Starting phenix.real_space_refine (version: dev) on Thu Apr 14 06:01:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ydw_10779/04_2022/6ydw_10779_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ydw_10779/04_2022/6ydw_10779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ydw_10779/04_2022/6ydw_10779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ydw_10779/04_2022/6ydw_10779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ydw_10779/04_2022/6ydw_10779_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ydw_10779/04_2022/6ydw_10779_neut_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 "BY TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bx TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 180836 Number of models: 1 Model: "" Number of chains: 124 Chain: "AI" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2650 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 313} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "BT" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1840 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 207, 'PCIS': 1} Chain: "BU" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "BV" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 144, 'PCIS': 1} Chain: "BW" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1374 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain: "BX" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 136} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "BY" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1678 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 17, 'TRANS': 188} Chain: "Ba" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3173 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 35, 'TRANS': 357} Chain: "Bb" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2952 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 32, 'TRANS': 321} Chain: "Bc" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2408 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "Bd" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1177 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 13, 'TRANS': 126} Chain: "Be" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "Bf" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 95} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "Bg" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain: "Bh" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2319 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "Bi" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2138 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 23, 'TRANS': 236} Chain: "Bj" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1775 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "Bk" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1246 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 1 Chain: "Bl" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 15, 'TRANS': 116, 'PCIS': 1} Chain: "Bm" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 893 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "Bn" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 837 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "Bo" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 772 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Bp" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Bq" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 697 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Bt" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "Bu" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Bv" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1131 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 12, 'TRANS': 122} Chain: "B0" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "Bw" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3126 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 25, 'TRANS': 360, 'PCIS': 1} Chain: "Bx" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1325 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 18, 'TRANS': 143} Chain: "AA" Number of atoms: 20411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 20411 Classifications: {'RNA': 960} Modifications used: {'rna3p_pyr': 373, 'rna2p_pur': 82, 'rna3p_pur': 440, 'rna2p_pyr': 65} Link IDs: {'rna3p': 812, 'rna2p': 147} Chain: "AB" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1762 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "AC" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1075 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "AE" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2732 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "AF" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "AG" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "AJ" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1155 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "AK" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1007 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "AL" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 10, 'TRANS': 98} Chain: "AN" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 858 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "AO" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1448 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "AP" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 932 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "AQ" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "AR" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 784 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "AU" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 734 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "AV" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1498 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 30, 'rna2p_pyr': 3, 'rna3p_pyr': 34} Link IDs: {'rna3p': 63, 'rna2p': 7} Chain: "AX" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 3, 'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 5} Chain: "AY" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1498 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 31, 'rna2p_pyr': 2, 'rna3p_pyr': 35} Link IDs: {'rna3p': 65, 'rna2p': 5} Chain: "AZ" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "Aa" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2378 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain: "Ab" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "Ac" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1367 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "Ad" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1467 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "Ae" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3109 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 375} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B1" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2036 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "Af" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 778 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "Ag" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2875 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain: "Ah" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1015 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 114, 'PCIS': 1} Chain: "Ai" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 824 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Aj" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1788 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 16, 'TRANS': 196} Chain: "Ak" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2222 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "Am" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "An" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 639 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Ao" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4525 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 27, 'TRANS': 544} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "Ap" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1564 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "CL" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 317 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 40} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "DL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "EL" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 222 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "FL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "GL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "HL" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 205 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "LL" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 537 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 66, 'PCIS': 1} Chain: "B2" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1548 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "B3" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "B4" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 474 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 57} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B5" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B6" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "B7" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B8" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 833 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "B9" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 335 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "BA" Number of atoms: 32844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 32844 Classifications: {'RNA': 1544} Modifications used: {'rna3p_pyr': 578, 'rna2p_pur': 172, 'rna3p_pur': 682, 'rna2p_pyr': 112} Link IDs: {'rna3p': 1260, 'rna2p': 283} Chain breaks: 1 Chain: "BB" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1427 Classifications: {'RNA': 67} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 27, 'p5*END': 1, 'rna3p_pur': 35, 'rna2p_pur': 2} Link IDs: {'rna3p': 61, 'rna2p': 5} Chain breaks: 2 Chain: "BC" Number of atoms: 5425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5425 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 30, 'TRANS': 663} Chain breaks: 2 Chain: "BD" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1860 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain: "BE" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 25, 'TRANS': 281} Chain: "BF" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2011 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Chain: "BI" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "BJ" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 18, 'TRANS': 193} Chain: "BK" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1339 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 166, 'PCIS': 1} Chain: "BN" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1444 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "BO" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 9, 'TRANS': 105} Chain: "BP" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2312 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 27, 'TRANS': 260} Chain: "BQ" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1803 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "BR" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "BS" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1168 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 136, 'PCIS': 1} Chain: "BW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Be" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bl" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bq" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bt" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bx" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 116 Unusual residues: {' MG': 102, 'SPM': 1} Classifications: {'undetermined': 103} Link IDs: {None: 102} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ac" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Am" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "An" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ap" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 252 Unusual residues: {' MG': 200, 'SPM': 2} Classifications: {'undetermined': 202, 'RNA': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 202} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'GNP': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BD" 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: "BF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BP" 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: "BQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "BC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43674 SG CYSBx 70 175.247 176.663 209.023 1.00 47.26 S ATOM 43695 SG CYSBx 73 176.161 180.042 207.615 1.00 42.12 S ATOM 43992 SG CYSBx 108 174.600 177.424 205.388 1.00 49.20 S ATOM A1H1P SG CYSBJ 64 172.536 179.104 208.059 1.00 64.08 S ATOM 71537 SG CYSAF 105 135.442 126.319 34.654 1.00102.28 S ATOM 80680 SG CYSAR 66 132.521 128.737 34.680 1.00 89.77 S ATOM 80702 SG CYSAR 69 132.102 125.287 33.275 1.00 96.06 S ATOM 80959 SG CYSAR 101 132.546 125.772 36.999 1.00 93.81 S ATOM 78838 SG CYSAP 26 144.732 63.653 119.536 1.00 65.44 S ATOM 89871 SG CYSAc 139 142.785 63.185 116.342 1.00 72.71 S ATOM 89885 SG CYSAc 141 142.428 60.680 119.131 1.00 70.44 S ATOM 89943 SG CYSAc 149 140.982 64.159 119.544 1.00 66.74 S ATOM A09SW SG CYSAp 94 114.006 76.157 121.165 1.00 69.29 S ATOM A09V1 SG CYSAp 105 114.212 76.777 117.457 1.00 68.27 S ATOM A09VM SG CYSAp 108 113.018 73.452 118.756 1.00 73.95 S ATOM A0A3J SG CYSAp 143 116.651 74.424 119.100 1.00 65.38 S ATOM A0EOY SG CYSB5 110 264.733 145.638 141.723 1.00 70.03 S ATOM A0EPK SG CYSB5 113 266.035 147.844 138.954 1.00 69.60 S ATOM A0ERT SG CYSB5 123 262.357 147.038 139.151 1.00 60.44 S ATOM A0ESF SG CYSB5 126 264.825 144.357 138.176 1.00 62.57 S ATOM A0GIW SG CYSB9 73 159.073 151.100 185.284 1.00 57.90 S ATOM A0GJL SG CYSB9 76 162.341 152.707 184.306 1.00 53.97 S ATOM A0GN1 SG CYSB9 89 162.133 148.966 184.730 1.00 55.97 S Time building chain proxies: 71.26, per 1000 atoms: 0.39 Number of scatterers: 180836 At special positions: 0 Unit cell: (326.65, 298.85, 300.24, 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 6 29.99 S 513 16.00 P 2724 15.00 Mg 325 11.99 O 40470 8.00 N 32857 7.00 C 103941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAm 45 " - pdb=" SG CYSAm 76 " distance=2.03 Simple disulfide: pdb=" SG CYSAm 55 " - pdb=" SG CYSAm 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.23 Conformation dependent library (CDL) restraints added in 13.