier: 3.642A pdb=" N ALALY 21 " --> pdb=" O ALALY 17 " (cutoff:3.500A) Processing helix chain 'LY' and resid 22 through 31 removed outlier: 4.030A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 4.470A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'LY' and resid 99 through 104' Processing helix chain 'LY' and resid 111 through 134 removed outlier: 3.746A pdb=" N ALALY 129 " --> pdb=" O ARGLY 125 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYSLY 134 " --> pdb=" O LYSLY 130 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 57 through 66 removed outlier: 3.579A pdb=" N GLULZ 62 " --> pdb=" O LYSLZ 58 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.732A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N METLZ 80 " --> pdb=" O TYRLZ 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 75 through 80' Processing helix chain 'LZ' and resid 97 through 103 removed outlier: 5.670A pdb=" N LYSLZ 101 " --> pdb=" O ALALZ 97 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLULZ 102 " --> pdb=" O ASPLZ 98 " (cutoff:3.500A) Proline residue: LZ 103 - end of helix No H-bonds generated for 'chain 'LZ' and resid 97 through 103' Processing helix chain 'LZ' and resid 104 through 124 removed outlier: 3.626A pdb=" N LYSLZ 111 " --> pdb=" O GLULZ 107 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRLZ 112 " --> pdb=" O GLULZ 108 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLYLZ 124 " --> pdb=" O ARGLZ 120 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 126 through 132 removed outlier: 3.754A pdb=" N PHELZ 130 " --> pdb=" O ASNLZ 126 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THRLZ 131 " --> pdb=" O ARGLZ 127 " (cutoff:3.500A) Proline residue: LZ 132 - end of helix No H-bonds generated for 'chain 'LZ' and resid 126 through 132' Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.978A pdb=" N LYSLa 10 " --> pdb=" O SERLa 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HISLa 11 " --> pdb=" O LYSLa 7 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARGLa 12 " --> pdb=" O THRLa 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 6 through 12' Processing helix chain 'La' and resid 41 through 49 removed outlier: 4.725A pdb=" N HISLa 49 " --> pdb=" O LEULa 45 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.550A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRPLa 69 " --> pdb=" O ARGLa 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 64 through 69' Processing helix chain 'La' and resid 74 through 82 removed outlier: 4.057A pdb=" N LEULa 78 " --> pdb=" O ASNLa 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VALLa 82 " --> pdb=" O LEULa 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 74 through 82' Processing helix chain 'La' and resid 83 through 93 removed outlier: 3.875A pdb=" N GLNLa 89 " --> pdb=" O ASPLa 85 " (cutoff:3.500A) Processing helix chain 'La' and resid 103 through 108 removed outlier: 3.758A pdb=" N HISLa 107 " --> pdb=" O ASPLa 103 " (cutoff:3.500A) Processing helix chain 'La' and resid 131 through 142 removed outlier: 3.629A pdb=" N ARGLa 136 " --> pdb=" O ALALa 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALALa 141 " --> pdb=" O LYSLa 137 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLYLa 142 " --> pdb=" O VALLa 138 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 11 through 20 removed outlier: 4.809A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLYLb 20 " --> pdb=" O ALALb 16 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 58 removed outlier: 3.597A pdb=" N ASNLb 42 " --> pdb=" O LYSLb 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HISLb 45 " --> pdb=" O ARGLb 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSLb 52 " --> pdb=" O HISLb 48 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYSLb 58 " --> pdb=" O LEULb 54 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 10 through 24 removed outlier: 4.629A pdb=" N GLYLc 14 " --> pdb=" O ALALc 10 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALALc 15 " --> pdb=" O GLNLc 11 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSLc 22 " --> pdb=" O ALALc 18 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 29 through 40 removed outlier: 3.733A pdb=" N THRLc 33 " --> pdb=" O GLYLc 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SERLc 39 " --> pdb=" O LYSLc 35 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 52 through 67 Processing helix chain 'Lc' and resid 76 through 85 removed outlier: 3.671A pdb=" N CYSLc 84 " --> pdb=" O LEULc 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLYLc 85 " --> pdb=" O GLYLc 81 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 23 through 29 removed outlier: 4.378A pdb=" N ARGLd 27 " --> pdb=" O HISLd 23 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HISLd 29 " --> pdb=" O HISLd 25 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 32 through 53 removed outlier: 5.281A pdb=" N ALALd 37 " --> pdb=" O PHELd 33 " (cutoff:3.500A) Proline residue: Ld 38 - end of helix removed outlier: 3.536A pdb=" N ILELd 41 " --> pdb=" O ALALd 37 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYSLd 42 " --> pdb=" O PROLd 38 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.044A pdb=" N PHELe 26 " --> pdb=" O GLNLe 22 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'Le' and resid 22 through 27' Processing helix chain 'Le' and resid 41 through 46 removed outlier: 3.509A pdb=" N ARGLe 46 " --> pdb=" O ARGLe 42 " (cutoff:3.500A) Processing helix chain 'Le' and resid 79 through 88 removed outlier: 3.710A pdb=" N VALLe 83 " --> pdb=" O ASNLe 79 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLULe 84 " --> pdb=" O VALLe 80 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'Le' and resid 79 through 88' Processing helix chain 'Le' and resid 102 through 117 removed outlier: 3.569A pdb=" N GLNLe 115 " --> pdb=" O THRLe 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEULe 116 " --> pdb=" O ARGLe 112 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 3.503A pdb=" N ASNLf 44 " --> pdb=" O THRLf 40 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 66 removed outlier: 4.054A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lg' and resid 59 through 66' Processing helix chain 'Lg' and resid 67 through 72 removed outlier: 3.807A pdb=" N LYSLg 71 " --> pdb=" O SERLg 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THRLg 72 " --> pdb=" O LYSLg 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lg' and resid 67 through 72' Processing helix chain 'Lg' and resid 82 through 109 removed outlier: 6.375A pdb=" N VALLg 86 " --> pdb=" O CYSLg 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLULg 97 " --> pdb=" O ALALg 93 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 8 through 13 removed outlier: 3.927A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TRPLh 13 " --> pdb=" O ALALh 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 8 through 13' Processing helix chain 'Lh' and resid 16 through 39 removed outlier: 3.539A pdb=" N THRLh 29 " --> pdb=" O GLYLh 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLULh 30 " --> pdb=" O GLULh 26 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEULh 31 " --> pdb=" O LEULh 27 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SERLh 32 " --> pdb=" O LYSLh 28 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLNLh 37 " --> pdb=" O GLNLh 33 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILELh 39 " --> pdb=" O ARGLh 35 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 43 through 76 removed outlier: 4.579A pdb=" N ASNLh 47 " --> pdb=" O GLYLh 43 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYSLh 48 " --> pdb=" O ALALh 44 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILELh 49 " --> pdb=" O LYSLh 45 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HISLh 50 " --> pdb=" O LEULh 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYSLh 54 " --> pdb=" O HISLh 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYSLh 76 " --> pdb=" O ARGLh 72 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 removed outlier: 3.920A pdb=" N ARGLh 95 " --> pdb=" O ARGLh 91 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARGLh 96 " --> pdb=" O ALALh 92 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 98 through 104 removed outlier: 3.537A pdb=" N ARGLh 104 " --> pdb=" O GLULh 100 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 106 through 116 removed outlier: 3.587A pdb=" N ARGLh 112 " --> pdb=" O LYSLh 108 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HISLh 115 " --> pdb=" O LYSLh 111 " (cutoff:3.500A) Processing helix chain 'Li' and resid 34 through 39 removed outlier: 4.639A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYSLi 39 " --> pdb=" O PROLi 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'Li' and resid 34 through 39' Processing helix chain 'Li' and resid 43 through 58 removed outlier: 3.672A pdb=" N VALLi 49 " --> pdb=" O ARGLi 45 " (cutoff:3.500A) Processing helix chain 'Li' and resid 60 through 73 removed outlier: 3.667A pdb=" N ARGLi 71 " --> pdb=" O ILELi 67 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASNLi 72 " --> pdb=" O GLULi 68 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLYLi 73 " --> pdb=" O LEULi 69 " (cutoff:3.500A) Processing helix chain 'Li' and resid 74 through 87 removed outlier: 4.202A pdb=" N ALALi 78 " --> pdb=" O LYSLi 74 " (cutoff:3.500A) Processing helix chain 'Li' and resid 88 through 109 removed outlier: 3.571A pdb=" N ILELi 102 " --> pdb=" O GLULi 98 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILELi 103 " --> pdb=" O LEULi 99 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 4 through 11 removed outlier: 3.784A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.793A pdb=" N LYSLj 54 " --> pdb=" O SERLj 50 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.322A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VALLj 70 " --> pdb=" O TYRLj 66 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix removed outlier: 3.801A pdb=" N ASNLj 76 " --> pdb=" O ARGLj 72 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 17 removed outlier: 4.024A pdb=" N PHELk 11 " --> pdb=" O ASPLk 7 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILELk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARGLk 17 " --> pdb=" O GLULk 13 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 51 through 62 removed outlier: 4.745A pdb=" N ALALk 55 " --> pdb=" O ASPLk 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLULk 56 " --> pdb=" O SERLk 52 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYSLk 57 " --> pdb=" O ASPLk 53 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEULk 62 " --> pdb=" O LEULk 58 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 3.533A pdb=" N ALALl 14 " --> pdb=" O LYSLl 10 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYSLl 15 " --> pdb=" O GLNLl 11 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASNLl 20 " --> pdb=" O ALALl 16 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.762A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARGLl 30 " --> pdb=" O TRPLl 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ll' and resid 24 through 30' Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 4.126A pdb=" N PHELm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASNLm 90 " --> pdb=" O ALALm 86 " (cutoff:3.500A) Processing helix chain 'Ln' and resid 2 through 24 removed outlier: 4.020A pdb=" N SERLn 24 " --> pdb=" O VALLn 20 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 2 through 24 removed outlier: 3.511A pdb=" N ARGLr 9 " --> pdb=" O TRPLr 5 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 37 through 49 removed outlier: 3.543A pdb=" N SERLo 48 " --> pdb=" O ASPLo 44 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLYLo 49 " --> pdb=" O ARGLo 45 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.513A pdb=" N GLNLp 29 " --> pdb=" O LEULp 25 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THRLp 32 " --> pdb=" O LYSLp 28 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLNLp 33 " --> pdb=" O GLNLp 29 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALALp 35 " --> pdb=" O VALLp 31 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 92 removed outlier: 3.717A pdb=" N SERLp 81 " --> pdb=" O ALALp 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILELp 89 " --> pdb=" O ARGLp 85 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 5 through 14 Processing helix chain 'Lq' and resid 44 through 49 removed outlier: 3.625A pdb=" N ASNLq 48 " --> pdb=" O ALALq 44 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lq' and resid 44 through 49' Processing helix chain 'Lq' and resid 86 through 102 removed outlier: 5.885A pdb=" N HISLq 101 " --> pdb=" O GLNLq 97 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLYLq 102 " --> pdb=" O ALALq 98 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 104 through 123 removed outlier: 4.097A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLNLq 122 " --> pdb=" O ILELq 118 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARGLq 123 " --> pdb=" O LEULq 119 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 134 through 141 removed outlier: 5.525A pdb=" N ALALq 138 " --> pdb=" O ARGLq 134 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARGLq 139 " --> pdb=" O GLYLq 135 " (cutoff:3.500A) Processing helix chain 'Ls' and resid 5 through 23 removed outlier: 3.512A pdb=" N ALALs 9 " --> pdb=" O SERLs 5 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLYLs 10 " --> pdb=" O GLYLs 6 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHELs 12 " --> pdb=" O LYSLs 8 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASPLs 13 " --> pdb=" O ALALs 9 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLULs 20 " --> pdb=" O LYSLs 16 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLULs 21 " --> pdb=" O GLYLs 17 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYRLs 22 " --> pdb=" O LEULs 18 " (cutoff:3.500A) Proline residue: Ls 23 - end of helix Processing helix chain 'Ls' and resid 34 through 46 removed outlier: 3.600A pdb=" N METLs 38 " --> pdb=" O SERLs 34 " (cutoff:3.500A) Processing helix chain 'Ls' and resid 57 through 67 removed outlier: 3.845A pdb=" N ARGLs 61 " --> pdb=" O THRLs 57 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALALs 62 " --> pdb=" O METLs 58 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYSLs 64 " --> pdb=" O ARGLs 60 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N METLs 67 " --> pdb=" O LEULs 63 " (cutoff:3.500A) Processing helix chain 'Ls' and resid 70 through 78 removed outlier: 4.574A pdb=" N GLULs 74 " --> pdb=" O HISLs 70 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARGLs 75 " --> pdb=" O PROLs 71 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEULs 76 " --> pdb=" O GLULs 72 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEULs 77 " --> pdb=" O TYRLs 73 " (cutoff:3.500A) Proline residue: Ls 78 - end of helix No H-bonds generated for 'chain 'Ls' and resid 70 through 78' Processing helix chain 'Ls' and resid 92 through 100 removed outlier: 4.379A pdb=" N GLULs 98 " --> pdb=" O LYSLs 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYSLs 99 " --> pdb=" O GLULs 95 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILELs 100 " --> pdb=" O VALLs 96 " (cutoff:3.500A) Processing helix chain 'Ls' and resid 132 through 140 removed outlier: 3.831A pdb=" N PHELs 136 " --> pdb=" O LYSLs 132 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEULs 139 " --> pdb=" O PHELs 135 " (cutoff:3.500A) Processing helix chain 'Ls' and resid 166 through 177 removed outlier: 3.744A pdb=" N ASNLs 174 " --> pdb=" O ALALs 170 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N METLs 175 " --> pdb=" O THRLs 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEULs 176 " --> pdb=" O LEULs 172 " (cutoff:3.500A) Processing helix chain 'SA' and resid 13 through 24 removed outlier: 3.660A pdb=" N ALASA 22 " --> pdb=" O GLUSA 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLNSA 24 " --> pdb=" O LEUSA 20 " (cutoff:3.500A) Processing helix chain 'SA' and resid 33 through 38 removed outlier: 3.715A pdb=" N GLNSA 37 " --> pdb=" O ASNSA 33 " (cutoff:3.500A) Proline residue: SA 38 - end of helix No H-bonds generated for 'chain 'SA' and resid 33 through 38' Processing helix chain 'SA' and resid 52 through 70 removed outlier: 3.784A pdb=" N ALASA 69 " --> pdb=" O ARGSA 65 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILESA 70 " --> pdb=" O ILESA 66 " (cutoff:3.500A) Processing helix chain 'SA' and resid 82 through 96 removed outlier: 3.752A pdb=" N GLNSA 86 " --> pdb=" O ARGSA 82 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARGSA 87 " --> pdb=" O PROSA 83 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALASA 88 " --> pdb=" O PHESA 84 " (cutoff:3.500A) Processing helix chain 'SA' and resid 128 through 133 Processing helix chain 'SA' and resid 134 through 143 removed outlier: 4.194A pdb=" N TYRSA 141 " --> pdb=" O LYSSA 137 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VALSA 142 " --> pdb=" O GLUSA 138 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASNSA 143 " --> pdb=" O ALASA 139 " (cutoff:3.500A) Processing helix chain 'SA' and resid 169 through 189 removed outlier: 4.018A pdb=" N GLYSA 174 " --> pdb=" O ARGSA 170 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLYSA 189 " --> pdb=" O LEUSA 185 " (cutoff:3.500A) Processing helix chain 'SA' and resid 201 through 207 removed outlier: 4.529A pdb=" N TYRSA 205 " --> pdb=" O METSA 201 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHESA 206 " --> pdb=" O PROSA 202 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TYRSA 207 " --> pdb=" O ASPSA 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 201 through 207' Processing helix chain 'SB' and resid 56 through 63 removed outlier: 4.167A pdb=" N ALASB 60 " --> pdb=" O ASNSB 56 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEUSB 61 " --> pdb=" O ALASB 57 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYSSB 62 " --> pdb=" O ASNSB 58 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLYSB 63 " --> pdb=" O ASPSB 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 56 through 63' Processing helix chain 'SB' and resid 69 through 75 Processing helix chain 'SB' and resid 76 through 81 removed outlier: 4.871A pdb=" N ALASB 80 " --> pdb=" O ASPSB 76 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHESB 81 " --> pdb=" O GLUSB 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 76 through 81' Processing helix chain 'SB' and resid 106 through 115 removed outlier: 3.593A pdb=" N LEUSB 110 " --> pdb=" O THRSB 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VALSB 114 " --> pdb=" O LEUSB 110 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARGSB 115 " --> pdb=" O ARGSB 111 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 177 Processing helix chain 'SB' and resid 180 through 191 removed outlier: 3.506A pdb=" N LYSSB 187 " --> pdb=" O GLNSB 183 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILESB 189 " --> pdb=" O VALSB 185 " (cutoff:3.500A) Proline residue: SB 190 - end of helix Processing helix chain 'SB' and resid 192 through 202 Processing helix chain 'SB' and resid 224 through 233 removed outlier: 3.639A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEUSB 231 " --> pdb=" O ALASB 227 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLYSB 233 " --> pdb=" O METSB 229 " (cutoff:3.500A) Processing helix chain 'SC' and resid 47 through 56 Processing helix chain 'SC' and resid 60 through 68 removed outlier: 4.022A pdb=" N ILESC 64 " --> pdb=" O SERSC 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HISSC 67 " --> pdb=" O GLUSC 63 " (cutoff:3.500A) Processing helix chain 'SC' and resid 73 through 81 removed outlier: 4.311A pdb=" N VALSC 77 " --> pdb=" O GLUSC 73 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASPSC 78 " --> pdb=" O TYRSC 74 " (cutoff:3.500A) Processing helix chain 'SC' and resid 128 through 144 removed outlier: 3.542A pdb=" N ILESC 138 " --> pdb=" O ARGSC 134 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SERSC 143 " --> pdb=" O ILESC 139 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VALSC 144 " --> pdb=" O ALASC 140 " (cutoff:3.500A) Processing helix chain 'SC' and resid 189 through 200 removed outlier: 3.543A pdb=" N ARGSC 194 " --> pdb=" O PROSC 190 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEUSC 195 " --> pdb=" O ALASC 191 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLYSC 200 " --> pdb=" O LEUSC 196 " (cutoff:3.500A) Processing helix chain 'SC' and resid 214 through 230 removed outlier: 3.959A pdb=" N THRSC 229 " --> pdb=" O ALASC 225 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYRSC 230 " --> pdb=" O VALSC 226 " (cutoff:3.500A) Processing helix chain 'SC' and resid 234 through 239 removed outlier: 3.992A pdb=" N TRPSC 238 " --> pdb=" O THRSC 234 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYSSC 239 " --> pdb=" O PROSC 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 234 through 239' Processing helix chain 'SC' and resid 246 through 251 Processing helix chain 'SD' and resid 9 through 32 removed outlier: 3.505A pdb=" N VALSD 15 " --> pdb=" O LYSSD 11 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLYSD 18 " --> pdb=" O PHESD 14 " (cutoff:3.500A) Processing helix chain 'SD' and resid 57 through 63 removed outlier: 4.936A pdb=" N GLYSD 63 " --> pdb=" O GLNSD 59 " (cutoff:3.500A) Processing helix chain 'SD' and resid 67 through 81 removed outlier: 6.272A pdb=" N GLUSD 71 " --> pdb=" O ARGSD 67 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEUSD 72 " --> pdb=" O ARGSD 68 " (cutoff:3.500A) Processing helix chain 'SD' and resid 100 through 115 removed outlier: 5.094A pdb=" N GLYSD 115 " --> pdb=" O LYSSD 111 " (cutoff:3.500A) Processing helix chain 'SD' and resid 117 through 133 removed outlier: 3.627A pdb=" N SERSD 132 " --> pdb=" O PHESD 128 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLYSD 133 " --> pdb=" O ILESD 129 " (cutoff:3.500A) Processing helix chain 'SD' and resid 164 through 170 removed outlier: 3.869A pdb=" N ARGSD 168 " --> pdb=" O GLYSD 164 " (cutoff:3.500A) Processing helix chain 'SE' and resid 43 through 49 Processing helix chain 'SE' and resid 57 through 68 removed outlier: 3.674A pdb=" N LYSSE 62 " --> pdb=" O TYRSE 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALASE 63 " --> pdb=" O ARGSE 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N METSE 65 " --> pdb=" O THRSE 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLNSE 67 " --> pdb=" O ALASE 63 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARGSE 68 " --> pdb=" O ILESE 64 " (cutoff:3.500A) Processing helix chain 'SE' and resid 115 through 120 removed outlier: 4.150A pdb=" N LYSSE 120 " --> pdb=" O ASPSE 116 " (cutoff:3.500A) Processing helix chain 'SE' and resid 221 through 226 removed outlier: 3.879A pdb=" N VALSE 225 " --> pdb=" O ARGSE 221 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHESE 226 " --> pdb=" O GLUSE 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'SE' and resid 221 through 226' Processing helix chain 'SE' and resid 246 through 262 removed outlier: 3.581A pdb=" N ARGSE 251 " --> pdb=" O ILESE 247 " (cutoff:3.500A) Processing helix chain 'SF' and resid 17 through 27 removed outlier: 3.507A pdb=" N LEUSF 21 " --> pdb=" O PROSF 17 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALASF 22 " --> pdb=" O LYSSF 18 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLUSF 23 " --> pdb=" O GLUSF 19 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLYSF 25 " --> pdb=" O LEUSF 21 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SERSF 26 " --> pdb=" O ALASF 22 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VALSF 27 " --> pdb=" O GLUSF 23 " (cutoff:3.500A) Processing helix chain 'SF' and resid 45 through 50 removed outlier: 3.785A pdb=" N ILESF 49 " --> pdb=" O LEUSF 45 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLNSF 50 " --> pdb=" O THRSF 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 45 through 50' Processing helix chain 'SF' and resid 69 through 74 removed outlier: 4.125A pdb=" N ASNSF 73 " --> pdb=" O PHESF 69 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYSSF 74 " --> pdb=" O ARGSF 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 69 through 74' Processing helix chain 'SF' and resid 75 through 85 removed outlier: 4.114A pdb=" N METSF 85 " --> pdb=" O THRSF 81 " (cutoff:3.500A) Processing helix chain 'SF' and resid 93 through 112 removed outlier: 3.533A pdb=" N ALASF 97 " --> pdb=" O LYSSF 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HISSF 109 " --> pdb=" O PHESF 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEUSF 110 " --> pdb=" O GLUSF 106 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N METSF 111 " --> pdb=" O ILESF 107 " (cutoff:3.500A) Processing helix chain 'SF' and resid 115 through 128 removed outlier: 3.621A pdb=" N ASPSF 122 " --> pdb=" O GLNSF 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLYSF 128 " --> pdb=" O ILESF 124 " (cutoff:3.500A) Processing helix chain 'SF' and resid 150 through 171 removed outlier: 3.515A pdb=" N ALASF 160 " --> pdb=" O ASNSF 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHESF 171 " --> pdb=" O ARGSF 167 " (cutoff:3.500A) Processing helix chain 'SF' and resid 176 through 191 removed outlier: 3.744A pdb=" N ALASF 182 " --> pdb=" O ALASF 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLUSF 184 " --> pdb=" O CYSSF 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILESF 186 " --> pdb=" O ALASF 182 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYSSF 190 " --> pdb=" O ILESF 186 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLYSF 191 " --> pdb=" O ASNSF 187 " (cutoff:3.500A) Processing helix chain 'SF' and resid 195 through 212 removed outlier: 3.514A pdb=" N ARGSF 212 " --> pdb=" O ALASF 208 " (cutoff:3.500A) Processing helix chain 'SG' and resid 20 through 26 removed outlier: 4.009A pdb=" N LEUSG 24 " --> pdb=" O ASPSG 20 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N HISSG 26 " --> pdb=" O ARGSG 22 " (cutoff:3.500A) Processing helix chain 'SG' and resid 38 through 43 removed outlier: 4.218A pdb=" N GLYSG 42 " --> pdb=" O GLYSG 38 " (cutoff:3.500A) Proline residue: SG 43 - end of helix No H-bonds generated for 'chain 'SG' and resid 38 through 43' Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 152 through 157 removed outlier: 4.243A pdb=" N TYRSG 156 " --> pdb=" O ASPSG 152 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VALSG 157 " --> pdb=" O VALSG 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'SG' and resid 152 through 157' Processing helix chain 'SG' and resid 183 through 231 removed outlier: 3.936A pdb=" N ASPSG 228 " --> pdb=" O ALASG 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEUSG 229 " --> pdb=" O GLNSG 225 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYSSG 231 " --> pdb=" O ALASG 227 " (cutoff:3.500A) Processing helix chain 'SH' and resid 20 through 37 removed outlier: 3.558A pdb=" N ALASH 25 " --> pdb=" O ASPSH 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEUSH 33 " --> pdb=" O ALASH 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THRSH 35 " --> pdb=" O TYRSH 31 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THRSH 37 " --> pdb=" O LEUSH 33 " (cutoff:3.500A) Processing helix chain 'SH' and resid 38 through 45 removed outlier: 5.659A pdb=" N ALASH 42 " --> pdb=" O ALASH 38 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALASH 43 " --> pdb=" O ASPSH 39 " (cutoff:3.500A) Processing helix chain 'SH' and resid 69 through 80 removed outlier: 4.795A pdb=" N GLNSH 74 " --> pdb=" O VALSH 70 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLYSH 75 " --> pdb=" O PROSH 71 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VALSH 79 " --> pdb=" O GLYSH 75 " (cutoff:3.500A) Processing helix chain 'SH' and resid 81 through 92 removed outlier: 3.745A pdb=" N ARGSH 85 " --> pdb=" O GLNSH 81 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLUSH 86 " --> pdb=" O ARGSH 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUSH 87 " --> pdb=" O LEUSH 83 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLUSH 88 " --> pdb=" O THRSH 84 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHESH 91 " --> pdb=" O LEUSH 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SERSH 92 " --> pdb=" O GLUSH 88 " (cutoff:3.500A) Processing helix chain 'SH' and resid 127 through 141 removed outlier: 3.513A pdb=" N ASPSH 133 " --> pdb=" O THRSH 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VALSH 140 " --> pdb=" O LEUSH 136 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYRSH 141 " --> pdb=" O THRSH 137 " (cutoff:3.500A) Processing helix chain 'SH' and resid 168 through 173 removed outlier: 3.993A pdb=" N VALSH 172 " --> pdb=" O GLUSH 168 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASPSH 173 " --> pdb=" O ARGSH 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'SH' and resid 168 through 173' Processing helix chain 'SH' and resid 174 through 187 removed outlier: 4.519A pdb=" N THRSH 178 " --> pdb=" O TYRSH 174 " (cutoff:3.500A) Processing helix chain 'SH' and resid 4 through 10 removed outlier: 4.261A pdb=" N ASNSH 7 " --> pdb=" O PROSH 4 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYSSH 8 " --> pdb=" O SERSH 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILESH 9 " --> pdb=" O LEUSH 6 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALASH 10 " --> pdb=" O ASNSH 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'SH' and resid 4 through 10' Processing helix chain 'SI' and resid 87 through 94 removed outlier: 4.074A pdb=" N VALSI 91 " --> pdb=" O ASNSI 87 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASNSI 94 " --> pdb=" O LEUSI 90 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 139 through 154 removed outlier: 5.437A pdb=" N GLUSI 143 " --> pdb=" O SERSI 139 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYSSI 144 " --> pdb=" O LYSSI 140 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLYSI 154 " --> pdb=" O PHESI 150 " (cutoff:3.500A) Processing helix chain 'SI' and resid 157 through 167 removed outlier: 4.097A pdb=" N GLNSI 163 " --> pdb=" O ALASI 159 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHESI 164 " --> pdb=" O LEUSI 160 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLUSI 165 " --> pdb=" O GLUSI 161 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALASI 166 " --> pdb=" O LYSSI 162 " (cutoff:3.500A) Processing helix chain 'SI' and resid 190 through 202 removed outlier: 3.528A pdb=" N TYRSI 196 " --> pdb=" O GLUSI 192 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HISSI 201 " --> pdb=" O GLNSI 197 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYSSI 202 " --> pdb=" O ARGSI 198 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 18 through 33 removed outlier: 3.562A pdb=" N ASPSJ 23 " --> pdb=" O ALASJ 19 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SERSJ 24 " --> pdb=" O ALASJ 20 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 36 through 61 removed outlier: 4.194A pdb=" N VALSJ 40 " --> pdb=" O ASNSJ 36 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILESJ 50 " --> pdb=" O THRSJ 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THRSJ 59 " --> pdb=" O ARGSJ 55 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEUSJ 60 " --> pdb=" O ILESJ 56 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASPSJ 61 " --> pdb=" O LEUSJ 57 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 64 through 82 Processing helix chain 'SJ' and resid 90 through 97 removed outlier: 3.728A pdb=" N VALSJ 94 " --> pdb=" O LYSSJ 90 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEUSJ 95 " --> pdb=" O LEUSJ 91 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALASJ 96 " --> pdb=" O ASPSJ 92 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEUSJ 97 " --> pdb=" O TYRSJ 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 90 through 97' Processing helix chain 'SJ' and resid 98 through 106 removed outlier: 4.013A pdb=" N PHESJ 102 " --> pdb=" O LYSSJ 98 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARGSJ 105 " --> pdb=" O ASPSJ 101 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARGSJ 106 " --> pdb=" O PHESJ 102 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 107 through 115 removed outlier: 3.596A pdb=" N TYRSJ 112 " --> pdb=" O GLNSJ 108 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLYSJ 115 " --> pdb=" O VALSJ 111 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 119 through 130 removed outlier: 3.692A pdb=" N ARGSJ 124 " --> pdb=" O ILESJ 120 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VALSJ 125 " --> pdb=" O HISSJ 121 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARGSJ 130 " --> pdb=" O LEUSJ 126 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 168 through 180 removed outlier: 3.553A pdb=" N LYSSJ 173 " --> pdb=" O ARGSJ 169 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 148 through 153 removed outlier: 4.427A pdb=" N LYSSJ 152 " --> pdb=" O ASPSJ 149 " (cutoff:3.500A) Processing helix chain 'SK' and resid 4 through 19 removed outlier: 4.555A pdb=" N ARGSK 8 " --> pdb=" O PROSK 4 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYSSK 9 " --> pdb=" O LYSSK 5 " (cutoff:3.500A) Processing helix chain 'SK' and resid 36 through 51 removed outlier: 3.848A pdb=" N LYSSK 42 " --> pdb=" O LEUSK 38 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARGSK 50 " --> pdb=" O SERSK 46 " (cutoff:3.500A) Processing helix chain 'SK' and resid 67 through 79 removed outlier: 3.983A pdb=" N HISSK 79 " --> pdb=" O ARGSK 75 " (cutoff:3.500A) Processing helix chain 'SK' and resid 85 through 90 removed outlier: 3.799A pdb=" N HISSK 89 " --> pdb=" O VALSK 85 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILESK 90 " --> pdb=" O PROSK 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'SK' and resid 85 through 90' Processing helix chain 'SL' and resid 31 through 36 removed outlier: 4.189A pdb=" N GLYSL 35 " --> pdb=" O ARGSL 31 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLYSL 36 " --> pdb=" O PROSL 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 31 through 36' Processing helix chain 'SL' and resid 50 through 56 removed outlier: 3.842A pdb=" N ILESL 54 " --> pdb=" O PROSL 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 29 through 41 removed outlier: 3.721A pdb=" N LEUSM 34 " --> pdb=" O LEUSM 30 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEUSM 36 " --> pdb=" O GLYSM 32 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SERSM 37 " --> pdb=" O VALSM 33 " (cutoff:3.500A) Processing helix chain 'SM' and resid 46 through 57 removed outlier: 3.746A pdb=" N LYSSM 52 " --> pdb=" O ARGSM 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARGSM 57 " --> pdb=" O ALASM 53 " (cutoff:3.500A) Processing helix chain 'SM' and resid 70 through 85 removed outlier: 3.743A pdb=" N LEUSM 76 " --> pdb=" O ALASM 72 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VALSM 77 " --> pdb=" O TYRSM 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILESM 78 " --> pdb=" O LYSSM 74 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N HISSM 84 " --> pdb=" O LEUSM 80 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYSSM 85 " --> pdb=" O CYSSM 81 " (cutoff:3.500A) Processing helix chain 'SM' and resid 93 through 102 removed outlier: 4.115A pdb=" N GLYSM 98 " --> pdb=" O GLYSM 94 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLUSM 99 " --> pdb=" O LYSSM 95 " (cutoff:3.500A) Processing helix chain 'SM' and resid 130 through 142 Processing helix chain 'SN' and resid 29 through 44 removed outlier: 3.644A pdb=" N LEUSN 40 " --> pdb=" O GLNSN 36 " (cutoff:3.500A) Processing helix chain 'SN' and resid 46 through 57 removed outlier: 3.655A pdb=" N GLYSN 51 " --> pdb=" O PROSN 47 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VALSN 52 " --> pdb=" O SERSN 48 " (cutoff:3.500A) Processing helix chain 'SN' and resid 62 through 68 removed outlier: 3.664A pdb=" N VALSN 66 " --> pdb=" O GLNSN 62 " (cutoff:3.500A) Processing helix chain 'SN' and resid 70 through 79 Processing helix chain 'SN' and resid 85 through 106 removed outlier: 3.966A pdb=" N ARGSN 104 " --> pdb=" O LYSSN 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARGSN 106 " --> pdb=" O LEUSN 102 " (cutoff:3.500A) Processing helix chain 'SN' and resid 108 through 133 removed outlier: 3.522A pdb=" N ARGSN 124 " --> pdb=" O SERSN 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYRSN 128 " --> pdb=" O ARGSN 124 " (cutoff:3.500A) Processing helix chain 'SN' and resid 145 through 151 removed outlier: 4.272A pdb=" N LEUSN 149 " --> pdb=" O THRSN 145 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VALSN 150 " --> pdb=" O ALASN 146 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALASN 151 " --> pdb=" O SERSN 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'SN' and resid 145 through 151' Processing helix chain 'SO' and resid 56 through 62 removed outlier: 4.435A pdb=" N LYSSO 60 " --> pdb=" O THRSO 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VALSO 61 " --> pdb=" O GLYSO 57 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYSSO 62 " --> pdb=" O GLYSO 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 56 through 62' Processing helix chain 'SO' and resid 63 through 68 removed outlier: 6.305A pdb=" N GLUSO 67 " --> pdb=" O ALASO 63 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N SERSO 68 " --> pdb=" O ASPSO 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 63 through 68' Processing helix chain 'SO' and resid 69 through 88 removed outlier: 3.616A pdb=" N ASPSO 79 " --> pdb=" O LEUSO 75 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VALSO 80 " --> pdb=" O ALASO 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALASO 81 " --> pdb=" O ALASO 77 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLUSO 86 " --> pdb=" O ALASO 82 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEUSO 87 " --> pdb=" O ARGSO 83 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLYSO 88 " --> pdb=" O CYSSO 84 " (cutoff:3.500A) Processing helix chain 'SO' and resid 108 through 122 removed outlier: 4.834A pdb=" N GLNSO 112 " --> pdb=" O GLYSO 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SERSO 113 " --> pdb=" O PROSO 109 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEUSO 115 " --> pdb=" O ALASO 111 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLYSO 122 " --> pdb=" O LEUSO 118 " (cutoff:3.500A) Processing helix chain 'SP' and resid 37 through 46 removed outlier: 3.550A pdb=" N LEUSP 45 " --> pdb=" O LEUSP 41 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HISSP 46 " --> pdb=" O ARGSP 42 " (cutoff:3.500A) Processing helix chain 'SP' and resid 47 through 56 removed outlier: 3.589A pdb=" N ARGSP 51 " --> pdb=" O ALASP 47 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLYSP 56 " --> pdb=" O LYSSP 52 " (cutoff:3.500A) Processing helix chain 'SP' and resid 58 through 75 removed outlier: 4.078A pdb=" N ILESP 65 " --> pdb=" O PROSP 61 " (cutoff:3.500A) Processing helix chain 'SP' and resid 123 through 129 removed outlier: 4.553A pdb=" N PHESP 127 " --> pdb=" O TYRSP 123 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SERSP 128 " --> pdb=" O LEUSP 124 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILESP 129 " --> pdb=" O GLYSP 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 123 through 129' Processing helix chain 'SP' and resid 30 through 35 removed outlier: 3.853A pdb=" N LEUSP 33 " --> pdb=" O