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNAR 500 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 69 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 66 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 101 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAF 105 " pdb=" ZNAc 500 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 141 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAP 26 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 139 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 149 " pdb=" ZNAp 500 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 105 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 94 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 108 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 143 " pdb=" ZNB5 500 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 113 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 123 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 110 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 126 " pdb=" ZNB9 500 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 76 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 73 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 89 " pdb="ZN ZNB9 500 " - pdb=" ND1 HISB9 95 " pdb=" ZNBx 500 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 108 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBJ 64 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 70 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 73 " Number of angles added : 33 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28630 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: 538 helices and 117 sheets defined 47.1% alpha, 12.0% beta 742 base pairs and 1311 stacking pairs defined. Time for finding SS restraints: 72.21 Creating SS restraints... Processing helix chain 'AI' and resid 70 through 93 Processing helix chain 'AI' and resid 100 through 113 removed outlier: 3.891A pdb=" N ARGAI 106 " --> pdb=" O GLUAI 102 " (cutoff:3.500A) Proline residue: AI 113 - end of helix Processing helix chain 'AI' and resid 118 through 123 removed outlier: 3.725A pdb=" N ARGAI 122 " --> pdb=" O GLUAI 118 " (cutoff:3.500A) Proline residue: AI 123 - end of helix No H-bonds generated for 'chain 'AI' and resid 118 through 123' Processing helix chain 'AI' and resid 127 through 133 Proline residue: AI 133 - end of helix Processing helix chain 'AI' and resid 155 through 183 removed outlier: 3.884A pdb=" N SERAI 160 " --> pdb=" O GLNAI 156 " (cutoff:3.500A) Processing helix chain 'AI' and resid 202 through 211 removed outlier: 3.840A pdb=" N METAI 209 " --> pdb=" O GLUAI 205 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VALAI 211 " --> pdb=" O GLUAI 207 " (cutoff:3.500A) Processing helix chain 'AI' and resid 215 through 233 removed outlier: 3.789A pdb=" N LEUAI 232 " --> pdb=" O ARGAI 228 " (cutoff:3.500A) Proline residue: AI 233 - end of helix Processing helix chain 'AI' and resid 235 through 247 removed outlier: 3.545A pdb=" N GLUAI 239 " --> pdb=" O GLYAI 235 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASPAI 240 " --> pdb=" O ALAAI 236 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHEAI 245 " --> pdb=" O PHEAI 241 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARGAI 246 " --> pdb=" O VALAI 242 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARGAI 247 " --> pdb=" O ASNAI 243 " (cutoff:3.500A) Processing helix chain 'AI' and resid 300 through 306 Proline residue: AI 306 - end of helix Processing helix chain 'AI' and resid 309 through 319 Proline residue: AI 317 - end of helix Processing helix chain 'AI' and resid 337 through 358 removed outlier: 3.898A pdb=" N GLNAI 341 " --> pdb=" O GLYAI 337 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALAAI 342 " --> pdb=" O ARGAI 338 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYSAI 354 " --> pdb=" O ALAAI 350 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SERAI 355 " --> pdb=" O ARGAI 351 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHEAI 356 " --> pdb=" O ALAAI 352 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VALAI 357 " --> pdb=" O LEUAI 353 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N THRAI 358 " --> pdb=" O CYSAI 354 " (cutoff:3.500A) Processing helix chain 'AI' and resid 359 through 369 Processing helix chain 'BT' and resid 88 through 107 removed outlier: 3.968A pdb=" N PHEBT 92 " --> pdb=" O ASNBT 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILEBT 105 " --> pdb=" O GLUBT 101 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HISBT 107 " --> pdb=" O ARGBT 103 " (cutoff:3.500A) Processing helix chain 'BT' and resid 189 through 194 removed outlier: 5.535A pdb=" N LEUBT 194 " --> pdb=" O LEUBT 190 " (cutoff:3.500A) Processing helix chain 'BT' and resid 195 through 200 removed outlier: 6.121A pdb=" N PHEBT 200 " --> pdb=" O GLUBT 196 " (cutoff:3.500A) Processing helix chain 'BT' and resid 244 through 249 removed outlier: 3.927A pdb=" N CYSBT 248 " --> pdb=" O ARGBT 244 " (cutoff:3.500A) Processing helix chain 'BT' and resid 250 through 262 removed outlier: 4.154A pdb=" N LYSBT 259 " --> pdb=" O ARGBT 255 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRPBT 260 " --> pdb=" O GLUBT 256 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SERBT 261 " --> pdb=" O ALABT 257 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLNBT 262 " --> pdb=" O GLNBT 258 " (cutoff:3.500A) Processing helix chain 'BT' and resid 263 through 268 removed outlier: 3.944A pdb=" N PHEBT 267 " --> pdb=" O PROBT 263 " (cutoff:3.500A) Processing helix chain 'BT' and resid 275 through 292 Processing helix chain 'BU' and resid 16 through 29 removed outlier: 3.960A pdb=" N VALBU 24 " --> pdb=" O ARGBU 20 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N HISBU 27 " --> pdb=" O GLUBU 23 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALABU 28 " --> pdb=" O VALBU 24 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARGBU 29 " --> pdb=" O LEUBU 25 " (cutoff:3.500A) Processing helix chain 'BU' and resid 33 through 38 removed outlier: 4.748A pdb=" N ARGBU 37 " --> pdb=" O GLYBU 33 " (cutoff:3.500A) Processing helix chain 'BU' and resid 46 through 79 removed outlier: 4.550A pdb=" N LYSBU 61 " --> pdb=" O ARGBU 57 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARGBU 62 " --> pdb=" O ARGBU 58 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HISBU 79 " --> pdb=" O ALABU 75 " (cutoff:3.500A) Processing helix chain 'BU' and resid 82 through 94 removed outlier: 3.713A pdb=" N GLNBU 94 " --> pdb=" O LEUBU 90 " (cutoff:3.500A) Processing helix chain 'BU' and resid 98 through 109 Processing helix chain 'BU' and resid 110 through 134 Processing helix chain 'BV' and resid 72 through 94 Processing helix chain 'BV' and resid 154 through 159 removed outlier: 4.712A pdb=" N ARGBV 159 " --> pdb=" O LYSBV 155 " (cutoff:3.500A) Processing helix chain 'BW' and resid 47 through 55 removed outlier: 4.685A pdb=" N LYSBW 51 " --> pdb=" O ARGBW 47 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASNBW 53 " --> pdb=" O TRPBW 49 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYSBW 54 " --> pdb=" O GLUBW 50 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILEBW 55 " --> pdb=" O LYSBW 51 " (cutoff:3.500A) Processing helix chain 'BW' and resid 81 through 93 removed outlier: 3.662A pdb=" N LEUBW 88 " --> pdb=" O LYSBW 84 " (cutoff:3.500A) Processing helix chain 'BW' and resid 96 through 107 removed outlier: 3.687A pdb=" N PHEBW 106 " --> pdb=" O ALABW 102 " (cutoff:3.500A) Processing helix chain 'BW' and resid 109 through 129 removed outlier: 4.572A pdb=" N GLNBW 113 " --> pdb=" O LYSBW 109 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILEBW 114 " --> pdb=" O LYSBW 110 " (cutoff:3.500A) Processing helix chain 'BW' and resid 189 through 204 removed outlier: 3.931A pdb=" N ARGBW 204 " --> pdb=" O GLUBW 200 " (cutoff:3.500A) Processing helix chain 'BX' and resid 49 through 60 Processing helix chain 'BX' and resid 114 through 136 Processing helix chain 'BY' and resid 28 through 36 Proline residue: BY 36 - end of helix Processing helix chain 'BY' and resid 116 through 121 removed outlier: 4.988A pdb=" N LYSBY 121 " --> pdb=" O HISBY 117 " (cutoff:3.500A) Processing helix chain 'BY' and resid 178 through 184 Processing helix chain 'BY' and resid 193 through 203 Processing helix chain 'Ba' and resid 47 through 52 removed outlier: 4.245A pdb=" N GLUBa 51 " --> pdb=" O ASPBa 47 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILEBa 52 " --> pdb=" O ARGBa 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 47 through 52' Processing helix chain 'Ba' and resid 116 through 125 Processing helix chain 'Ba' and resid 133 through 142 Processing helix chain 'Ba' and resid 149 through 163 Processing helix chain 'Ba' and resid 172 through 196 Proline residue: Ba 178 - end of helix removed outlier: 4.186A pdb=" N GLNBa 191 " --> pdb=" O LEUBa 187 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILEBa 192 " --> pdb=" O CYSBa 188 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEUBa 193 " --> pdb=" O LYSBa 189 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYSBa 194 " --> pdb=" O SERBa 190 " (cutoff:3.500A) Proline residue: Ba 196 - end of helix Processing helix chain 'Ba' and resid 241 through 252 removed outlier: 4.033A pdb=" N LYSBa 249 " --> pdb=" O VALBa 245 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASNBa 250 " --> pdb=" O GLUBa 246 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HISBa 251 " --> pdb=" O ALABa 247 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VALBa 252 " --> pdb=" O THRBa 248 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 299 through 304 removed outlier: 5.279A pdb=" N PHEBa 304 " --> pdb=" O ARGBa 300 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 305 through 329 Processing helix chain 'Ba' and resid 407 through 420 removed outlier: 4.307A pdb=" N PHEBa 411 " --> pdb=" O GLNBa 407 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 44 through 49 removed outlier: 3.778A pdb=" N LEUBb 48 " --> pdb=" O ASPBb 44 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYSBb 49 " --> pdb=" O LEUBb 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 44 through 49' Processing helix chain 'Bb' and resid 53 through 67 removed outlier: 3.780A pdb=" N ARGBb 66 " --> pdb=" O GLUBb 62 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYSBb 67 " --> pdb=" O GLNBb 63 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 73 through 79 removed outlier: 3.772A pdb=" N HISBb 77 " --> pdb=" O THRBb 73 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 98 through 116 removed outlier: 3.889A pdb=" N ASNBb 116 " --> pdb=" O GLUBb 112 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 117 through 126 Processing helix chain 'Bb' and resid 131 through 143 Processing helix chain 'Bb' and resid 144 through 156 Processing helix chain 'Bb' and resid 157 through 162 Processing helix chain 'Bb' and resid 194 through 199 Processing helix chain 'Bb' and resid 244 through 249 removed outlier: 3.796A pdb=" N GLYBb 248 " --> pdb=" O ARGBb 244 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLNBb 249 " --> pdb=" O VALBb 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 244 through 249' Processing helix chain 'Bb' and resid 292 through 297 removed outlier: 3.640A pdb=" N THRBb 297 " --> pdb=" O LEUBb 293 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 299 through 308 Processing helix chain 'Bb' and resid 324 through 333 removed outlier: 4.488A pdb=" N THRBb 328 " --> pdb=" O ASPBb 324 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARGBb 329 " --> pdb=" O ASPBb 325 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VALBb 330 " --> pdb=" O SERBb 326 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 364 through 370 removed outlier: 3.566A pdb=" N ARGBb 368 " --> pdb=" O ARGBb 364 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYRBb 369 " --> pdb=" O TYRBb 365 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 33 through 57 removed outlier: 4.285A pdb=" N THRBc 56 " --> pdb=" O GLNBc 52 " (cutoff:3.500A) Proline residue: Bc 57 - end of helix Processing helix chain 'Bc' and resid 84 through 93 Processing helix chain 'Bc' and resid 94 through 100 Processing helix chain 'Bc' and resid 132 through 155 removed outlier: 3.992A pdb=" N PHEBc 155 " --> pdb=" O ILEBc 151 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 192 through 210 removed outlier: 3.686A pdb=" N LYSBc 209 " --> pdb=" O ALABc 205 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASPBc 210 " --> pdb=" O LEUBc 206 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 219 through 228 removed outlier: 4.060A pdb=" N GLUBc 225 " --> pdb=" O LYSBc 221 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 230 through 245 removed outlier: 3.991A pdb=" N GLNBc 243 " --> pdb=" O GLUBc 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASNBc 244 " --> pdb=" O LYSBc 240 " (cutoff:3.500A) Proline residue: Bc 245 - end of helix Processing helix chain 'Bc' and resid 305 through 318 removed outlier: 4.265A pdb=" N LYSBc 318 " --> pdb=" O GLUBc 314 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 184 through 189 removed outlier: 3.578A pdb=" N ASPBc 187 " --> pdb=" O LYSBc 184 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLUBc 188 " --> pdb=" O ARGBc 185 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRPBc 189 " --> pdb=" O LEUBc 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 184 through 189' Processing helix chain 'Bc' and resid 268 through 273 removed outlier: 4.084A pdb=" N ILEBc 271 " --> pdb=" O ARGBc 268 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHEBc 273 " --> pdb=" O SERBc 270 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 17 through 35 removed outlier: 4.029A pdb=" N LYSBd 21 " --> pdb=" O ASPBd 17 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SERBd 35 " --> pdb=" O LEUBd 31 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 41 through 46 removed outlier: 3.774A pdb=" N ILEBd 45 " --> pdb=" O ILEBd 41 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THRBd 46 " --> pdb=" O GLUBd 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 41 through 46' Processing helix chain 'Bd' and resid 47 through 57 removed outlier: 5.036A pdb=" N LEUBd 51 " --> pdb=" O PROBd 47 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASNBd 52 " --> pdb=" O VALBd 48 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYSBd 53 " --> pdb=" O LYSBd 49 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLUBd 54 " --> pdb=" O PHEBd 50 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARGBd 55 " --> pdb=" O LEUBd 51 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLNBd 56 " --> pdb=" O ASNBd 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARGBd 57 " --> pdb=" O LYSBd 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 47 through 57' Processing helix chain 'Bd' and resid 63 through 110 Processing helix chain 'Bd' and resid 111 through 119 removed outlier: 4.088A pdb=" N LYSBd 119 " --> pdb=" O ALABd 115 " (cutoff:3.500A) Processing helix chain 'Be' and resid 22 through 27 removed outlier: 4.390A pdb=" N GLYBe 26 " --> pdb=" O THRBe 22 " (cutoff:3.500A) Proline residue: Be 27 - end of helix No H-bonds generated for 'chain 'Be' and resid 22 through 27' Processing helix chain 'Be' and resid 51 through 56 removed outlier: 3.680A pdb=" N ILEBe 55 " --> pdb=" O ILEBe 51 " (cutoff:3.500A) Proline residue: Be 56 - end of helix No H-bonds generated for 'chain 'Be' and resid 51 through 56' Processing helix chain 'Be' and resid 62 through 67 removed outlier: 4.997A pdb=" N PHEBe 66 " --> pdb=" O GLUBe 62 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYSBe 67 " --> pdb=" O LEUBe 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Be' and resid 62 through 67' Processing helix chain 'Be' and resid 85 through 94 Processing helix chain 'Be' and resid 95 through 105 Processing helix chain 'Bf' and resid 88 through 98 removed outlier: 3.783A pdb=" N THRBf 94 " --> pdb=" O LEUBf 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEUBf 96 " --> pdb=" O LEUBf 92 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLUBf 97 " --> pdb=" O LYSBf 93 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 104 through 117 Processing helix chain 'Bf' and resid 119 through 124 removed outlier: 4.737A pdb=" N TRPBf 123 " --> pdb=" O THRBf 119 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYRBf 124 " --> pdb=" O LYSBf 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 119 through 124' Processing helix chain 'Bf' and resid 127 through 134 removed outlier: 3.898A pdb=" N ARGBf 133 " --> pdb=" O TYRBf 129 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARGBf 134 " --> pdb=" O HISBf 130 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 2 through 7 removed outlier: 4.767A pdb=" N ALABg 7 " --> pdb=" O ALABg 3 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 16 through 21 removed outlier: 4.770A pdb=" N GLYBg 20 " --> pdb=" O HISBg 16 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARGBg 21 " --> pdb=" O ASNBg 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bg' and resid 16 through 21' Processing helix chain 'Bg' and resid 37 through 50 removed outlier: 3.990A pdb=" N ARGBg 41 " --> pdb=" O ALABg 37 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLYBg 42 " --> pdb=" O PROBg 38 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALABg 43 " --> pdb=" O SERBg 39 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 51 through 59 Proline residue: Bg 59 - end of helix Processing helix chain 'Bg' and resid 93 through 107 Processing helix chain 'Bh' and resid 34 through 54 removed outlier: 5.097A pdb=" N ALABh 38 " --> pdb=" O GLYBh 34 " (cutoff:3.500A) Proline residue: Bh 54 - end of helix Processing helix chain 'Bh' and resid 59 through 64 Proline residue: Bh 64 - end of helix Processing helix chain 'Bh' and resid 67 through 80 removed outlier: 4.058A pdb=" N LEUBh 79 " --> pdb=" O PHEBh 75 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLNBh 80 " --> pdb=" O GLYBh 76 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 84 through 93 removed outlier: 4.056A pdb=" N VALBh 93 " --> pdb=" O LYSBh 89 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 94 through 109 Processing helix chain 'Bh' and resid 114 through 119 removed outlier: 5.102A pdb=" N ASNBh 118 " --> pdb=" O ALABh 114 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEUBh 119 " --> pdb=" O ALABh 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bh' and resid 114 through 119' Processing helix chain 'Bh' and resid 122 through 145 Processing helix chain 'Bh' and resid 149 through 162 Processing helix chain 'Bh' and resid 163 through 174 Processing helix chain 'Bh' and resid 187 through 206 Processing helix chain 'Bh' and resid 207 through 224 removed outlier: 3.676A pdb=" N ILEBh 220 " --> pdb=" O ARGBh 216 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THRBh 221 " --> pdb=" O ASPBh 217 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLNBh 222 " --> pdb=" O PHEBh 218 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N METBh 223 " --> pdb=" O LEUBh 219 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THRBh 224 " --> pdb=" O ILEBh 220 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 227 through 233 removed outlier: 4.036A pdb=" N METBh 231 " --> pdb=" O GLUBh 227 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 236 through 249 Processing helix chain 'Bh' and resid 288 through 306 Processing helix chain 'Bi' and resid 48 through 54 removed outlier: 4.526A pdb=" N SERBi 52 " --> pdb=" O PROBi 48 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYSBi 54 " --> pdb=" O TYRBi 50 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 65 through 72 removed outlier: 3.912A pdb=" N LEUBi 72 " --> pdb=" O PROBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 93 through 101 removed outlier: 4.594A pdb=" N SERBi 99 " --> pdb=" O ALABi 95 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEUBi 100 " --> pdb=" O ARGBi 96 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SERBi 101 " --> pdb=" O ILEBi 97 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 102 through 115 removed outlier: 4.261A pdb=" N GLNBi 107 " --> pdb=" O GLUBi 103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASNBi 115 " --> pdb=" O ARGBi 111 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 116 through 129 Processing helix chain 'Bi' and resid 133 through 155 removed outlier: 3.871A pdb=" N PHEBi 137 " --> pdb=" O LYSBi 133 " (cutoff:3.500A) Proline residue: Bi 138 - end of helix Processing helix chain 'Bi' and resid 156 through 164 Processing helix chain 'Bi' and resid 165 through 177 Proline residue: Bi 170 - end of helix removed outlier: 5.751A pdb=" N ASPBi 175 " --> pdb=" O ASPBi 171 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILEBi 176 " --> pdb=" O METBi 172 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 64 through 82 Processing helix chain 'Bj' and resid 85 through 104 removed outlier: 3.890A pdb=" N SERBj 103 " --> pdb=" O ALABj 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASPBj 104 " --> pdb=" O LYSBj 100 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 116 through 132 removed outlier: 3.945A pdb=" N LEUBj 120 " --> pdb=" O LEUBj 116 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYSBj 132 " --> pdb=" O PHEBj 128 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 137 through 143 removed outlier: 4.335A pdb=" N ASPBj 141 " --> pdb=" O LEUBj 137 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYSBj 142 " --> pdb=" O THRBj 138 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 183 through 195 Processing helix chain 'Bj' and resid 256 through 265 removed outlier: 5.358A pdb=" N LYSBj 265 " --> pdb=" O GLYBj 261 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 266 through 276 removed outlier: 3.612A pdb=" N GLNBj 271 " --> pdb=" O LYSBj 267 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VALBj 272 " --> pdb=" O TYRBj 268 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARGBj 273 " --> pdb=" O LEUBj 269 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARGBj 274 " --> pdb=" O ALABj 270 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHEBj 275 " --> pdb=" O GLNBj 271 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 59 through 64 removed outlier: 3.775A pdb=" N VALBk 63 " --> pdb=" O TYRBk 59 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYSBk 64 " --> pdb=" O LYSBk 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bk' and resid 59 through 64' Processing helix chain 'Bk' and resid 99 through 118 Processing helix chain 'Bk' and resid 163 through 178 Processing helix chain 'Bk' and resid 190 through 199 removed outlier: 4.029A pdb=" N ARGBk 197 " --> pdb=" O ASPBk 193 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHEBk 198 " --> pdb=" O PHEBk 194 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYSBk 199 " --> pdb=" O LYSBk 195 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 201 through 212 Processing helix chain 'Bl' and resid 44 through 52 removed outlier: 4.560A pdb=" N VALBl 48 " --> pdb=" O GLUBl 44 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLUBl 49 " --> pdb=" O TYRBl 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARGBl 50 " --> pdb=" O HISBl 46 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEUBl 51 " --> pdb=" O PHEBl 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEUBl 52 " --> pdb=" O VALBl 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bl' and resid 44 through 52' Processing helix chain 'Bl' and resid 116 through 132 removed outlier: 3.766A pdb=" N LEUBl 120 " --> pdb=" O ASPBl 116 " (cutoff:3.500A) Proline residue: Bl 130 - end of helix Processing helix chain 'Bl' and resid 153 through 165 Processing helix chain 'Bm' and resid 66 through 80 Processing helix chain 'Bm' and resid 94 through 110 Processing helix chain 'Bm' and resid 114 through 122 removed outlier: 4.047A pdb=" N LEUBm 118 " --> pdb=" O PROBm 114 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HISBm 119 " --> pdb=" O ASNBm 115 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLNBm 120 " --> pdb=" O SERBm 116 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N CYSBm 122 " --> pdb=" O LEUBm 118 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 123 through 134 removed outlier: 3.630A pdb=" N VALBm 127 " --> pdb=" O ARGBm 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VALBm 133 " --> pdb=" O ASPBm 129 " (cutoff:3.500A) Proline residue: Bm 134 - end of helix Processing helix chain 'Bm' and resid 139 through 148 removed outlier: 3.753A pdb=" N ALABm 146 " --> pdb=" O ASPBm 142 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SERBm 147 " --> pdb=" O GLUBm 143 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASNBm 148 " --> pdb=" O LEUBm 144 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 48 through 54 Processing helix chain 'Bn' and resid 59 through 64 Processing helix chain 'Bn' and resid 69 through 74 removed outlier: 4.583A pdb=" N LEUBn 73 " --> pdb=" O HISBn 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILEBn 74 " --> pdb=" O PROBn 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bn' and resid 69 through 74' Processing helix chain 'Bn' and resid 86 through 98 Processing helix chain 'Bn' and resid 103 through 123 Processing helix chain 'Bo' and resid 24 through 32 removed outlier: 3.920A pdb=" N ARGBo 28 " --> pdb=" O GLYBo 24 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 41 through 46 removed outlier: 3.591A pdb=" N LEUBo 46 " --> pdb=" O PROBo 42 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 60 through 108 removed outlier: 3.531A pdb=" N GLNBo 106 " --> pdb=" O GLUBo 102 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 114 through 119 removed outlier: 4.956A pdb=" N GLNBo 118 " --> pdb=" O GLYBo 114 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASNBo 119 " --> pdb=" O ALABo 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bo' and resid 114 through 119' Processing helix chain 'Bp' and resid 2 through 9 removed outlier: 4.072A pdb=" N GLYBp 9 " --> pdb=" O LEUBp 5 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 27 