LEUSP 30 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASPSP 35 " --> pdb=" O ALASP 32 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 35 through 40 removed outlier: 4.027A pdb=" N PHESQ 39 " --> pdb=" O PROSQ 35 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ALASQ 40 " --> pdb=" O LEUSQ 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'SQ' and resid 35 through 40' Processing helix chain 'SQ' and resid 41 through 56 removed outlier: 4.965A pdb=" N ALASQ 46 " --> pdb=" O GLUSQ 42 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYSSQ 47 " --> pdb=" O ILESQ 43 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEUSQ 48 " --> pdb=" O LEUSQ 44 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYRSQ 49 " --> pdb=" O ARGSQ 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLUSQ 50 " --> pdb=" O ALASQ 46 " (cutoff:3.500A) Proline residue: SQ 51 - end of helix removed outlier: 4.013A pdb=" N LEUSQ 55 " --> pdb=" O PROSQ 51 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 74 through 97 removed outlier: 3.624A pdb=" N ALASQ 86 " --> pdb=" O ARGSQ 82 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 98 through 113 removed outlier: 4.202A pdb=" N LYSSQ 102 " --> pdb=" O ASPSQ 98 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHESQ 112 " --> pdb=" O GLUSQ 108 " (cutoff:3.500A) Processing helix chain 'SR' and resid 6 through 20 removed outlier: 3.540A pdb=" N GLUSR 18 " --> pdb=" O LYSSR 14 " (cutoff:3.500A) Processing helix chain 'SR' and resid 27 through 39 removed outlier: 3.747A pdb=" N ARGSR 33 " --> pdb=" O GLUSR 29 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASPSR 36 " --> pdb=" O LYSSR 32 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUSR 37 " --> pdb=" O ARGSR 33 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILESR 38 " --> pdb=" O VALSR 34 " (cutoff:3.500A) Processing helix chain 'SR' and resid 43 through 64 removed outlier: 3.681A pdb=" N LYSSR 59 " --> pdb=" O THRSR 55 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARGSR 60 " --> pdb=" O HISSR 56 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARGSR 63 " --> pdb=" O LYSSR 59 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLYSR 64 " --> pdb=" O ARGSR 60 " (cutoff:3.500A) Processing helix chain 'SR' and resid 71 through 83 removed outlier: 3.711A pdb=" N GLUSR 79 " --> pdb=" O GLUSR 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGSR 80 " --> pdb=" O GLUSR 76 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLNSR 83 " --> pdb=" O GLUSR 79 " (cutoff:3.500A) Processing helix chain 'SR' and resid 92 through 97 removed outlier: 4.669A pdb=" N ASNSR 96 " --> pdb=" O ASPSR 92 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SERSR 97 " --> pdb=" O PHESR 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 92 through 97' Processing helix chain 'SR' and resid 105 through 116 removed outlier: 3.596A pdb=" N LYSSR 109 " --> pdb=" O ASPSR 105 " (cutoff:3.500A) Processing helix chain 'SS' and resid 27 through 35 removed outlier: 3.936A pdb=" N THRSS 33 " --> pdb=" O VALSS 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLNSS 34 " --> pdb=" O TYRSS 30 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILESS 35 " --> pdb=" O ALASS 31 " (cutoff:3.500A) Processing helix chain 'SS' and resid 39 through 51 removed outlier: 3.652A pdb=" N SERSS 43 " --> pdb=" O GLYSS 39 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASNSS 44 " --> pdb=" O ARGSS 40 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASPSS 51 " --> pdb=" O CYSSS 47 " (cutoff:3.500A) Processing helix chain 'SS' and resid 62 through 76 removed outlier: 3.998A pdb=" N LEUSS 66 " --> pdb=" O THRSS 62 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLUSS 67 " --> pdb=" O SERSS 63 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARGSS 68 " --> pdb=" O GLUSS 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILESS 72 " --> pdb=" O ARGSS 68 " (cutoff:3.500A) Proline residue: SS 76 - end of helix Processing helix chain 'SS' and resid 101 through 120 removed outlier: 3.716A pdb=" N ASPSS 106 " --> pdb=" O ALASS 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGSS 110 " --> pdb=" O ASPSS 106 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLUSS 111 " --> pdb=" O SERSS 107 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASPSS 112 " --> pdb=" O LYSSS 108 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEUSS 113 " --> pdb=" O LEUSS 109 " (cutoff:3.500A) Processing helix chain 'SS' and resid 121 through 130 Processing helix chain 'ST' and resid 6 through 11 removed outlier: 4.060A pdb=" N VALST 10 " --> pdb=" O THRST 6 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASPST 11 " --> pdb=" O VALST 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'ST' and resid 6 through 11' Processing helix chain 'ST' and resid 12 through 27 Processing helix chain 'ST' and resid 52 through 69 removed outlier: 3.764A pdb=" N ALAST 58 " --> pdb=" O TRPST 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEUST 67 " --> pdb=" O ARGST 63 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYSST 69 " --> pdb=" O VALST 65 " (cutoff:3.500A) Processing helix chain 'ST' and resid 72 through 81 removed outlier: 3.585A pdb=" N LYSST 78 " --> pdb=" O GLYST 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYST 81 " --> pdb=" O ARGST 77 " (cutoff:3.500A) Processing helix chain 'ST' and resid 97 through 112 removed outlier: 4.008A pdb=" N ASPST 101 " --> pdb=" O SERST 97 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N METST 105 " --> pdb=" O ASPST 101 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEUST 108 " --> pdb=" O ILEST 104 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYSST 110 " --> pdb=" O GLNST 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILEST 111 " --> pdb=" O ALAST 107 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLNST 112 " --> pdb=" O LEUST 108 " (cutoff:3.500A) Processing helix chain 'ST' and resid 126 through 144 removed outlier: 3.789A pdb=" N ARGST 131 " --> pdb=" O GLNST 127 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEUST 133 " --> pdb=" O GLYST 129 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEST 136 " --> pdb=" O ASPST 132 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALAST 137 " --> pdb=" O LEUST 133 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLNST 138 " --> pdb=" O ASPST 134 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THRST 139 " --> pdb=" O ARGST 135 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALST 140 " --> pdb=" O ILEST 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUST 142 " --> pdb=" O GLNST 138 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAST 143 " --> pdb=" O THRST 139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASPST 144 " --> pdb=" O VALST 140 " (cutoff:3.500A) Processing helix chain 'SU' and resid 27 through 46 removed outlier: 4.574A pdb=" N LEUSU 31 " --> pdb=" O LYSSU 27 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSSU 33 " --> pdb=" O GLNSU 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VALSU 34 " --> pdb=" O SERSU 30 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLUSU 40 " --> pdb=" O GLNSU 36 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYSSU 45 " --> pdb=" O ARGSU 41 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASPSU 46 " --> pdb=" O ALASU 42 " (cutoff:3.500A) Processing helix chain 'SU' and resid 93 through 102 removed outlier: 4.092A pdb=" N VALSU 97 " --> pdb=" O PROSU 93 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYSSU 98 " --> pdb=" O THRSU 94 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLNSU 99 " --> pdb=" O GLUSU 95 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILESU 100 " --> pdb=" O ILESU 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILESU 101 " --> pdb=" O VALSU 97 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILESU 102 " --> pdb=" O LYSSU 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 93 through 102' Processing helix chain 'SV' and resid 56 through 63 removed outlier: 3.528A pdb=" N METSV 62 " --> pdb=" O PHESV 58 " (cutoff:3.500A) Processing helix chain 'SV' and resid 64 through 77 Processing helix chain 'SW' and resid 5 through 21 Processing helix chain 'SW' and resid 31 through 45 removed outlier: 3.569A pdb=" N VALSW 40 " --> pdb=" O LYSSW 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HISSW 44 " --> pdb=" O VALSW 40 " (cutoff:3.500A) Processing helix chain 'SW' and resid 82 through 94 removed outlier: 3.726A pdb=" N LEUSW 86 " --> pdb=" O ARGSW 82 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLUSW 87 " --> pdb=" O LEUSW 83 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYSSW 88 " --> pdb=" O ALASW 84 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRPSW 89 " --> pdb=" O GLUSW 85 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VALSW 90 " --> pdb=" O LEUSW 86 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEUSW 94 " --> pdb=" O VALSW 90 " (cutoff:3.500A) Processing helix chain 'SW' and resid 112 through 120 removed outlier: 3.776A pdb=" N ARGSW 117 " --> pdb=" O HISSW 113 " (cutoff:3.500A) Processing helix chain 'SX' and resid 11 through 24 removed outlier: 4.340A pdb=" N TRPSX 24 " --> pdb=" O ARGSX 20 " (cutoff:3.500A) Processing helix chain 'SX' and resid 26 through 35 Processing helix chain 'SX' and resid 92 through 97 removed outlier: 4.080A pdb=" N VALSX 96 " --> pdb=" O CYSSX 92 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASPSX 97 " --> pdb=" O LEUSX 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'SX' and resid 92 through 97' Processing helix chain 'SX' and resid 131 through 138 removed outlier: 3.518A pdb=" N LEUSX 135 " --> pdb=" O GLYSX 131 " (cutoff:3.500A) Processing helix chain 'SX' and resid 36 through 41 removed outlier: 3.630A pdb=" N SERSX 41 " --> pdb=" O THRSX 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'SX' and resid 36 through 41' Processing helix chain 'SY' and resid 39 through 52 removed outlier: 4.139A pdb=" N LYSSY 52 " --> pdb=" O ALASY 48 " (cutoff:3.500A) Processing helix chain 'SY' and resid 81 through 89 removed outlier: 3.600A pdb=" N LYSSY 86 " --> pdb=" O PROSY 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYSSY 87 " --> pdb=" O GLUSY 83 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHESY 88 " --> pdb=" O ALASY 84 " (cutoff:3.500A) Processing helix chain 'SY' and resid 90 through 98 Processing helix chain 'SY' and resid 107 through 122 removed outlier: 3.810A pdb=" N LYSSY 119 " --> pdb=" O LYSSY 115 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THRSY 120 " --> pdb=" O ASNSY 116 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEUSY 121 " --> pdb=" O ARGSY 117 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARGSY 122 " --> pdb=" O LEUSY 118 " (cutoff:3.500A) Processing helix chain 'SY' and resid 129 through 135 removed outlier: 4.755A pdb=" N LYSSY 133 " --> pdb=" O GLYSY 129 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYSSY 134 " --> pdb=" O ALASY 130 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLUSY 135 " --> pdb=" O LYSSY 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'SY' and resid 129 through 135' Processing helix chain 'SZ' and resid 32 through 47 removed outlier: 4.458A pdb=" N LYSSZ 38 " --> pdb=" O ALASZ 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEUSZ 39 " --> pdb=" O THRSZ 35 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRSZ 40 " --> pdb=" O SERSZ 36 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLNSZ 44 " --> pdb=" O TYRSZ 40 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SERSZ 45 " --> pdb=" O LYSSZ 41 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYRSZ 46 " --> pdb=" O ASPSZ 42 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARGSZ 47 " --> pdb=" O VALSZ 43 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 50 through 58 Processing helix chain 'SZ' and resid 61 through 76 removed outlier: 3.703A pdb=" N LEUSZ 72 " --> pdb=" O CYSSZ 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLUSZ 73 " --> pdb=" O LEUSZ 69 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLUSZ 74 " --> pdb=" O LYSSZ 70 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYSSZ 75 " --> pdb=" O ASPSZ 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLYSZ 76 " --> pdb=" O LEUSZ 72 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 31 through 36 removed outlier: 5.915A pdb=" N ILESa 36 " --> pdb=" O LYSSa 32 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 46 through 57 removed outlier: 3.623A pdb=" N ILESa 50 " --> pdb=" O GLUSa 46 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ARGSa 51 " --> pdb=" O SERSa 47 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASPSa 52 " --> pdb=" O ALASa 48 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 74 through 82 removed outlier: 3.803A pdb=" N HISSa 80 " --> pdb=" O SERSa 76 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 88 through 93 removed outlier: 4.667A pdb=" N ARGSa 93 " --> pdb=" O ARGSa 89 " (cutoff:3.500A) Processing helix chain 'Sb' and resid 11 through 19 removed outlier: 4.104A pdb=" N ARGSb 17 " --> pdb=" O ALASb 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYSSb 18 " --> pdb=" O SERSb 14 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N HISSb 19 " --> pdb=" O GLUSb 15 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 39 through 47 removed outlier: 3.761A pdb=" N GLUSd 45 " --> pdb=" O GLNSd 41 " (cutoff:3.500A) Processing helix chain 'Se' and resid 12 through 18 Processing helix chain 'Se' and resid 32 through 44 removed outlier: 3.583A pdb=" N LYSSe 36 " --> pdb=" O GLYSe 32 " (cutoff:3.500A) Processing helix chain 'Sf' and resid 100 through 106 removed outlier: 4.420A pdb=" N LYSSf 104 " --> pdb=" O LEUSf 100 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYRSf 105 " --> pdb=" O ALASf 101 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYRSf 106 " --> pdb=" O VALSf 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'Sf' and resid 100 through 106' Processing sheet with id= 1, first strand: chain 'A' and resid 4 through 8 removed outlier: 5.584A pdb=" N GLN A 4 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 309 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN A 296 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N THR A 297 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 288 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 19 through 23 removed outlier: 6.256A pdb=" N ASN A 29 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 31 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 42 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR A 52 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 67 through 72 removed outlier: 5.983A pdb=" N TYR A 77 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.978A pdb=" N ARG A 99 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 120 through 123 removed outlier: 3.505A pdb=" N SER A 122 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 130 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 129 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 140 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 153 through 157 removed outlier: 5.416A pdb=" N CYS A 153 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL A 164 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR A 186 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 196 through 201 removed outlier: 3.746A pdb=" N THR A 197 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 210 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU A 206 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N SER A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 221 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 247 through 251 removed outlier: 6.893A pdb=" N ILE A 258 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 39 through 42 removed outlier: 4.266A pdb=" N LEU A 40 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 57 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 255 through 258 removed outlier: 4.275A pdb=" N ASP A 268 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.802A pdb=" N GLULA 47 " --> pdb=" O ARGLA 60 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LA' and resid 134 through 137 removed outlier: 6.764A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYSLA 145 " --> pdb=" O ASNLA 140 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLYLA 138 " --> pdb=" O ARGLA 147 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.325A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LB' and resid 40 through 43 removed outlier: 5.289A pdb=" N GLYLB 187 " --> pdb=" O PROLB 40 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N GLYLB 186 " --> pdb=" O THRLB 157 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N THRLB 157 " --> pdb=" O GLYLB 186 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VALLB 158 " --> pdb=" O TYRLB 92 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LB' and resid 50 through 55 removed outlier: 5.332A pdb=" N LYSLB 50 " --> pdb=" O ASPLB 80 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASPLB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLYLB 52 " --> pdb=" O ILELB 78 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LC' and resid 5 through 8 Processing sheet with id= 18, first strand: chain 'LC' and resid 209 through 212 Processing sheet with id= 19, first strand: chain 'LD' and resid 72 through 75 removed outlier: 6.566A pdb=" N METLD 64 " --> pdb=" O PHELD 75 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYRLD 49 " --> pdb=" O LYSLD 146 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LE' and resid 57 through 61 removed outlier: 4.555A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LE' and resid 81 through 84 Processing sheet with id= 22, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.975A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id= 24, first strand: chain 'LG' and resid 179 through 183 Processing sheet with id= 25, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.966A pdb=" N GLYLH 51 " --> pdb=" O VALLH 12 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VALLH 52 " --> pdb=" O VALLH 48 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LH' and resid 17 through 20 Processing sheet with id= 27, first strand: chain 'LH' and resid 100 through 103 removed outlier: 8.821A pdb=" N GLYLH 110 " --> pdb=" O PROLH 132 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYRLH 112 " --> pdb=" O METLH 130 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LH' and resid 134 through 139 removed outlier: 5.782A pdb=" N GLULH 145 " --> pdb=" O SERLH 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASPLH 144 " --> pdb=" O TYRLH 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYRLH 92 " --> pdb=" O ASPLH 144 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLYLH 150 " --> pdb=" O PHELH 86 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LH' and resid 86 through 90 removed outlier: 3.866A pdb=" N GLULH 185 " --> pdb=" O LYSLH 89 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LI' and resid 34 through 37 removed outlier: 6.333A pdb=" N TYRLI 34 " --> pdb=" O VALLI 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILELI 136 " --> pdb=" O LEULI 52 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N CYSLI 49 " --> pdb=" O SERLI 168 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LI' and resid 95 through 100 removed outlier: 6.425A pdb=" N HISLI 95 " --> pdb=" O THRLI 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THRLI 125 " --> pdb=" O HISLI 95 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILELI 97 " --> pdb=" O GLNLI 123 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LI' and resid 189 through 192 removed outlier: 7.568A pdb=" N ARGLI 189 " --> pdb=" O LEULI 200 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LJ' and resid 46 through 49 removed outlier: 4.111A pdb=" N ALALJ 67 " --> pdb=" O SERLJ 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYSLJ 17 " --> pdb=" O CYSLJ 131 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHELJ 103 " --> pdb=" O CYSLJ 130 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LK' and resid 12 through 16 removed outlier: 4.378A pdb=" N ILELK 12 " --> pdb=" O GLNLK 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLNLK 65 " --> pdb=" O ILELK 12 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARGLK 61 " --> pdb=" O ARGLK 16 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 36, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.770A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LN' and resid 59 through 67 removed outlier: 6.820A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.857A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 40, first strand: chain 'LP' and resid 14 through 20 removed outlier: 6.744A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 42, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 43, first strand: chain 'LQ' and resid 126 through 129 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'LR' and resid 21 through 25 removed outlier: 6.417A pdb=" N LYSLR 21 " --> pdb=" O LYSLR 53 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEULR 49 " --> pdb=" O ASPLR 25 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.674A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LS' and resid 88 through 96 removed outlier: 3.547A pdb=" N LEULS 79 " --> pdb=" O METLS 90 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRPLS 78 " --> pdb=" O LEULS 124 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.396A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SERLS 60 " --> pdb=" O ILELS 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LS' and resid 74 through 78 removed outlier: 4.928A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSLS 125 " --> pdb=" O TRPLS 78 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LT' and resid 39 through 43 removed outlier: 4.515A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LT' and resid 72 through 79 Processing sheet with id= 51, first strand: chain 'LU' and resid 60 through 64 removed outlier: 3.743A pdb=" N SERLU 63 " --> pdb=" O GLULU 71 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N TRPLU 99 " --> pdb=" O TYRLU 115 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LV' and resid 34 through 38 removed outlier: 6.251A pdb=" N ARGLV 34 " --> pdb=" O CYSLV 27 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYSLV 27 " --> pdb=" O ARGLV 34 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASNLV 100 " --> pdb=" O ILELV 24 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILELV 104 " --> pdb=" O ALALV 28 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LV' and resid 81 through 84 removed outlier: 3.692A pdb=" N ARGLV 82 " --> pdb=" O ALALV 101 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LW' and resid 18 through 23 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'LX' and resid 94 through 99 removed outlier: 3.943A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LY' and resid 71 through 74 removed outlier: 3.624A pdb=" N SERLY 71 " --> pdb=" O HISLY 80 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALLY 78 " --> pdb=" O TYRLY 73 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LZ' and resid 9 through 13 removed outlier: 4.216A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LZ' and resid 26 through 29 removed outlier: 3.617A pdb=" N GLNLZ 26 " --> pdb=" O LEULZ 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYSLZ 72 " --> pdb=" O VALLZ 42 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Lc' and resid 68 through 74 removed outlier: 3.606A pdb=" N ILELc 45 " --> pdb=" O PROLc 69 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALALc 49 " --> pdb=" O TYRLc 73 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEULc 44 " --> pdb=" O ILELc 95 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 5.470A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERLd 115 " --> pdb=" O GLULd 19 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 62, first strand: chain 'Lf' and resid 13 through 16 removed outlier: 7.096A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.271A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.455A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILELg 24 " --> pdb=" O ARGLg 32 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 3.624A pdb=" N GLNLk 3 " --> pdb=" O LEULk 44 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSLk 69 " --> pdb=" O ALALk 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VALLk 71 " --> pdb=" O ILELk 25 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Lm' and resid 93 through 97 removed outlier: 6.093A pdb=" N LYSLm 93 " --> pdb=" O LYSLm 124 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLNLm 120 " --> pdb=" O ARGLm 97 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Lo' and resid 6 through 10 removed outlier: 6.227A pdb=" N LYSLo 6 " --> pdb=" O VALLo 25 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEULo 22 " --> pdb=" O SERLo 75 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VALLo 69 " --> pdb=" O TYRLo 28 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Lp' and resid 53 through 57 removed outlier: 5.506A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Lq' and resid 19 through 22 removed outlier: 5.976A pdb=" N PHELq 19 " --> pdb=" O ARGLq 30 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Lq' and resid 51 through 56 removed outlier: 5.388A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYSLq 66 " --> pdb=" O ALALq 51 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Ls' and resid 25 through 29 Processing sheet with id= 72, first strand: chain 'Ls' and resid 104 through 107 removed outlier: 4.048A pdb=" N PHELs 181 " --> pdb=" O ALALs 107 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Ls' and resid 112 through 115 removed outlier: 6.606A pdb=" N ALALs 113 " --> pdb=" O LYSLs 164 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYSLs 164 " --> pdb=" O ALALs 113 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALALs 115 " --> pdb=" O GLYLs 162 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Ls' and resid 143 through 146 Processing sheet with id= 75, first strand: chain 'SA' and resid 41 through 44 removed outlier: 3.962A pdb=" N LYSSA 42 " --> pdb=" O ILESA 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VALSA 48 " --> pdb=" O ARGSA 44 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SA' and resid 98 through 102 removed outlier: 3.530A pdb=" N GLNSA 99 " --> pdb=" O VALSA 76 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SB' and resid 44 through 50 removed outlier: 4.613A pdb=" N GLYSB 44 " --> pdb=" O ILESB 32 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARGSB 26 " --> pdb=" O ARGSB 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THRSB 98 " --> pdb=" O LYSSB 33 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHESB 100 " --> pdb=" O PROSB 35 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEUSB 97 " --> pdb=" O ASPSB 89 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYSSB 85 " --> pdb=" O HISSB 101 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEUSB 103 " --> pdb=" O LYSSB 83 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYSSB 83 " --> pdb=" O LEUSB 103 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARGSB 64 " --> pdb=" O VALSB 88 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'SB' and resid 119 through 128 removed outlier: 5.947A pdb=" N THRSB 119 " --> pdb=" O THRSB 143 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SB' and resid 134 through 139 removed outlier: 6.477A pdb=" N LEUSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYSSB 214 " --> pdb=" O PHESB 138 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'SC' and resid 84 through 89 removed outlier: 3.528A pdb=" N LEUSC 111 " --> pdb=" O GLUSC 87 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILESC 109 " --> pdb=" O METSC 89 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'SC' and resid 165 through 169 removed outlier: 4.247A pdb=" N ALASC 180 " --> pdb=" O ASPSC 203 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASPSC 203 " --> pdb=" O ALASC 180 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'SC' and resid 106 through 114 removed outlier: 6.438A pdb=" N HISSC 118 " --> pdb=" O ASPSC 114 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'SD' and resid 49 through 56 Processing sheet with id= 84, first strand: chain 'SD' and resid 151 through 158 removed outlier: 3.770A pdb=" N GLYSD 183 " --> pdb=" O LEUSD 180 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'SE' and resid 88 through 91 removed outlier: 4.403A pdb=" N ASPSE 88 " --> pdb=" O LEUSE 101 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N HISSE 112 " --> pdb=" O ARGSE 100 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILESE 102 " --> pdb=" O THRSE 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THRSE 110 " --> pdb=" O ILESE 102 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'SE' and resid 122 through 126 removed outlier: 4.862A pdb=" N ASPSE 158 " --> pdb=" O VALSE 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THRSE 159 " --> pdb=" O ILESE 173 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASPSE 171 " --> pdb=" O LYSSE 161 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'SE' and resid 197 through 200 removed outlier: 3.578A pdb=" N HISSE 197 " --> pdb=" O HISSE 209 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHESE 218 " --> pdb=" O LEUSE 210 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASNSE 216 " --> pdb=" O ASPSE 212 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'SG' and resid 11 through 18 removed outlier: 3.884A pdb=" N VALSG 18 " --> pdb=" O METSG 1 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SERSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILESG 52 " --> pdb=" O SERSG 112 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VALSG 114 " --> pdb=" O LEUSG 50 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEUSG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALASG 34 " --> pdb=" O ILESG 52 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'SG' and resid 72 through 76 Processing sheet with id= 90, first strand: chain 'SG' and resid 159 through 163 removed outlier: 3.781A pdb=" N ARGSG 160 " --> pdb=" O LYSSG 174 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'SH' and resid 50 through 56 removed outlier: 3.959A pdb=" N SERSH 51 " --> pdb=" O PHESH 67 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'SH' and resid 147 through 152 removed outlier: 4.859A pdb=" N ASNSH 190 " --> pdb=" O LYSSH 158 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'SI' and resid 42 through 48 removed outlier: 6.646A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASNSI 52 " --> pdb=" O THRSI 48 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'SI' and resid 72 through 75 removed outlier: 3.667A pdb=" N CYSSI 72 " --> pdb=" O TRPSI 67 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASNSI 64 " --> pdb=" O ALASI 183 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASPSI 184 " --> pdb=" O SERSI 174 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALASI 100 " --> pdb=" O ILESI 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VALSI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLYSI 80 " --> pdb=" O GLNSI 103 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'SK' and resid 20 through 24 removed outlier: 3.630A pdb=" N ALASK 23 " --> pdb=" O TYRSK 62 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'SL' and resid 74 through 79 removed outlier: 6.217A pdb=" N ARGSL 74 " --> pdb=" O GLNSL 132 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VALSL 129 " --> pdb=" O LEUSL 145 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'SL' and resid 88 through 100 removed outlier: 6.530A pdb=" N THRSL 88 " --> pdb=" O HISSL 115 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HISSL 115 " --> pdb=" O THRSL 88 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILESL 90 " --> pdb=" O ALASL 113 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALASL 113 " --> pdb=" O ILESL 90 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARGSL 92 " --> pdb=" O ASNSL 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASNSL 111 " --> pdb=" O ARGSL 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLUSL 94 " --> pdb=" O HISSL 109 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HISSL 109 " --> pdb=" O GLUSL 94 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEUSL 96 " --> pdb=" O LYSSL 107 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYSSL 107 " --> pdb=" O LEUSL 96 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYRSL 98 " --> pdb=" O TYRSL 105 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYRSL 105 " --> pdb=" O TYRSL 98 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'SM' and resid 42 through 45 removed outlier: 4.845A pdb=" N GLYSM 42 " --> pdb=" O LYSSM 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VALSM 122 " --> pdb=" O ALASM 44 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'SO' and resid 39 through 45 removed outlier: 3.533A pdb=" N VALSO 29 " --> pdb=" O THRSO 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILESO 94 " --> pdb=" O GLYSO 126 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'SP' and resid 83 through 86 removed outlier: 3.867A pdb=" N ILESP 102 " --> pdb=" O VALSP 113 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALSP 113 " --> pdb=" O ILESP 102 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'SQ' and resid 5 through 12 removed outlier: 6.448A pdb=" N GLNSQ 5 " --> pdb=" O GLNSQ 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILESQ 67 " --> pdb=" O LYSSQ 30 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'SS' and resid 13 through 16 removed outlier: 6.580A pdb=" N HISSS 13 " --> pdb=" O GLYSS 24 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLYSS 24 " --> pdb=" O HISSS 13 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'ST' and resid 114 through 117 removed outlier: 4.464A pdb=" N GLYST 122 " --> pdb=" O ASPST 117 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'SU' and resid 55 through 65 removed outlier: 5.219A pdb=" N LYSSU 85 " --> pdb=" O PROSU 56 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THRSU 64 " --> pdb=" O ASPSU 77 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'SW' and resid 23 through 28 removed outlier: 5.518A pdb=" N ARGSW 23 " --> pdb=" O LEUSW 65 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLUSW 49 " --> pdb=" O GLNSW 64 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'SW' and resid 78 through 81 removed outlier: 4.257A pdb=" N TYRSW 79 " --> pdb=" O ILESW 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLYSW 123 " --> pdb=" O VALSW 81 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'SX' and resid 48 through 51 removed outlier: 3.632A pdb=" N ALASX 49 " --> pdb=" O LEUSX 104 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEUSX 103 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'SX' and resid 55 through 61 removed outlier: 3.922A pdb=" N GLUSX 55 " --> pdb=" O ARGSX 73 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VALSX 59 " --> pdb=" O ARGSX 69 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALASX 67 " --> pdb=" O ALASX 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYSSX 81 " --> pdb=" O LEUSX 76 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'SY' and resid 8 through 13 removed outlier: 3.606A pdb=" N THRSY 9 " --> pdb=" O LEUSY 31 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'SY' and resid 57 through 61 removed outlier: 5.722A pdb=" N GLNSY 57 " --> pdb=" O TYRSY 79 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYSSY 71 " --> pdb=" O GLNSY 66 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'SY' and resid 23 through 31 Processing sheet with id=112, first strand: chain 'Sa' and resid 20 through 23 removed outlier: 6.344A pdb=" N ILESa 21 " --> pdb=" O CYSSa 29 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYSSa 29 " --> pdb=" O ILESa 21 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N CYSSa 23 " --> pdb=" O ALASa 27 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'Sa' and resid 37 through 43 Processing sheet with id=114, first strand: chain 'Sb' and resid 32 through 37 removed outlier: 6.417A pdb=" N PHESb 32 " --> pdb=" O LYSSb 82 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SERSb 78 " --> pdb=" O LYSSb 36 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'Sc' and resid 42 through 46 removed outlier: 6.842A pdb=" N ARGSc 30 " --> pdb=" O THRSc 14 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASPSc 53 " --> pdb=" O VALSc 13 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'Sf' and resid 138 through 141 removed outlier: 6.331A pdb=" N GLNSf 139 " --> pdb=" O THRSf 147 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THRSf 147 " --> pdb=" O GLNSf 139 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYSSf 141 " --> pdb=" O HISSf 145 " (cutoff:3.500A) 3185 hydrogen bonds defined for protein. 9453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1962 hydrogen bonds 3226 hydrogen bond angles 0 basepair planarities 835 basepair parallelities 2953 stacking parallelities Total time for adding SS restraints: 379.24 Time building geometry restraints manager: 75.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 22759 1.31 - 1.44: 89021 1.44 - 1.56: 98030 1.56 - 1.69: 10453 1.69 - 1.81: 453 Bond restraints: 220716 Sorted by residual: bond pdb=" C4 B8N 21188 " pdb=" C5 B8N 21188 " ideal model delta sigma weight residual 1.634 1.391 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C4 B8N 21188 " pdb=" O4 B8N 21188 " ideal model delta sigma weight residual 1.183 1.422 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" N1 B8N 21188 " pdb=" C2 B8N 21188 " ideal model delta sigma weight residual 1.552 1.327 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" N1 B8N 21188 " pdb=" C6 B8N 21188 " ideal model delta sigma weight residual 1.547 1.326 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C2 OMG 12578 " pdb=" N3 OMG 12578 " ideal model delta sigma weight residual 1.462 1.303 0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 220711 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.92: 29246 105.92 - 113.00: 126784 113.00 - 120.09: 80543 120.09 - 127.17: 75167 127.17 - 134.26: 11561 Bond angle restraints: 323301 Sorted by residual: angle pdb=" C1' OMG 12578 " pdb=" N9 OMG 12578 " pdb=" C8 OMG 12578 " ideal model delta sigma weight residual 106.81 126.72 -19.91 3.00e+00 1.11e-01 4.41e+01 angle pdb=" C ALASO 63 " pdb=" N ASPSO 64 " pdb=" CA ASPSO 64 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C3' U 11587 " pdb=" O3' U 11587 " pdb=" P C 11588 " ideal model delta sigma weight residual 120.20 127.23 -7.03 1.50e+00 4.44e-01 2.20e+01 angle pdb=" O3' U 11587 " pdb=" C3' U 11587 " pdb=" C2' U 11587 " ideal model delta sigma weight residual 109.50 116.34 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" C1' B8N 21188 " pdb=" C5 B8N 21188 " pdb=" C6 B8N 21188 " ideal model delta sigma weight residual 108.00 121.45 -13.45 3.00e+00 1.11e-01 2.01e+01 ... (remaining 323296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 118852 35.81 - 71.62: 3005 71.62 - 107.43: 222 107.43 - 143.24: 41 143.24 - 179.05: 43 Dihedral angle restraints: 122163 sinusoidal: 87975 harmonic: 34188 Sorted by residual: dihedral