through 39 Processing helix chain 'Bp' and resid 40 through 47 removed outlier: 3.578A pdb=" N ASNBp 46 " --> pdb=" O VALBp 42 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEUBp 47 " --> pdb=" O ARGBp 43 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 82 through 98 removed outlier: 3.636A pdb=" N GLYBp 98 " --> pdb=" O ILEBp 94 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 65 through 71 removed outlier: 4.808A pdb=" N THRBq 69 " --> pdb=" O PROBq 65 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 88 through 93 removed outlier: 4.043A pdb=" N TYRBq 92 " --> pdb=" O PROBq 88 " (cutoff:3.500A) Proline residue: Bq 93 - end of helix No H-bonds generated for 'chain 'Bq' and resid 88 through 93' Processing helix chain 'Bq' and resid 94 through 99 removed outlier: 4.012A pdb=" N METBq 99 " --> pdb=" O TRPBq 95 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 106 through 111 removed outlier: 5.611A pdb=" N ASPBq 111 " --> pdb=" O LEUBq 107 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 114 through 134 removed outlier: 4.212A pdb=" N TRPBq 118 " --> pdb=" O THRBq 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYSBq 134 " --> pdb=" O ASNBq 130 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 72 through 77 removed outlier: 4.416A pdb=" N VALBq 75 " --> pdb=" O ALABq 72 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASNBq 76 " --> pdb=" O METBq 73 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILEBq 77 " --> pdb=" O GLYBq 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bq' and resid 72 through 77' Processing helix chain 'Bt' and resid 28 through 51 removed outlier: 3.919A pdb=" N SERBt 50 " --> pdb=" O GLNBt 46 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARGBt 51 " --> pdb=" O TYRBt 47 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 55 through 60 removed outlier: 3.806A pdb=" N ARGBt 60 " --> pdb=" O ALABt 56 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 63 through 81 removed outlier: 4.739A pdb=" N ARGBt 67 " --> pdb=" O ALABt 63 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARGBt 81 " --> pdb=" O ALABt 77 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 87 through 100 removed outlier: 4.029A pdb=" N GLNBt 91 " --> pdb=" O ARGBt 87 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HISBt 94 " --> pdb=" O GLUBt 90 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEUBt 95 " --> pdb=" O GLNBt 91 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEUBt 96 " --> pdb=" O LEUBt 92 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VALBt 97 " --> pdb=" O GLYBt 93 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THRBt 98 " --> pdb=" O HISBt 94 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARGBt 99 " --> pdb=" O LEUBt 95 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYSBt 100 " --> pdb=" O LEUBt 96 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 44 through 50 Proline residue: Bu 50 - end of helix Processing helix chain 'Bu' and resid 62 through 67 removed outlier: 4.236A pdb=" N LYSBu 66 " --> pdb=" O PROBu 62 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLNBu 67 " --> pdb=" O ASPBu 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 62 through 67' Processing helix chain 'Bu' and resid 72 through 77 removed outlier: 3.642A pdb=" N LEUBu 76 " --> pdb=" O PROBu 72 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THRBu 77 " --> pdb=" O VALBu 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 72 through 77' Processing helix chain 'Bu' and resid 111 through 122 Processing helix chain 'Bu' and resid 141 through 163 Proline residue: Bu 163 - end of helix Processing helix chain 'Bu' and resid 170 through 189 removed outlier: 4.483A pdb=" N LEUBu 174 " --> pdb=" O GLUBu 170 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARGBu 176 " --> pdb=" O ALABu 172 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SERBu 177 " --> pdb=" O GLUBu 173 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEUBu 187 " --> pdb=" O ASNBu 183 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 54 through 59 removed outlier: 3.630A pdb=" N THRBu 57 " --> pdb=" O GLYBu 54 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALABu 58 " --> pdb=" O SERBu 55 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRPBu 59 " --> pdb=" O ASPBu 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 54 through 59' Processing helix chain 'Bv' and resid 48 through 53 removed outlier: 3.868A pdb=" N LEUBv 52 " --> pdb=" O PROBv 48 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 54 through 64 Processing helix chain 'Bv' and resid 71 through 76 removed outlier: 4.478A pdb=" N LEUBv 75 " --> pdb=" O ALABv 71 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TRPBv 76 " --> pdb=" O ALABv 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bv' and resid 71 through 76' Processing helix chain 'Bv' and resid 78 through 93 Processing helix chain 'Bv' and resid 95 through 159 removed outlier: 3.735A pdb=" N LYSBv 127 " --> pdb=" O GLUBv 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N METBv 128 " --> pdb=" O CYSBv 124 " (cutoff:3.500A) Proline residue: Bv 129 - end of helix removed outlier: 3.670A pdb=" N GLUBv 159 " --> pdb=" O ARGBv 155 " (cutoff:3.500A) Processing helix chain 'B0' and resid 110 through 120 Processing helix chain 'Bw' and resid 55 through 73 Processing helix chain 'Bw' and resid 75 through 85 Processing helix chain 'Bw' and resid 101 through 111 removed outlier: 4.574A pdb=" N TRPBw 105 " --> pdb=" O ASNBw 101 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 132 through 149 Processing helix chain 'Bw' and resid 164 through 184 Proline residue: Bw 169 - end of helix removed outlier: 4.651A pdb=" N VALBw 184 " --> pdb=" O GLYBw 180 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 186 through 193 removed outlier: 4.212A pdb=" N ALABw 190 " --> pdb=" O ASNBw 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALABw 191 " --> pdb=" O PROBw 187 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALABw 193 " --> pdb=" O LEUBw 189 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 261 through 266 removed outlier: 4.719A pdb=" N LEUBw 265 " --> pdb=" O LYSBw 261 " (cutoff:3.500A) Proline residue: Bw 266 - end of helix No H-bonds generated for 'chain 'Bw' and resid 261 through 266' Processing helix chain 'Bw' and resid 301 through 309 Processing helix chain 'Bw' and resid 311 through 338 removed outlier: 4.918A pdb=" N GLUBw 315 " --> pdb=" O ALABw 311 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VALBw 316 " --> pdb=" O ASPBw 312 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHEBw 318 " --> pdb=" O ILEBw 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHEBw 327 " --> pdb=" O ILEBw 323 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 374 through 382 removed outlier: 3.755A pdb=" N GLNBw 379 " --> pdb=" O ALABw 375 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASNBw 380 " --> pdb=" O GLNBw 376 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASNBw 381 " --> pdb=" O ALABw 377 " (cutoff:3.500A) Proline residue: Bw 382 - end of helix Processing helix chain 'Bw' and resid 408 through 421 removed outlier: 4.022A pdb=" N LEUBw 412 " --> pdb=" O ASNBw 408 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 70 through 76 Processing helix chain 'Bx' and resid 85 through 93 removed outlier: 3.642A pdb=" N LEUBx 89 " --> pdb=" O ASPBx 85 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLNBx 91 " --> pdb=" O LEUBx 87 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHEBx 92 " --> pdb=" O LEUBx 88 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILEBx 93 " --> pdb=" O LEUBx 89 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 101 through 106 Processing helix chain 'Bx' and resid 108 through 126 Processing helix chain 'Bx' and resid 135 through 142 removed outlier: 4.244A pdb=" N VALBx 140 " --> pdb=" O PROBx 136 " (cutoff:3.500A) Proline residue: Bx 141 - end of helix Processing helix chain 'AB' and resid 55 through 69 removed outlier: 3.507A pdb=" N ASPAB 59 " --> pdb=" O ASNAB 55 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARGAB 60 " --> pdb=" O ASPAB 56 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILEAB 61 " --> pdb=" O LEUAB 57 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEUAB 62 " --> pdb=" O ARGAB 58 " (cutoff:3.500A) Proline residue: AB 65 - end of helix removed outlier: 4.289A pdb=" N HISAB 68 " --> pdb=" O GLUAB 64 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALAAB 69 " --> pdb=" O PROAB 65 " (cutoff:3.500A) Processing helix chain 'AB' and resid 74 through 79 removed outlier: 4.631A pdb=" N PHEAB 78 " --> pdb=" O LEUAB 74 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SERAB 79 " --> pdb=" O LYSAB 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 74 through 79' Processing helix chain 'AB' and resid 80 through 87 removed outlier: 3.941A pdb=" N ALAAB 86 " --> pdb=" O SERAB 82 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARGAB 87 " --> pdb=" O LEUAB 83 " (cutoff:3.500A) Processing helix chain 'AB' and resid 116 through 138 Processing helix chain 'AB' and resid 150 through 162 Processing helix chain 'AB' and resid 177 through 182 Processing helix chain 'AB' and resid 205 through 215 removed outlier: 4.189A pdb=" N ARGAB 209 " --> pdb=" O HISAB 205 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALAAB 212 " --> pdb=" O VALAB 208 " (cutoff:3.500A) Processing helix chain 'AB' and resid 241 through 274 removed outlier: 3.996A pdb=" N GLYAB 274 " --> pdb=" O TYRAB 270 " (cutoff:3.500A) Processing helix chain 'AC' and resid 52 through 58 removed outlier: 4.033A pdb=" N HISAC 57 " --> pdb=" O TYRAC 53 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALAAC 58 " --> pdb=" O GLUAC 54 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 101 removed outlier: 3.911A pdb=" N ARGAC 85 " --> pdb=" O HISAC 81 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLUAC 88 " --> pdb=" O GLUAC 84 " (cutoff:3.500A) Proline residue: AC 101 - end of helix Processing helix chain 'AC' and resid 128 through 148 removed outlier: 4.027A pdb=" N SERAC 144 " --> pdb=" O GLUAC 140 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HISAC 145 " --> pdb=" O THRAC 141 " (cutoff:3.500A) Processing helix chain 'AE' and resid 94 through 104 Processing helix chain 'AE' and resid 107 through 113 removed outlier: 4.129A pdb=" N ARGAE 111 " --> pdb=" O GLYAE 107 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYSAE 112 " --> pdb=" O ALAAE 108 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLYAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'AE' and resid 107 through 113' Processing helix chain 'AE' and resid 161 through 180 removed outlier: 4.115A pdb=" N GLNAE 165 " --> pdb=" O SERAE 161 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLUAE 166 " --> pdb=" O LYSAE 162 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYSAE 167 " --> pdb=" O GLUAE 163 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASPAE 180 " --> pdb=" O ARGAE 176 " (cutoff:3.500A) Processing helix chain 'AE' and resid 263 through 279 removed outlier: 4.022A pdb=" N VALAE 276 " --> pdb=" O LYSAE 272 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N HISAE 277 " --> pdb=" O ASNAE 273 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYRAE 278 " --> pdb=" O ARGAE 274 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEUAE 279 " --> pdb=" O ALAAE 275 " (cutoff:3.500A) Processing helix chain 'AE' and resid 317 through 328 removed outlier: 3.715A pdb=" N THRAE 322 " --> pdb=" O ARGAE 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUAE 326 " --> pdb=" O THRAE 322 " (cutoff:3.500A) Processing helix chain 'AE' and resid 341 through 356 removed outlier: 3.806A pdb=" N GLNAE 356 " --> pdb=" O GLYAE 352 " (cutoff:3.500A) Processing helix chain 'AE' and resid 358 through 367 Processing helix chain 'AE' and resid 407 through 416 removed outlier: 3.537A pdb=" N ALAAE 413 " --> pdb=" O GLUAE 409 " (cutoff:3.500A) Processing helix chain 'AE' and resid 420 through 425 removed outlier: 4.496A pdb=" N GLYAE 424 " --> pdb=" O SERAE 420 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEUAE 425 " --> pdb=" O VALAE 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'AE' and resid 420 through 425' Processing helix chain 'AF' and resid 14 through 33 removed outlier: 3.720A pdb=" N GLYAF 33 " --> pdb=" O LEUAF 29 " (cutoff:3.500A) Processing helix chain 'AF' and resid 71 through 86 removed outlier: 4.167A pdb=" N VALAF 75 " --> pdb=" O PROAF 71 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLUAF 76 " --> pdb=" O ALAAF 72 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SERAF 77 " --> pdb=" O THRAF 73 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARGAF 84 " --> pdb=" O GLUAF 80 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASPAF 85 " --> pdb=" O HISAF 81 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILEAF 86 " --> pdb=" O LEUAF 82 " (cutoff:3.500A) Processing helix chain 'AF' and resid 96 through 101 removed outlier: 4.407A pdb=" N GLNAF 100 " --> pdb=" O HISAF 96 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLUAF 101 " --> pdb=" O PROAF 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 96 through 101' Processing helix chain 'AG' and resid 47 through 54 removed outlier: 4.129A pdb=" N TYRAG 51 " --> pdb=" O ASPAG 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYSAG 53 " --> pdb=" O GLUAG 49 " (cutoff:3.500A) Proline residue: AG 54 - end of helix Processing helix chain 'AG' and resid 57 through 71 removed outlier: 4.215A pdb=" N GLUAG 61 " --> pdb=" O GLUAG 57 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYSAG 63 " --> pdb=" O THRAG 59 