pdb=" O4' U 2 677 " pdb=" C1' U 2 677 " pdb=" N1 U 2 677 " pdb=" C2 U 2 677 " ideal model delta sinusoidal sigma weight residual 200.00 44.43 155.57 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U 2 74 " pdb=" C1' U 2 74 " pdb=" N1 U 2 74 " pdb=" C2 U 2 74 " ideal model delta sinusoidal sigma weight residual 200.00 45.23 154.77 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" O4' C 2 277 " pdb=" C1' C 2 277 " pdb=" N1 C 2 277 " pdb=" C2 C 2 277 " ideal model delta sinusoidal sigma weight residual 200.00 46.78 153.22 1 1.50e+01 4.44e-03 8.08e+01 ... (remaining 122160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 38442 0.071 - 0.143: 1770 0.143 - 0.214: 62 0.214 - 0.285: 5 0.285 - 0.356: 1 Chirality restraints: 40280 Sorted by residual: chirality pdb=" CA HISLB 257 " pdb=" N HISLB 257 " pdb=" C HISLB 257 " pdb=" CB HISLB 257 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C3' G 11290 " pdb=" C4' G 11290 " pdb=" O3' G 11290 " pdb=" C2' G 11290 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILESM 86 " pdb=" CA ILESM 86 " pdb=" CG1 ILESM 86 " pdb=" CG2 ILESM 86 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 40277 not shown) Planarity restraints: 21636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12578 " 0.016 2.00e-02 2.50e+03 5.42e-01 6.60e+03 pdb=" C4' OMG 12578 " 0.423 2.00e-02 2.50e+03 pdb=" O4' OMG 12578 " 0.588 2.00e-02 2.50e+03 pdb=" C3' OMG 12578 " -0.585 2.00e-02 2.50e+03 pdb=" O3' OMG 12578 " -0.512 2.00e-02 2.50e+03 pdb=" C2' OMG 12578 " -0.230 2.00e-02 2.50e+03 pdb=" O2' OMG 12578 " 0.867 2.00e-02 2.50e+03 pdb=" C1' OMG 12578 " 0.238 2.00e-02 2.50e+03 pdb=" N9 OMG 12578 " -0.805 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HISLs 70 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PROLs 71 " 0.191 5.00e-02 4.00e+02 pdb=" CA PROLs 71 " -0.058 5.00e-02 4.00e+02 pdb=" CD PROLs 71 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALASO 63 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ALASO 63 " 0.058 2.00e-02 2.50e+03 pdb=" O ALASO 63 " -0.021 2.00e-02 2.50e+03 pdb=" N ASPSO 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 21633 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 2663 2.46 - 3.07: 120607 3.07 - 3.68: 329053 3.68 - 4.29: 517860 4.29 - 4.90: 754388 Nonbonded interactions: 1724571 Sorted by model distance: nonbonded pdb="MG MG 13440 " pdb=" O HOH 14176 " model vdw 1.848 2.170 nonbonded pdb=" OP1 G 1 916 " pdb="MG MG 13509 " model vdw 1.862 2.170 nonbonded pdb="MG MG 13491 " pdb=" O HOH 14398 " model vdw 1.869 2.170 nonbonded pdb="MG MG 13440 " pdb=" O HOH 14432 " model vdw 1.871 2.170 nonbonded pdb="MG MG 13514 " pdb=" O HOH 13904 " model vdw 1.877 2.170 ... (remaining 1724566 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 'Ln' selection = chain 'Lr' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 5231 5.49 5 Mg 571 5.21 5 S 290 5.16 5 C 109238 2.51 5 N 38171 2.21 5 O 53835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.110 Extract box with map and model: 30.860 Check model and map are aligned: 2.020 Convert atoms to be neutral: 1.140 Process input model: 754.580 Find NCS groups from input model: 6.160 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 810.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.003 0.243 220716 Z= 0.201 Angle : 0.450 19.913 323301 Z= 0.237 Chirality : 0.031 0.356 40280 Planarity : 0.005 0.542 21636 Dihedral : 14.063 179.047 100109 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.61 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.07), residues: 11697 helix: -0.15 (0.08), residues: 3548 sheet: -0.25 (0.12), residues: 1764 loop : -1.19 (0.07), residues: 6385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2064 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2060 time to evaluate : 10.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 7 residues processed: 2061 average time/residue: 2.3109 time to fit residues: 7143.9354 Evaluate side-chains 1655 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1648 time to evaluate : 10.102 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 4 average time/residue: 1.8799 time to fit residues: 24.0832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 1413 optimal weight: 2.9990 chunk 1268 optimal weight: 6.9990 chunk 704 optimal weight: 20.0000 chunk 433 optimal weight: 20.0000 chunk 855 optimal weight: 6.9990 chunk 677 optimal weight: 3.9990 chunk 1312 optimal weight: 6.9990 chunk 507 optimal weight: 7.9990 chunk 797 optimal weight: 0.3980 chunk 976 optimal weight: 3.9990 chunk 1520 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** LC 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 89 ASN LD 181 ASN LD 225 GLN LE 116 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LG 246 GLN LH 35 GLN ** LH 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 102 ASN LL 7 GLN LL 66 ASN LM 106 GLN LP 89 GLN LP 118 GLN LP 120 ASN LQ 122 GLN LR 91 GLN LS 19 ASN LS 21 ASN LU 55 ASN LX 81 ASN LX 93 ASN LY 92 GLN Lf 58 GLN Lf 79 ASN Li 100 GLN Lk 28 ASN Lk 67 GLN Ll 43 HIS Lo 82 GLN ** Ls 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 193 ASN SC 95 GLN SC 102 GLN SD 7 GLN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 201 HIS SE 253 GLN ** SH 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SH 120 GLN SI 88 ASN ** SK 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SN 78 ASN SQ 77 GLN SR 48 ASN ST 42 ASN ** SV 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 12 ASN SW 15 ASN SY 18 ASN SY 25 GLN ** SZ 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 51 GLN Sb 61 ASN Sb 65 GLN Sc 28 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 220716 Z= 0.322 Angle : 0.619 13.878 323301 Z= 0.322 Chirality : 0.040 0.390 40280 Planarity : 0.005 0.132 21636 Dihedral : 13.465 177.962 76033 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.18 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.07), residues: 11697 helix: 0.57 (0.08), residues: 3780 sheet: -0.14 (0.12), residues: 1737 loop : -1.32 (0.07), residues: 6180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1940 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1717 time to evaluate : 10.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 124 residues processed: 1800 average time/residue: 2.2992 time to fit residues: 6233.6079 Evaluate side-chains 1730 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1606 time to evaluate : 10.168 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 46 residues processed: 82 average time/residue: 1.5024 time to fit residues: 229.2437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 844 optimal weight: 5.9990 chunk 471 optimal weight: 20.0000 chunk 1265 optimal weight: 5.9990 chunk 1035 optimal weight: 6.9990 chunk 419 optimal weight: 8.9990 chunk 1522 optimal weight: 10.0000 chunk 1645 optimal weight: 8.9990 chunk 1356 optimal weight: 9.9990 chunk 1510 optimal weight: 5.9990 chunk 519 optimal weight: 10.0000 chunk 1221 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 585 GLN LA 140 ASN LB 379 GLN ** LC 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 89 ASN LD 225 GLN LE 172 ASN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LG 246 GLN LH 35 GLN LM 106 GLN ** LM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 111 ASN LQ 122 GLN LR 91 GLN LR 125 HIS LR 177 GLN LS 19 ASN LS 21 ASN LU 55 ASN LV 134 ASN LX 81 ASN LY 92 GLN LZ 122 ASN Ld 49 GLN Lf 79 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Li 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 82 GLN SC 95 GLN SC 160 HIS SD 25 ASN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 253 GLN SF 156 ASN ** SH 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SI 88 ASN ** SK 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SN 105 ASN SP 136 HIS SR 48 ASN ** SV 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 15 ASN ** SZ 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 51 GLN Sb 65 GLN Sc 28 GLN Sf 139 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.084 220716 Z= 0.511 Angle : 0.699 12.963 323301 Z= 0.361 Chirality : 0.045 0.547 40280 Planarity : 0.005 0.136 21636 Dihedral : 13.823 178.575 76033 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.07), residues: 11697 helix: 0.56 (0.08), residues: 3798 sheet: -0.33 (0.12), residues: 1760 loop : -1.50 (0.07), residues: 6139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1930 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1603 time to evaluate : 10.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 327 outliers final: 196 residues processed: 1762 average time/residue: 2.3936 time to fit residues: 6358.5337 Evaluate side-chains 1762 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1566 time to evaluate : 11.278 Switching outliers to nearest non-outliers outliers start: 196 outliers final: 99 residues processed: 101 average time/residue: 1.5877 time to fit residues: 300.6892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 1504 optimal weight: 1.9990 chunk 1144 optimal weight: 0.6980 chunk 790 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 726 optimal weight: 4.9990 chunk 1022 optimal weight: 8.9990 chunk 1528 optimal weight: 30.0000 chunk 1618 optimal weight: 9.9990 chunk 798 optimal weight: 1.9990 chunk 1448 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 257 HIS LB 379 GLN ** LC 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 89 ASN LD 225 GLN LE 172 ASN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN ** LH 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 103 ASN LM 106 GLN LM 110 GLN LP 89 GLN LQ 122 GLN LR 91 GLN LR 125 HIS LU 55 ASN LV 134 ASN LX 81 ASN LY 92 GLN Lf 58 GLN Lf 79 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 82 GLN SB 149 GLN SC 95 GLN SC 102 GLN SD 7 GLN SD 177 HIS SE 130 GLN SE 201 HIS SE 253 GLN ** SF 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SI 88 ASN SI 127 GLN SN 21 ASN SN 105 ASN SQ 77 GLN SR 48 ASN ST 128 GLN SW 15 ASN SY 25 GLN ** SZ 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 51 GLN Sb 65 GLN Sc 28 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 220716 Z= 0.224 Angle : 0.569 12.502 323301 Z= 0.299 Chirality : 0.037 0.350 40280 Planarity : 0.004 0.125 21636 Dihedral : 13.628 179.546 76033 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.37 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.07), residues: 11697 helix: 0.87 (0.08), residues: 3793 sheet: -0.25 (0.12), residues: 1744 loop : -1.46 (0.07), residues: 6160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1982 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1663 time to evaluate : 11.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 319 outliers final: 175 residues processed: 1845 average time/residue: 2.2600 time to fit residues: 6319.6989 Evaluate side-chains 1765 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1590 time to evaluate : 10.095 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 111 residues processed: 70 average time/residue: 1.3920 time to fit residues: 188.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 1347 optimal weight: 0.9980 chunk 918 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 1204 optimal weight: 5.9990 chunk 667 optimal weight: 7.9990 chunk 1380 optimal weight: 3.9990 chunk 1118 optimal weight: 0.0980 chunk 1 optimal weight: 8.9990 chunk 826 optimal weight: 10.0000 chunk 1452 optimal weight: 10.0000 chunk 408 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 257 HIS LB 379 GLN LC 60 GLN LD 89 ASN LD 225 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LH 35 GLN ** LH 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 106 GLN LM 110 GLN LP 97 ASN LQ 122 GLN LR 125 HIS LU 55 ASN LV 134 ASN LX 81 ASN LY 92 GLN Lf 79 ASN Lh 33 GLN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 100 GLN ** Lo 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 95 GLN SD 7 GLN SD 177 HIS SE 130 GLN SE 201 HIS SE 253 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SN 21 ASN SN 105 ASN SQ 77 GLN SR 48 ASN ST 13 HIS ST 130 GLN SW 15 ASN SY 25 GLN SZ 84 HIS Sb 51 GLN Sb 65 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 220716 Z= 0.218 Angle : 0.551 13.422 323301 Z= 0.289 Chirality : 0.036 0.345 40280 Planarity : 0.004 0.127 21636 Dihedral : 13.526 179.983 76033 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.18 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.08), residues: 11697 helix: 1.02 (0.09), residues: 3814 sheet: -0.17 (0.12), residues: 1730 loop : -1.42 (0.07), residues: 6153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1991 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1663 time to evaluate : 10.