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARGAG 66 " --> pdb=" O GLUAG 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHEAG 68 " --> pdb=" O TYRAG 64 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYSAG 69 " --> pdb=" O GLUAG 65 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THRAG 71 " --> pdb=" O ASPAG 67 " (cutoff:3.500A) Processing helix chain 'AG' and resid 88 through 99 Processing helix chain 'AG' and resid 103 through 129 removed outlier: 3.847A pdb=" N ALAAG 107 " --> pdb=" O ASNAG 103 " (cutoff:3.500A) Processing helix chain 'AG' and resid 130 through 137 removed outlier: 3.810A pdb=" N ALAAG 135 " --> pdb=" O ALAAG 131 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THRAG 136 " --> pdb=" O GLUAG 132 " (cutoff:3.500A) Processing helix chain 'AG' and resid 140 through 153 Processing helix chain 'AG' and resid 175 through 194 Processing helix chain 'AG' and resid 200 through 215 removed outlier: 3.643A pdb=" N LEUAG 210 " --> pdb=" O SERAG 206 " (cutoff:3.500A) Processing helix chain 'AG' and resid 217 through 238 removed outlier: 5.059A pdb=" N ALAAG 235 " --> pdb=" O GLUAG 231 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEUAG 236 " --> pdb=" O ALAAG 232 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALAAG 237 " --> pdb=" O ASNAG 233 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N HISAG 238 " --> pdb=" O ARGAG 234 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 84 through 103 removed outlier: 3.970A pdb=" N LEUAJ 88 " --> pdb=" O ASPAJ 84 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLUAJ 101 " --> pdb=" O LEUAJ 97 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEUAJ 102 " --> pdb=" O ALAAJ 98 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 149 through 164 removed outlier: 3.984A pdb=" N ASNAJ 163 " --> pdb=" O TYRAJ 159 " (cutoff:3.500A) Processing helix chain 'AK' and resid 113 through 118 removed outlier: 4.070A pdb=" N GLYAK 118 " --> pdb=" O CYSAK 114 " (cutoff:3.500A) Processing helix chain 'AK' and resid 121 through 126 removed outlier: 4.187A pdb=" N GLYAK 125 " --> pdb=" O ASNAK 121 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THRAK 126 " --> pdb=" O ALAAK 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'AK' and resid 121 through 126' Processing helix chain 'AK' and resid 127 through 145 removed outlier: 3.865A pdb=" N LYSAK 144 " --> pdb=" O LYSAK 140 " (cutoff:3.500A) Processing helix chain 'AK' and resid 159 through 171 removed outlier: 3.917A pdb=" N LEUAK 167 " --> pdb=" O ALAAK 163 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THRAK 168 " --> pdb=" O ILEAK 164 " (cutoff:3.500A) Processing helix chain 'AL' and resid 32 through 40 Processing helix chain 'AN' and resid 31 through 48 Processing helix chain 'AN' and resid 49 through 59 removed outlier: 3.968A pdb=" N SERAN 56 " --> pdb=" O LEUAN 52 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEUAN 57 " --> pdb=" O ARGAN 53 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARGAN 58 " --> pdb=" O ILEAN 54 " (cutoff:3.500A) Processing helix chain 'AN' and resid 64 through 79 removed outlier: 3.622A pdb=" N GLNAN 68 " --> pdb=" O PROAN 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VALAN 70 " --> pdb=" O ASPAN 66 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEUAN 78 " --> pdb=" O GLUAN 74 " (cutoff:3.500A) Proline residue: AN 79 - end of helix Processing helix chain 'AN' and resid 83 through 88 removed outlier: 4.718A pdb=" N ILEAN 87 " --> pdb=" O CYSAN 83 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ARGAN 88 " --> pdb=" O PROAN 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 83 through 88' Processing helix chain 'AN' and resid 107 through 118 removed outlier: 3.611A pdb=" N ARGAN 112 " --> pdb=" O ARGAN 108 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HISAN 117 " --> pdb=" O HISAN 113 " (cutoff:3.500A) Processing helix chain 'AO' and resid 87 through 95 removed outlier: 3.675A pdb=" N LEUAO 93 " --> pdb=" O VALAO 89 " (cutoff:3.500A) Processing helix chain 'AO' and resid 100 through 116 removed outlier: 3.579A pdb=" N LYSAO 104 " --> pdb=" O ASNAO 100 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYSAO 115 " --> pdb=" O GLNAO 111 " (cutoff:3.500A) Processing helix chain 'AO' and resid 125 through 148 removed outlier: 3.567A pdb=" N VALAO 131 " --> pdb=" O GLUAO 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYSAO 136 " --> pdb=" O ALAAO 132 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAO 146 " --> pdb=" O GLUAO 142 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARGAO 148 " --> pdb=" O METAO 144 " (cutoff:3.500A) Processing helix chain 'AO' and resid 150 through 175 Processing helix chain 'AO' and resid 176 through 187 Processing helix chain 'AO' and resid 201 through 239 removed outlier: 3.558A pdb=" N GLNAO 238 " --> pdb=" O ALAAO 234 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLYAO 239 " --> pdb=" O ALAAO 235 " (cutoff:3.500A) Processing helix chain 'AP' and resid 69 through 80 Processing helix chain 'AP' and resid 84 through 95 Processing helix chain 'AP' and resid 100 through 126 removed outlier: 4.182A pdb=" N ASPAP 126 " --> pdb=" O SERAP 122 " (cutoff:3.500A) Processing helix chain 'AR' and resid 77 through 86 removed outlier: 3.901A pdb=" N GLNAR 83 " --> pdb=" O GLNAR 79 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHEAR 84 " --> pdb=" O LEUAR 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILEAR 85 " --> pdb=" O LEUAR 81 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SERAR 86 " --> pdb=" O SERAR 82 " (cutoff:3.500A) Processing helix chain 'AR' and resid 94 through 99 Processing helix chain 'AR' and resid 101 through 119 removed outlier: 3.546A pdb=" N GLNAR 105 " --> pdb=" O CYSAR 101 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYSAR 106 " --> pdb=" O GLYAR 102 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLUAR 107 " --> pdb=" O LYSAR 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILEAR 117 " --> pdb=" O LYSAR 113 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLYAR 119 " --> pdb=" O ALAAR 115 " (cutoff:3.500A) Processing helix chain 'AR' and resid 127 through 132 removed outlier: 3.685A pdb=" N LEUAR 131 " --> pdb=" O ASPAR 127 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYSAR 132 " --> pdb=" O PROAR 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'AR' and resid 127 through 132' Processing helix chain 'AU' and resid 18 through 34 removed outlier: 3.974A pdb=" N ALAAU 22 " --> pdb=" O ASNAU 18 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 45 removed outlier: 4.939A pdb=" N TYRAU 44 " --> pdb=" O LYSAU 40 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYRAU 45 " --> pdb=" O ARGAU 41 " (cutoff:3.500A) Processing helix chain 'AU' and resid 47 through 80 removed outlier: 3.859A pdb=" N GLNAU 53 " --> pdb=" O CYSAU 49 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARGAU 77 " --> pdb=" O ASNAU 73 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LYSAU 78 " --> pdb=" O PHEAU 74 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASNAU 79 " --> pdb=" O LEUAU 75 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARGAU 80 " --> pdb=" O METAU 76 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 698 through 707 removed outlier: 3.519A pdb=" N ALAAZ 702 " --> pdb=" O ALAAZ 698 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 94 through 106 removed outlier: 4.272A pdb=" N ILEAa 100 " --> pdb=" O GLUAa 96 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 108 through 114 removed outlier: 4.629A pdb=" N LYSAa 114 " --> pdb=" O GLNAa 110 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 129 through 149 removed outlier: 3.828A pdb=" N VALAa 146 " --> pdb=" O GLUAa 142 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 207 through 219 removed outlier: 3.522A pdb=" N ARGAa 213 " --> pdb=" O GLUAa 209 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 233 through 244 Processing helix chain 'Aa' and resid 245 through 257 removed outlier: 3.544A pdb=" N ALAAa 255 " --> pdb=" O ASNAa 251 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 261 through 279 removed outlier: 4.076A pdb=" N ILEAa 265 " --> pdb=" O SERAa 261 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASPAa 276 " --> pdb=" O TYRAa 272 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 280 through 286 removed outlier: 4.269A pdb=" N LEUAa 284 " --> pdb=" O LYSAa 280 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARGAa 285 " --> pdb=" O TYRAa 281 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SERAa 286 " --> pdb=" O ASPAa 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 280 through 286' Processing helix chain 'Aa' and resid 289 through 301 removed outlier: 3.541A pdb=" N ASNAa 299 " --> pdb=" O TRPAa 295 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 303 through 314 removed outlier: 3.900A pdb=" N ASPAa 314 " --> pdb=" O GLNAa 310 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 315 through 331 removed outlier: 3.794A pdb=" N ALAAa 319 " --> pdb=" O LEUAa 315 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEUAa 322 " --> pdb=" O ASPAa 318 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HISAa 324 " --> pdb=" O THRAa 320 " (cutoff:3.500A) Proline residue: Aa 331 - end of helix Processing helix chain 'Aa' and resid 333 through 343 removed outlier: 3.562A pdb=" N ALAAa 339 " --> pdb=" O SERAa 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSAa 340 " --> pdb=" O ALAAa 336 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 345 through 357 removed outlier: 3.805A pdb=" N ILEAa 350 " --> pdb=" O GLYAa 346 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYSAa 351 " --> pdb=" O LEUAa 347 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 360 through 379 removed outlier: 4.250A pdb=" N THRAa 377 " --> pdb=" O GLUAa 373 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 11 through 23 removed outlier: 4.172A pdb=" N ASPAb 18 " --> pdb=" O SERAb 14 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEUAb 19 " --> pdb=" O ARGAb 15 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 29 through 39 removed outlier: 4.247A pdb=" N ASPAb 33 " --> pdb=" O PROAb 29 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILEAb 34 " --> pdb=" O LEUAb 30 " (cutoff:3.500A) Proline residue: Ab 39 - end of helix Processing helix chain 'Ab' and resid 65 through 78 removed outlier: 3.785A pdb=" N ARGAb 69 " --> pdb=" O TYRAb 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILEAb 70 " --> pdb=" O HISAb 66 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYSAb 73 " --> pdb=" O ARGAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 94 through 110 removed outlier: 3.718A pdb=" N ARGAb 108 " --> pdb=" O ILEAb 104 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEUAb 109 " --> pdb=" O GLUAb 105 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLYAb 110 " --> pdb=" O LEUAb 106 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 113 through 129 removed outlier: 3.565A pdb=" N GLUAb 120 " --> pdb=" O LYSAb 116 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALAAb 121 " --> pdb=" O LEUAb 117 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLYAb 122 " --> pdb=" O PHEAb 118 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEUAb 126 " --> pdb=" O GLYAb 122 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALAAb 127 " --> pdb=" O LYSAb 123 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLUAb 128 " --> pdb=" O ALAAb 124 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 7 through 12 removed outlier: 4.640A pdb=" N ARGAc 11 " --> pdb=" O PHEAc 7 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THRAc 12 " --> pdb=" O PROAc 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 7 through 12' Processing helix chain 'Ac' and resid 13 through 19 removed outlier: 3.816A pdb=" N GLYAc 19 " --> pdb=" O TYRAc 15 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 41 through 60 removed outlier: 4.326A pdb=" N ILEAc 52 " --> pdb=" O VALAc 48 " (cutoff:3.500A) Proline residue: Ac 53 - end of helix removed outlier: 3.753A pdb=" N LYSAc 58 " --> pdb=" O GLNAc 54 " (cutoff:3.500A) Proline residue: Ac 60 - end of helix Processing helix chain 'Ac' and resid 94 through 106 removed outlier: 3.590A pdb=" N ILEAc 98 " --> pdb=" O SERAc 94 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VALAc 99 " --> pdb=" O ASNAc 95 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 109 through 125 removed outlier: 3.508A pdb=" N GLUAc 116 " --> pdb=" O THRAc 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSAc 121 " --> pdb=" O GLUAc 117 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLNAc 122 " --> pdb=" O GLNAc 118 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEUAc 123 " --> pdb=" O GLUAc 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SERAc 124 " --> pdb=" O LYSAc 120 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N HISAc 125 " --> pdb=" O LYSAc 121 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 161 removed outlier: 3.507A pdb=" N THRAc 160 " --> pdb=" O PROAc 156 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLYAc 161 " --> pdb=" O LYSAc 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 156 through 161' Processing helix chain 'Ac' and resid 162 through 170 removed outlier: 3.795A pdb=" N ALAAc 169 " --> pdb=" O ALAAc 165 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THRAc 170 " --> pdb=" O ALAAc 166 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 35 through 42 removed outlier: 4.442A pdb=" N GLYAd 40 " --> pdb=" O LYSAd 36 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARGAd 41 " --> pdb=" O SERAd 37 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VALAd 