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 328 outliers final: 200 residues processed: 1850 average time/residue: 2.3800 time to fit residues: 6753.4457 Evaluate side-chains 1776 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1576 time to evaluate : 10.184 Switching outliers to nearest non-outliers outliers start: 200 outliers final: 129 residues processed: 74 average time/residue: 1.4108 time to fit residues: 202.0161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 544 optimal weight: 30.0000 chunk 1457 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 950 optimal weight: 0.6980 chunk 399 optimal weight: 40.0000 chunk 1619 optimal weight: 6.9990 chunk 1344 optimal weight: 0.9990 chunk 749 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 535 optimal weight: 6.9990 chunk 850 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 257 HIS LB 379 GLN LD 39 GLN LD 89 ASN LD 225 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LM 106 GLN LM 110 GLN LP 97 ASN LQ 122 GLN LR 125 HIS LU 55 ASN LV 134 ASN LX 81 ASN LY 92 GLN Lf 7 HIS Lf 58 GLN Lf 79 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 95 GLN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 130 GLN SE 201 HIS SE 224 ASN SE 253 GLN SG 201 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SN 21 ASN SN 105 ASN SQ 77 GLN ST 130 GLN SW 15 ASN SW 42 GLN Sb 51 GLN Sb 61 ASN Sb 65 GLN ** Sf 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 220716 Z= 0.348 Angle : 0.608 12.750 323301 Z= 0.317 Chirality : 0.039 0.427 40280 Planarity : 0.005 0.130 21636 Dihedral : 13.644 178.735 76033 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.08), residues: 11697 helix: 0.97 (0.09), residues: 3808 sheet: -0.23 (0.12), residues: 1737 loop : -1.48 (0.07), residues: 6152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1931 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1584 time to evaluate : 10.430 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 outliers start: 347 outliers final: 230 residues processed: 1797 average time/residue: 2.2781 time to fit residues: 6238.5141 Evaluate side-chains 1778 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1548 time to evaluate : 10.087 Switching outliers to nearest non-outliers outliers start: 230 outliers final: 155 residues processed: 78 average time/residue: 1.4454 time to fit residues: 215.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 1561 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 922 optimal weight: 0.9980 chunk 1182 optimal weight: 1.9990 chunk 916 optimal weight: 10.0000 chunk 1363 optimal weight: 9.9990 chunk 904 optimal weight: 0.9990 chunk 1613 optimal weight: 6.9990 chunk 1009 optimal weight: 5.9990 chunk 983 optimal weight: 2.9990 chunk 744 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LB 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LD 89 ASN LD 225 GLN LE 116 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LM 106 GLN LM 110 GLN LO 152 GLN LQ 122 GLN LR 91 GLN LT 24 GLN LU 55 ASN LV 134 ASN LX 81 ASN LY 92 GLN Lf 79 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 44 GLN SC 95 GLN SC 97 GLN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 130 GLN SE 201 HIS SE 224 ASN SE 253 GLN SF 118 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SN 21 ASN SN 105 ASN SQ 77 GLN ST 130 GLN SW 15 ASN ** SY 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sf 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 220716 Z= 0.238 Angle : 0.576 12.691 323301 Z= 0.302 Chirality : 0.037 0.380 40280 Planarity : 0.005 0.127 21636 Dihedral : 13.607 179.352 76033 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.14 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.08), residues: 11697 helix: 1.03 (0.09), residues: 3810 sheet: -0.20 (0.12), residues: 1732 loop : -1.46 (0.07), residues: 6155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1889 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1582 time to evaluate : 10.211 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 outliers start: 307 outliers final: 224 residues processed: 1786 average time/residue: 2.2831 time to fit residues: 6240.6162 Evaluate side-chains 1772 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1548 time to evaluate : 10.071 Switching outliers to nearest non-outliers outliers start: 224 outliers final: 164 residues processed: 64 average time/residue: 1.4783 time to fit residues: 181.4252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 998 optimal weight: 10.0000 chunk 644 optimal weight: 0.8980 chunk 963 optimal weight: 6.9990 chunk 486 optimal weight: 40.0000 chunk 317 optimal weight: 8.9990 chunk 312 optimal weight: 6.9990 chunk 1025 optimal weight: 4.9990 chunk 1099 optimal weight: 6.9990 chunk 797 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 1268 optimal weight: 0.5980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 379 GLN LD 89 ASN LD 225 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LH 15 ASN LI 203 HIS LM 106 GLN LM 110 GLN LQ 122 GLN LR 91 GLN LR 125 HIS LT 24 GLN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 134 ASN LX 81 ASN LY 92 GLN Lf 79 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 100 GLN SC 44 GLN SC 95 GLN SD 177 HIS SE 130 GLN SE 201 HIS SE 253 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SN 105 ASN SQ 77 GLN ST 130 GLN SW 15 ASN Sb 51 GLN ** Sf 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 220716 Z= 0.316 Angle : 0.603 12.924 323301 Z= 0.314 Chirality : 0.039 0.367 40280 Planarity : 0.005 0.129 21636 Dihedral : 13.651 179.070 76033 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.73 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.08), residues: 11697 helix: 0.99 (0.09), residues: 3806 sheet: -0.25 (0.12), residues: 1742 loop : -1.50 (0.07), residues: 6149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1881 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1579 time to evaluate : 10.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 302 outliers final: 221 residues processed: 1789 average time/residue: 2.3213 time to fit residues: 6339.6047 Evaluate side-chains 1774 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1553 time to evaluate : 10.079 Switching outliers to nearest non-outliers outliers start: 221 outliers final: 169 residues processed: 54 average time/residue: 1.3577 time to fit residues: 148.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 1467 optimal weight: 1.9990 chunk 1545 optimal weight: 20.0000 chunk 1410 optimal weight: 1.9990 chunk 1503 optimal weight: 9.9990 chunk 904 optimal weight: 4.9990 chunk 655 optimal weight: 5.9990 chunk 1180 optimal weight: 0.8980 chunk 461 optimal weight: 20.0000 chunk 1358 optimal weight: 10.0000 chunk 1422 optimal weight: 0.6980 chunk 1498 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 379 GLN LC 284 GLN LD 225 GLN LE 116 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN LM 106 GLN LM 110 GLN LQ 122 GLN LR 91 GLN LR 125 HIS ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 134 ASN LX 81 ASN LY 92 GLN Lf 58 GLN Lf 79 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 44 GLN SC 95 GLN SC 97 GLN SC 102 GLN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 130 GLN SE 201 HIS SE 224 ASN SE 253 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SI 88 ASN SN 21 ASN SN 105 ASN SQ 77 GLN SS 99 GLN ** ST 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 130 GLN SW 15 ASN SW 39 GLN Sb 51 GLN ** Sf 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 220716 Z= 0.196 Angle : 0.578 12.963 323301 Z= 0.303 Chirality : 0.036 0.315 40280 Planarity : 0.005 0.125 21636 Dihedral : 13.605 179.485 76033 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.20 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.08), residues: 11697 helix: 1.06 (0.09), residues: 3802 sheet: -0.22 (0.12), residues: 1745 loop : -1.45 (0.07), residues: 6150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1598 time to evaluate : 11.405 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 outliers start: 253 outliers final: 205 residues processed: 1787 average time/residue: 2.2720 time to fit residues: 6203.8895 Evaluate side-chains 1769 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1564 time to evaluate : 10.068 Switching outliers to nearest non-outliers outliers start: 205 outliers final: 169 residues processed: 40 average time/residue: 1.5360 time to fit residues: 120.8181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 987 optimal weight: 0.6980 chunk 1589 optimal weight: 5.9990 chunk 970 optimal weight: 3.9990 chunk 754 optimal weight: 7.9990 chunk 1105 optimal weight: 0.9990 chunk 1667 optimal weight: 0.0970 chunk 1534 optimal weight: 0.0030 chunk 1328 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 1025 optimal weight: 3.9990 chunk 814 optimal weight: 50.0000 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 379 GLN LD 89 ASN LD 225 GLN LF 192 HIS ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 35 GLN LM 106 GLN LM 110 GLN LP 97 ASN LQ 122 GLN LR 125 HIS ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 134 ASN LX 81 ASN LY 92 GLN Ld 105 ASN Lh 70 GLN Li 42 GLN SC 44 GLN SC 95 GLN SC 102 GLN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 130 GLN SE 201 HIS SE 224 ASN SE 253 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SH 81 GLN SN 78 ASN SN 105 ASN SQ 77 GLN ** ST 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 130 GLN SW 15 ASN ** Sb 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sf 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.116 220716 Z= 0.160 Angle : 0.566 18.702 323301 Z= 0.294 Chirality : 0.035 0.346 40280 Planarity : 0.005 0.273 21636 Dihedral : 13.525 179.820 76033 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.42 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.08), residues: 11697 helix: 1.10 (0.09), residues: 3801 sheet: -0.16 (0.12), residues: 1746 loop : -1.41 (0.07), residues: 6150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23394 Ramachandran restraints generated. 11697 Oldfield, 0 Emsley, 11697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1834 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1620 time to evaluate : 10.130 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 outliers start: 214 outliers final: 175 residues processed: 1796 average time/residue: 2.2973 time to fit residues: 6327.6092 Evaluate side-chains 1742 residues out of total 10010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1567 time to evaluate : 10.205 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 160 residues processed: 19 average time/residue: 1.4716 time to fit residues: 62.5575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1674 random chunks: chunk 1054 optimal weight: 5.9990 chunk 1414 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 1224 optimal weight: 0.0770 chunk 196 optimal weight: 7.9990 chunk 369 optimal weight: 10.0000 chunk 1330 optimal weight: 2.9990 chunk 556 optimal weight: 10.0000 chunk 1365 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LB 379 GLN LC 284 GLN LD 89 ASN LD 225 GLN LE 116 GLN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 203 HIS LL 7 GLN LM 106 GLN LM 110 GLN LP 89 GLN LP 97 ASN LR 125 HIS LS 19 ASN LT 24 GLN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 134 ASN LX 81 ASN LY 92 GLN ** Lh 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 42 GLN Li 100 GLN ** Lo 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 44 GLN SC 95 GLN SC 97 GLN SD 29 GLN ** SD 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 177 HIS SE 130 GLN SE 201 HIS SE 224 ASN SE 253 GLN ** SH 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SN 21 ASN SN 105 ASN SQ 77 GLN ** ST 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 130 GLN SW 15 ASN SZ 84 HIS ** Sb 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sf 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.063130 restraints weight = 362495.735| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 1.47 r_work: 0.2651 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work: 0.2635 rms_B_bonded: 1.41 restraints_weight: 0.1250 r_work: 0.2627 rms_B_bonded: 1.45 restraints_weight: 0.0625 r_work: 0.2620 rms_B_bonded: 1.51 restraints_weight: 0.0312 r_work: 0.2611 rms_B_bonded: 1.59 restraints_weight: 0.0156 r_work: 0.2603 rms_B_bonded: 1.68 restraints_weight: 0.0078 r_work: 0.2595 rms_B_bonded: 1.78 restraints_weight: 0.0039 r_work: 0.2586 rms_B_bonded: 1.90 restraints_weight: 0.0020 r_work: 0.2577 rms_B_bonded: 2.03 restraints_weight: 0.0010 r_work: 0.2567 rms_B_bonded: 2.17 restraints_weight: 0.0005 r_work: 0.2558 rms_B_bonded: 2.32 restraints_weight: 0.0002 r_work: 0.2548 rms_B_bonded: 2.49 restraints_weight: 0.0001 r_work: 0.2537 rms_B_bonded: 2.67 restraints_weight: 0.0001 r_work: 0.2526 rms_B_bonded: 2.87 restraints_weight: 0.0000 r_work: 0.2514 rms_B_bonded: 3.08 restraints_weight: 0.0000 r_work: 0.2502 rms_B_bonded: 3.31 restraints_weight: 0.0000 r_work: 0.2490 rms_B_bonded: 3.55 restraints_weight: 0.0000 r_work: 0.2476 rms_B_bonded: 3.82 restraints_weight: 0.0000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.125 220716 Z= 0.381 Angle : 0.639 14.870 323301 Z= 0.331 Chirality : 0.040 0.392 40280 Planarity : 0.005 0.131 21636 Dihedral : 13.679 178.626 76033 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 11697 helix: 0.95 (0.09), residues: 3810 sheet: -0.24 (0.12), residues: 1758 loop : -1.50 (0.07), residues: 6129 =============================================================================== Job complete usr+sys time: 78948.37 seconds wall clock time: 1357 minutes 13.45 seconds (81433.45 seconds total)