42 " --> pdb=" O LYSAd 38 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 50 through 150 removed outlier: 3.934A pdb=" N VALAd 55 " --> pdb=" O THRAd 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARGAd 59 " --> pdb=" O VALAd 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRAd 66 " --> pdb=" O GLNAd 62 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VALAd 89 " --> pdb=" O ALAAd 85 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLNAd 90 " --> pdb=" O ARGAd 86 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALAAd 91 " --> pdb=" O ALAAd 87 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARGAd 93 " --> pdb=" O VALAd 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYSAd 94 " --> pdb=" O GLNAd 90 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALAAd 99 " --> pdb=" O ALAAd 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VALAd 140 " --> pdb=" O ALAAd 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLNAd 147 " --> pdb=" O ALAAd 143 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALAAd 148 " --> pdb=" O ARGAd 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRPAd 149 " --> pdb=" O GLUAd 145 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 156 through 161 Processing helix chain 'Ad' and resid 169 through 184 removed outlier: 5.045A pdb=" N GLUAd 174 " --> pdb=" O ARGAd 170 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALAAd 175 " --> pdb=" O GLUAd 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAd 178 " --> pdb=" O GLUAd 174 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASPAd 182 " --> pdb=" O GLUAd 178 " (cutoff:3.500A) Proline residue: Ad 184 - end of helix Processing helix chain 'Ae' and resid 68 through 75 removed outlier: 4.426A pdb=" N ALAAe 72 " --> pdb=" O CYSAe 68 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALAAe 73 " --> pdb=" O LEUAe 69 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALAe 75 " --> pdb=" O SERAe 71 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 84 removed outlier: 4.002A pdb=" N GLUAe 81 " --> pdb=" O SERAe 77 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALAAe 82 " --> pdb=" O HISAe 78 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARGAe 83 " --> pdb=" O LYSAe 79 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASPAe 84 " --> pdb=" O TRPAe 80 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 89 through 104 Processing helix chain 'Ae' and resid 108 through 119 removed outlier: 3.730A pdb=" N ILEAe 112 " --> pdb=" O SERAe 108 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHEAe 115 " --> pdb=" O THRAe 111 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASNAe 118 " --> pdb=" O ARGAe 114 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILEAe 119 " --> pdb=" O PHEAe 115 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 121 through 139 removed outlier: 3.837A pdb=" N HISAe 137 " --> pdb=" O TYRAe 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SERAe 138 " --> pdb=" O LYSAe 134 " (cutoff:3.500A) Proline residue: Ae 139 - end of helix Processing helix chain 'Ae' and resid 145 through 160 removed outlier: 3.915A pdb=" N ILEAe 149 " --> pdb=" O ARGAe 145 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYSAe 158 " --> pdb=" O ARGAe 154 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYRAe 159 " --> pdb=" O GLNAe 155 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLYAe 160 " --> pdb=" O CYSAe 156 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 161 through 172 removed outlier: 5.820A pdb=" N ALAAe 165 " --> pdb=" O ALAAe 161 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEUAe 166 " --> pdb=" O GLNAe 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THRAe 168 " --> pdb=" O LYSAe 164 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEUAe 169 " --> pdb=" O ALAAe 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASNAe 171 " --> pdb=" O TYRAe 167 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYSAe 172 " --> pdb=" O THRAe 168 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 181 through 195 removed outlier: 4.485A pdb=" N ASNAe 185 " --> pdb=" O ASNAe 181 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILEAe 192 " --> pdb=" O METAe 188 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYSAe 193 " --> pdb=" O ASPAe 189 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYSAe 194 " --> pdb=" O TYRAe 190 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 197 through 211 removed outlier: 4.011A pdb=" N LEUAe 201 " --> pdb=" O TYRAe 197 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SERAe 202 " --> pdb=" O LYSAe 198 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VALAe 203 " --> pdb=" O ASPAe 199 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VALAe 204 " --> pdb=" O ALAAe 200 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHEAe 205 " --> pdb=" O LEUAe 201 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 217 through 233 removed outlier: 3.670A pdb=" N TYRAe 224 " --> pdb=" O LEUAe 220 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEUAe 230 " --> pdb=" O LEUAe 226 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALAAe 231 " --> pdb=" O TYRAe 227 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYSAe 233 " --> pdb=" O CYSAe 229 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 237 through 251 removed outlier: 3.574A pdb=" N PHEAe 244 " --> pdb=" O GLUAe 240 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLYAe 245 " --> pdb=" O GLUAe 241 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEUAe 248 " --> pdb=" O PHEAe 244 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEUAe 249 " --> pdb=" O GLYAe 245 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEUAe 250 " --> pdb=" O ALAAe 246 " (cutoff:3.500A) Proline residue: Ae 251 - end of helix Processing helix chain 'Ae' and resid 257 through 278 removed outlier: 3.804A pdb=" N LEUAe 261 " --> pdb=" O ASNAe 257 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLNAe 264 " --> pdb=" O GLYAe 260 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEUAe 265 " --> pdb=" O LEUAe 261 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEUAe 270 " --> pdb=" O TYRAe 266 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYSAe 273 " --> pdb=" O ALAAe 269 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALAe 274 " --> pdb=" O LEUAe 270 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLUAe 275 " --> pdb=" O LEUAe 271 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEUAe 276 " --> pdb=" O GLYAe 272 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 279 through 287 removed outlier: 4.619A pdb=" N VALAe 283 " --> pdb=" O GLYAe 279 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYRAe 284 " --> pdb=" O LEUAe 280 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASNAe 286 " --> pdb=" O ALAAe 282 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N METAe 287 " --> pdb=" O VALAe 283 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 294 through 310 removed outlier: 4.355A pdb=" N ARGAe 298 " --> pdb=" O GLYAe 294 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N METAe 303 " --> pdb=" O ALAAe 299 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VALAe 306 " --> pdb=" O VALAe 302 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALAAe 307 " --> pdb=" O METAe 303 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SERAe 308 " --> pdb=" O GLUAe 304 " (cutoff:3.500A) Proline residue: Ae 310 - end of helix Processing helix chain 'Ae' and resid 313 through 335 removed outlier: 6.545A pdb=" N GLYAe 317 " --> pdb=" O GLYAe 313 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLUAe 318 " --> pdb=" O GLNAe 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALAAe 332 " --> pdb=" O LYSAe 328 " (cutoff:3.500A) Proline residue: Ae 333 - end of helix Processing helix chain 'Ae' and resid 345 through 353 removed outlier: 4.507A pdb=" N GLNAe 349 " --> pdb=" O GLYAe 345 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLUAe 352 " --> pdb=" O SERAe 348 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 363 through 386 removed outlier: 3.867A pdb=" N LYSAe 367 " --> pdb=" O THRAe 363 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEUAe 368 " --> pdb=" O GLUAe 364 " (cutoff:3.500A) Proline residue: Ae 369 - end of helix removed outlier: 3.790A pdb=" N SERAe 380 " --> pdb=" O GLUAe 376 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYSAe 381 " --> pdb=" O ALAAe 377 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLNAe 383 " --> pdb=" O ARGAe 379 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALAAe 384 " --> pdb=" O SERAe 380 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 403 through 452 removed outlier: 4.281A pdb=" N THRAe 407 " --> pdb=" O ALAAe 403 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAAe 410 " --> pdb=" O PROAe 406 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLUAe 411 " --> pdb=" O THRAe 407 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILEAe 413 " --> pdb=" O GLUAe 409 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALAAe 414 " --> pdb=" O ALAAe 410 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VALAe 415 " --> pdb=" O GLUAe 411 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLNAe 418 " --> pdb=" O ALAAe 414 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VALAe 428 " --> pdb=" O HISAe 424 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 337 through 343 removed outlier: 4.362A pdb=" N GLUAe 340 " --> pdb=" O THRAe 337 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLNAe 341 " --> pdb=" O SERAe 338 " (cutoff:3.500A) Proline residue: Ae 342 - end of helix No H-bonds generated for 'chain 'Ae' and resid 337 through 343' Processing helix chain 'B1' and resid 7 through 19 removed outlier: 3.873A pdb=" N TRPB1 11 " --> pdb=" O PROB1 7 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYSB1 12 " --> pdb=" O VALB1 8 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLNB1 13 " --> pdb=" O GLYB1 9 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLYB1 19 " --> pdb=" O ARGB1 15 " (cutoff:3.500A) Processing helix chain 'B1' and resid 25 through 35 removed outlier: 5.880A pdb=" N ALAB1 35 " --> pdb=" O SERB1 31 " (cutoff:3.500A) Processing helix chain 'B1' and resid 72 through 79 removed outlier: 3.956A pdb=" N GLNB1 76 " --> pdb=" O PROB1 72 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEUB1 77 " --> pdb=" O PROB1 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLYB1 78 " --> pdb=" O GLUB1 74 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEUB1 79 " --> pdb=" O SERB1 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 72 through 79' Processing helix chain 'B1' and resid 128 through 139 Processing helix chain 'B1' and resid 140 through 148 Processing helix chain 'B1' and resid 149 through 154 Processing helix chain 'B1' and resid 155 through 172 Processing helix chain 'B1' and resid 180 through 192 removed outlier: 3.589A pdb=" N ARGB1 190 " --> pdb=" O ALAB1 186 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYRB1 191 " --> pdb=" O ILEB1 187 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYSB1 192 " --> pdb=" O TYRB1 188 " (cutoff:3.500A) Processing helix chain 'B1' and resid 197 through 202 removed outlier: 4.207A pdb=" N GLUB1 202 " --> pdb=" O GLUB1 198 " (cutoff:3.500A) Processing helix chain 'B1' and resid 207 through 220 Processing helix chain 'B1' and resid 225 through 245 removed outlier: 3.808A pdb=" N ILEB1 229 " --> pdb=" O PROB1 225 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLUB1 245 " --> pdb=" O GLNB1 241 " (cutoff:3.500A) Processing helix chain 'Af' and resid 80 through 88 removed outlier: 3.507A pdb=" N METAf 84 " --> pdb=" O SERAf 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARGAf 86 " --> pdb=" O ALAAf 82 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HISAf 87 " --> pdb=" O SERAf 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SERAf 88 " --> pdb=" O METAf 84 " (cutoff:3.500A) Processing helix chain 'Af' and resid 89 through 94 Processing helix chain 'Af' and resid 131 through 136 removed outlier: 3.635A pdb=" N TYRAf 135 " --> pdb=" O GLYAf 132 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLNAf 136 " --> pdb=" O GLUAf 133 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 70 through 78 removed outlier: 3.676A pdb=" N LEUAg 74 " --> pdb=" O SERAg 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYSAg 75 " --> pdb=" O LEUAg 71 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THRAg 76 " --> pdb=" O GLNAg 72 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 83 through 94 removed outlier: 3.895A pdb=" N GLNAg 89 " --> pdb=" O ARGAg 85 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSAg 91 " --> pdb=" O ALAAg 87 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 101 through 114 removed outlier: 3.710A pdb=" N ASNAg 113 " --> pdb=" O HISAg 109 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 132 through 148 removed outlier: 3.666A pdb=" N SERAg 136 " --> pdb=" O GLYAg 132 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 156 through 162 removed outlier: 3.966A pdb=" N TRPAg 160 " --> pdb=" O ASPAg 156 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 179 through 195 removed outlier: 3.559A pdb=" N TRPAg 186 " --> pdb=" O GLUAg 182 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASNAg 189 " --> pdb=" O THRAg 185 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THRAg 192 " --> pdb=" O LYSAg 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASNAg 194 " --> pdb=" O PHEAg 190 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLUAg 195 " --> pdb=" O LYSAg 191 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 196 through 201 removed outlier: 4.450A pdb=" N GLNAg 200 " --> pdb=" O HISAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 220 through 232 removed outlier: 4.093A pdb=" N VALAg 224 " --> pdb=" O PROAg 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VALAg 225 " --> pdb=" O LEUAg 221 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLUAg 226 " --> pdb=" O GLYAg 222 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLYAg 228 " --> pdb=" O VALAg 224 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VALAg 232 " --> pdb=" O GLYAg 228 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 233 through 250 removed outlier: 5.745A pdb=" N ASPAg 237 " --> pdb=" O ARGAg 233 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLYAg 240 " --> pdb=" O THRAg 236 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYSAg 247 " --> pdb=" O LEUAg 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARGAg 248 " --> pdb=" O LYSAg 244 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 263 through 269 removed outlier: 4.597A pdb=" N LEUAg 267 " --> pdb=" O GLYAg 263 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TRPAg 268 " --> pdb=" O VALAg 264 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 286 through 298 removed outlier: 3.829A pdb=" N ASNAg 291 " --> pdb=" O ALAAg 287 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEUAg 292 " --> pdb=" O LEUAg 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYSAg 294 " --> pdb=" O HISAg 290 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N METAg 295 " --> pdb=" O ASNAg 291 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VALAg 296 " --> pdb=" O LEUAg 292 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYSAg 297 " --> pdb=" O ARGAg 293 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASNAg 298 " --> pdb=" O LYSAg 294 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 323 through 329 Processing helix chain 'Ag' and resid 330 through 336 removed outlier: 3.860A pdb=" N ASPAg 334 " --> pdb=" O LYSAg 330 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALAAg 335 " --> pdb=" O GLUAg 331 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUAg 336 " --> pdb=" O GLYAg 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 330 through 336' Processing helix chain 'Ag' and resid 348 through 363 removed outlier: 3.789A pdb=" N GLUAg 353 " --> pdb=" O PROAg 349 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 372 through 384 Processing helix chain 'Ag' and resid 386 through 397 removed outlier: 3.747A pdb=" N ALAAg 395 " --> pdb=" O GLUAg 391 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYRAg 396 " --> pdb=" O ARGAg 392 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEUAg 397 " --> pdb=" O LEUAg 393 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 268 through 283 removed outlier: 3.722A pdb=" N ILEAh 272 " --> pdb=" O SERAh 268 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALAh 281 " --> pdb=" O GLNAh 277 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 288 through 300 removed outlier: 3.572A pdb=" N TRPAh 296 " --> pdb=" O GLUAh 292 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 319 through 324 removed outlier: 3.619A pdb=" N HISAh 323 " --> pdb=" O GLUAh 319 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 326 through 331 removed outlier: 4.399A pdb=" N LEUAh 330 " --> pdb=" O LEUAh 326 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLNAh 331 " --> pdb=" O ASPAh 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 326 through 331' Processing helix chain 'Ah' and resid 337 through 354 removed outlier: 3.990A pdb=" N HISAh 341 " --> pdb=" O GLYAh 337 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEUAh 345 " --> pdb=" O HISAh 341 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VALAh 346 " --> pdb=" O PHEAh 342 " (cutoff:3.500A) Proline residue: Ah 354 - end of helix Processing helix chain 'Ah' and resid 357 through 376 removed outlier: 3.541A pdb=" N LYSAh 361 " --> pdb=" O SERAh 357 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARGAh 376 " --> pdb=" O PHEAh 372 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 377 through 383 removed outlier: 3.967A pdb=" N GLYAh 383 " --> pdb=" O LEUAh 379 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 5 through 20 Processing helix chain 'Ai' and resid 27 through 39 removed outlier: 3.849A pdb=" N METAi 31 " --> pdb=" O ASPAi 27 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYSAi 32 " --> pdb=" O SERAi 28 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VALAi 33 " --> pdb=" O LYSAi 29 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VALAi 34 " --> pdb=" O SERAi 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHEAi 37 " --> pdb=" O VALAi 33 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 45 through 51 removed outlier: 4.107A pdb=" N TRPAi 51 " --> pdb=" O GLUAi 47 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 54 through 69 Processing helix chain 'Ai' and resid 73 through 90 Processing helix chain 'Aj' and resid 9 through 26 removed outlier: 4.588A pdb=" N GLUAj 13 " --> pdb=" O ARGAj 9 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARGAj 16 " --> pdb=" O ALAAj 12 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 29 through 35 Processing helix chain 'Aj' and resid 51 through 61 removed outlier: 3.836A pdb=" N TRPAj 55 " --> pdb=" O PROAj 51 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALAAj 56 " --> pdb=" O METAj 52 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASPAj 57 " --> pdb=" O ARGAj 53 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARGAj 59 " --> pdb=" O TRPAj 55 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 63 through 71 removed outlier: 3.775A pdb=" N LEUAj 67 " --> pdb=" O ARGAj 63 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ARGAj 70 " --> pdb=" O GLNAj 66 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEUAj 71 " --> pdb=" O LEUAj 67 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 82 through 89 Processing helix chain 'Aj' and resid 143 through 152 removed outlier: 4.583A pdb=" N GLUAj 148 " --> pdb=" O LYSAj 144 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALAAj 149 " --> pdb=" O HISAj 145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THRAj 151 " --> pdb=" O GLUAj 147 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALAAj 152 " --> pdb=" O GLUAj 148 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 167 through 182 removed outlier: 3.622A pdb=" N ARGAj 178 " --> pdb=" O ILEAj 174 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLNAj 179 " --> pdb=" O LEUAj 175 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYSAj 180 " --> pdb=" O ALAAj 176 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYRAj 181 " --> pdb=" O GLNAj 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLYAj 182 " --> pdb=" O ARGAj 178 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 57 through 62 removed outlier: 4.689A pdb=" N LYSAk 61 " --> pdb=" O PROAk 57 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 67 through 73 removed outlier: 3.730A pdb=" N VALAk 71 " --> pdb=" O ASPAk 67 " (cutoff:3.500A) Proline residue: Ak 73 - end of helix Processing helix chain 'Ak' and resid 79 through 84 removed outlier: 3.894A pdb=" N VALAk 83 " --> pdb=" O LYSAk 79 " (cutoff:3.500A) Proline residue: Ak 84 - end of helix No H-bonds generated for 'chain 'Ak' and resid 79 through 84' Processing helix chain 'Ak' and resid 104 through 111 removed outlier: 3.563A pdb=" N LEUAk 108 " --> pdb=" O ASNAk 104 " (cutoff:3.500A) Proline residue: Ak 111 - end of helix Processing helix chain 'Ak' and resid 117 through 133 removed outlier: 3.925A pdb=" N ALAAk 127 " --> pdb=" O ARGAk 123 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYSAk 129 " --> pdb=" O CYSAk 125 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASPAk 130 " --> pdb=" O GLUAk 126 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHEAk 131 " --> pdb=" O ALAAk 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYSAk 132 " --> pdb=" O LEUAk 128 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N THRAk 133 " --> pdb=" O LYSAk 129 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 141 through 149 Processing helix chain 'Ak' and resid 178 through 183 removed outlier: 4.384A pdb=" N LEUAk 182 " --> pdb=" O LYSAk 178 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASNAk 183 " --> pdb=" O LEUAk 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 178 through 183' Processing helix chain 'Ak' and resid 185 through 197 removed outlier: 3.603A pdb=" N LYSAk 194 " --> pdb=" O LYSAk 190 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 216 through 238 removed outlier: 4.382A pdb=" N TRPAk 236 " --> pdb=" O TYRAk 232 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYSAk 237 " --> pdb=" O HISAk 233 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N THRAk 238 " --> pdb=" O GLUAk 234 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 239 through 245 removed outlier: 4.463A pdb=" N LYSAk 243 " --> pdb=" O GLUAk 239 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYSAk 244 " --> pdb=" O GLUAk 240 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYSAk 245 " --> pdb=" O TRPAk 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 239 through 245' Processing helix chain 'Ak' and resid 246 through 251 removed outlier: 3.742A pdb=" N METAk 250 " --> pdb=" O THRAk 246 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLUAk 251 " --> pdb=" O GLUAk 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 246 through 251' Processing helix chain 'Ak' and resid 258 through 276 removed outlier: 3.605A pdb=" N LEUAk 269 " --> pdb=" O LEUAk 265 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLNAk 270 " --> pdb=" O GLUAk 266 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 281 through 288 removed outlier: 4.422A pdb=" N THRAk 288 " --> pdb=" O GLUAk 284 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 289 through 304 removed outlier: 3.730A pdb=" N VALAk 299 " --> pdb=" O ARGAk 295 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SERAk 300 " --> pdb=" O LYSAk 296 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 307 through 323 removed outlier: 3.897A pdb=" N SERAk 312 " --> pdb=" O GLUAk 308 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 167 through 172 removed outlier: 3.752A pdb=" N ARGAk 171 " --> pdb=" O PROAk 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VALAk 172 " --> pdb=" O LYSAk 169 " (cutoff:3.500A) Processing helix chain 'Am' and resid 45 through 60 removed outlier: 3.752A pdb=" N CYSAm 55 " --> pdb=" O VALAm 51 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRPAm 56 " --> pdb=" O METAm 52 " (cutoff:3.500A) Processing helix chain 'Am' and resid 62 through 67 removed outlier: 4.545A pdb=" N CYSAm 66 " --> pdb=" O ARGAm 62 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARGAm 67 " --> pdb=" O ASPAm 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Am' and resid 62 through 67' Processing helix chain 'Am' and resid 68 through 91 removed outlier: 4.001A pdb=" N PHEAm 73 " --> pdb=" O GLUAm 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHEAm 74 " --> pdb=" O ILEAm 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSAm 85 " --> pdb=" O GLUAm 81 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SERAm 88 " --> pdb=" O ARGAm 84 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILEAm 89 " --> pdb=" O LYSAm 85 " (cutoff:3.500A) Processing helix chain 'Am' and resid 100 through 112 removed outlier: 4.063A pdb=" N LYSAm 106 " --> pdb=" O LYSAm 102 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHEAm 111 " --> pdb=" O LEUAm 107 " (cutoff:3.500A) Proline residue: Am 112 - end of helix Processing helix chain 'An' and resid 128 through 151 removed outlier: 4.335A pdb=" N LYSAn 132 " --> pdb=" O LYSAn 128 " (cutoff:3.500A) Processing helix chain 'An' and resid 152 through 181 removed outlier: 3.644A pdb=" N ILEAn 176 " --> pdb=" O ASPAn 172 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRPAn 177 " --> pdb=" O LEUAn 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLNAn 178 " --> pdb=" O LYSAn 174 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 68 through 79 removed outlier: 3.745A pdb=" N THRAo 77 " --> pdb=" O ALAAo 73 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VALAo 78 " --> pdb=" O LEUAo 74 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HISAo 79 " --> pdb=" O ALAAo 75 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 99 through 125 removed outlier: 3.731A pdb=" N LEUAo 107 " --> pdb=" O SERAo 103 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEUAo 108 " --> pdb=" O HISAo 104 " (cutoff:3.500A) Proline residue: Ao 125 - end of helix Processing helix chain 'Ao' and resid 137 through 142 removed outlier: 4.350A pdb=" N METAo 141 " --> pdb=" O ILEAo 137 " (cutoff:3.500A) Proline residue: Ao 142 - end of helix No H-bonds generated for 'chain 'Ao' and resid 137 through 142' Processing helix chain 'Ao' and resid 152 through 163 removed outlier: 3.839A pdb=" N GLNAo 158 " --> pdb=" O GLUAo 154 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLUAo 159 " --> pdb=" O ALAAo 155 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYSAo 162 " --> pdb=" O GLNAo 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEUAo 163 " --> pdb=" O GLUAo 159 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 201 through 215 removed outlier: 4.196A pdb=" N GLUAo 214 " --> pdb=" O SERAo 210 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLUAo 215 " --> pdb=" O GLUAo 211 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 219 through 234 removed outlier: 3.843A pdb=" N LYSAo 223 " --> pdb=" O ALAAo 219 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SERAo 224 " --> pdb=" O ASPAo 220 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYSAo 225 " --> pdb=" O ASNAo 221 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HISAo 230 " --> pdb=" O THRAo 226 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLYAo 233 " --> pdb=" O GLYAo 229 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 240 through 252 removed outlier: 3.758A pdb=" N PHEAo 251 " --> pdb=" O ALAAo 247 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 257 through 273 removed outlier: 4.422A pdb=" N CYSAo 263 " --> pdb=" O ALAAo 259 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THRAo 264 " --> pdb=" O HISAo 260 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARGAo 267 " --> pdb=" O CYSAo 263 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VALAo 270 " --> pdb=" O ILEAo 266 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYSAo 271 " --> pdb=" O ARGAo 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HISAo 272 " --> pdb=" O GLYAo 268 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 274 through 289 removed outlier: 4.319A pdb=" N ALAAo 278 " --> pdb=" O ALAAo 274 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUAo 279 " --> pdb=" O PROAo 275 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASNAo 280 " --> pdb=" O THRAo 276 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUAo 281 " --> pdb=" O GLNAo 277 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYRAo 282 " --> pdb=" O ALAAo 278 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THRAo 283 " --> pdb=" O LEUAo 279 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 293 through 308 removed outlier: 3.849A pdb=" N PHEAo 297 " --> pdb=" O ASPAo 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SERAo 299 " --> pdb=" O TYRAo 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILEAo 301 " --> pdb=" O PHEAo 297 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLUAo 302 " --> pdb=" O ASNAo 298 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VALAo 307 " --> pdb=" O ALAAo 303 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VALAo 308 " --> pdb=" O THRAo 304 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 311 through 330 removed outlier: 5.404A pdb=" N LYSAo 315 " --> pdb=" O LYSAo 311 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRPAo 316 " --> pdb=" O PHEAo 312 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASNAo 330 " --> pdb=" O METAo 326 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 334 through 349 removed outlier: 3.671A pdb=" N ILEAo 341 " --> pdb=" O THRAo 337 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUAo 342 " --> pdb=" O PHEAo 338 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEUAo 345 " --> pdb=" O ILEAo 341 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARGAo 346 " --> pdb=" O LEUAo 342 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARGAo 347 " --> pdb=" O LYSAo 343 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHEAo 348 " --> pdb=" O CYSAo 344 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYRAo 349 " --> pdb=" O LEUAo 345 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 352 through 367 removed outlier: 3.548A pdb=" N ALAAo 356 " --> pdb=" O GLYAo 352 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLYAo 367 " --> pdb=" O METAo 363 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 371 through 387 removed outlier: 3.782A pdb=" N TYRAo 375 " --> pdb=" O SERAo 371 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYRAo 377 " --> pdb=" O ALAAo 373 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALAo 378 " --> pdb=" O THRAo 374 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SERAo 387 " --> pdb=" O TYRAo 383 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 390 through 405 removed outlier: 4.689A pdb=" N LEUAo 394 " --> pdb=" O LYSAo 390 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILEAo 395 " --> pdb=" O GLYAo 391 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLYAo 405 " --> pdb=" O ASNAo 401 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 415 through 430 removed outlier: 5.383A pdb=" N PHEAo 419 " --> pdb=" O ASPAo 415 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLNAo 420 " --> pdb=" O ASPAo 416 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYSAo 426 " --> pdb=" O ALAAo 422 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 431 through 446 removed outlier: 3.900A pdb=" N GLNAo 437 " --> pdb=" O GLUAo 433 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASNAo 443 " --> pdb=" O HISAo 439 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THRAo 444 " --> pdb=" O GLYAo 440 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLYAo 445 " --> pdb=" O LEUAo 441 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASPAo 446 " --> pdb=" O LEUAo 442 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 453 through 471 removed outlier: 3.796A pdb=" N ARGAo 457 " --> pdb=" O SERAo 453 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHEAo 459 " --> pdb=" O HISAo 455 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEUAo 467 " --> pdb=" O LYSAo 463 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHEAo 470 " --> pdb=" O ASNAo 466 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 473 through 485 removed outlier: 3.595A pdb=" N LYSAo 482 " --> pdb=" O LEUAo 478 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASPAo 483 " --> pdb=" O LYSAo 479 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 492 through 507 removed outlier: 3.724A pdb=" N METAo 496 " --> pdb=" O HISAo 492 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILEAo 497 " --> pdb=" O SERAo 493 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALAAo 506 " --> pdb=" O ALAAo 502 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASNAo 507 " --> pdb=" O LEUAo 503 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 509 through 523 Proline residue: Ao 513 - end of helix removed outlier: 3.979A pdb=" N ASPAo 518 " --> pdb=" O GLNAo 514 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLUAo 521 " --> pdb=" O LYSAo 517 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 526 through 542 removed outlier: 5.812A pdb=" N GLUAo 532 " --> pdb=" O ASNAo 528 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLUAo 533 " --> pdb=" O GLUAo 529 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILEAo 534 " --> pdb=" O LEUAo 530 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEUAo 535 " --> pdb=" O LYSAo 531 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N METAo 536 " --> pdb=" O GLUAo 532 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEUAo 537 " --> pdb=" O GLUAo 533 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N METAo 538 " --> pdb=" O ILEAo 534 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALAAo 539 " --> pdb=" O LEUAo 535 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARGAo 540 " --> pdb=" O METAo 536 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASPAo 541 " --> pdb=" O LEUAo 537 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLNAo 542 " --> pdb=" O METAo 538 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 547 through 565 removed outlier: 3.698A pdb=" N ALAAo 555 " --> pdb=" O PHEAo 551 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILEAo 558 " --> pdb=" O CYSAo 554 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THRAo 561 " --> pdb=" O ASPAo 557 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYRAo 562 " --> pdb=" O ILEAo 558 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLUAo 563 " --> pdb=" O LYSAo 559 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SERAo 564 " --> pdb=" O SERAo 560 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLNAo 565 " --> pdb=" O THRAo 561 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 575 through 590 removed outlier: 4.403A pdb=" N LEUAo 579 " --> pdb=" O PROAo 575 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASNAo 580 " --> pdb=" O ALAAo 576 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHEAo 586 " --> pdb=" O VALAo 582 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARGAo 588 " --> pdb=" O VALAo 584 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALAAo 589 " --> pdb=" O LEUAo 585 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 591 through 606 removed outlier: 3.786A pdb=" N ALAAo 595 " --> pdb=" O ARGAo 591 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYSAo 597 " --> pdb=" O GLNAo 593 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N METAo 598 " --> pdb=" O GLUAo 594 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEUAo 599 " --> pdb=" O ALAAo 595 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARGAo 603 " --> pdb=" O LEUAo 599 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYSAo 604 " --> pdb=" O GLYAo 600 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HISAo 605 " --> pdb=" O LEUAo 601 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASNAo 606 " --> pdb=" O PHEAo 602 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 610 through 625 removed outlier: 4.018A pdb=" N LEUAo 614 " --> pdb=" O ARGAo 610 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 626 through 641 removed outlier: 4.516A pdb=" N ALAAo 630 " --> pdb=" O SERAo 626 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILEAo 631 " --> pdb=" O PROAo 627 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLUAo 632 " --> pdb=" O ALAAo 628 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSAo 635 " --> pdb=" O ILEAo 631 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHEAo 640 " --> pdb=" O LEUAo 636 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 644 through 660 removed outlier: 3.554A pdb=" N METAo 653 " --> pdb=" O THRAo 649 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 661 through 674 removed outlier: 4.032A pdb=" N SERAo 674 " --> pdb=" O THRAo 670 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 54 through 61 removed outlier: 4.353A pdb=" N TYRAp 58 " --> pdb=" O GLUAp 54 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEUAp 59 " --> pdb=" O PROAp 55 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASPAp 60 " --> pdb=" O TRPAp 56 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 62 through 68 removed outlier: 4.023A pdb=" N ARGAp 67 " --> pdb=" O GLUAp 63 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 105 through 111 removed outlier: 4.520A pdb=" N ASPAp 110 " --> pdb=" O PROAp 106 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLNAp 111 " --> pdb=" O ILEAp 107 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 119 through 128 removed outlier: 3.757A pdb=" N LEUAp 123 " --> pdb=" O ASNAp 119 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLNAp 125 " --> pdb=" O LYSAp 121 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHEAp 126 " --> pdb=" O LEUAp 122 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VALAp 127 " --> pdb=" O LEUAp 123 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYSAp 128 " --> pdb=" O GLUAp 124 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 136 through 141 Processing helix chain 'Ap' and resid 143 through 161 removed outlier: 3.645A pdb=" N LYSAp 149 " --> pdb=" O LYSAp 145 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 190 through 196 removed outlier: 3.572A pdb=" N GLYAp 196 " --> pdb=" O THRAp 192 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 209 through 221 removed outlier: 3.624A pdb=" N GLNAp 221 " --> pdb=" O ARGAp 217 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 200 through 205 removed outlier: 3.550A pdb=" N SERAp 204 " --> pdb=" O PROAp 201 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TRPAp 205 " --> pdb=" O TRPAp 202 " (cutoff:3.500A) Processing helix chain 'CL' and resid 61 through 75 removed outlier: 3.717A pdb=" N GLNCL 65 " --> pdb=" O PROCL 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEUCL 74 " --> pdb=" O ASPCL 70 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THRCL 75 " --> pdb=" O ILECL 71 " (cutoff:3.500A) Processing helix chain 'CL' and resid 76 through 90 Processing helix chain 'DL' and resid 64 through 74 removed outlier: 3.843A pdb=" N VALDL 68 " --> pdb=" O ILEDL 64 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALADL 72 " --> pdb=" O VALDL 68 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SERDL 73 " --> pdb=" O GLNDL 69 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEUDL 74 " --> pdb=" O ASPDL 70 " (cutoff:3.500A) Processing helix chain 'DL' and resid 75 through 90 removed outlier: 3.574A pdb=" N LYSDL 88 " --> pdb=" O GLUDL 84 " (cutoff:3.500A) Processing helix chain 'FL' and resid 64 through 74 removed outlier: 3.617A pdb=" N ASPFL 70 " --> pdb=" O GLNFL 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILEFL 71 " --> pdb=" O LEUFL 67 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SERFL 73 " --> pdb=" O GLNFL 69 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEUFL 74 " --> pdb=" O ASPFL 70 " (cutoff:3.500A) Processing helix chain 'FL' and resid 75 through 90 Processing helix chain 'GL' and resid 64 through 74 removed outlier: 4.124A pdb=" N LEUGL 74 " --> pdb=" O ASPGL 70 " (cutoff:3.500A) Processing helix chain 'GL' and resid 75 through 90 removed outlier: 3.972A pdb=" N LEUGL 90 " --> pdb=" O LEUGL 86 " (cutoff:3.500A) Processing helix chain 'EL' and resid 64 through 75 removed outlier: 4.365A pdb=" N VALEL 68 " --> pdb=" O ILEEL 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEUEL 74 " --> pdb=" O ASPEL 70 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THREL 75 " --> pdb=" O ILEEL 71 " (cutoff:3.500A) Processing helix chain 'EL' and resid 76 through 90 Processing helix chain 'HL' and resid 64 through 75 removed outlier: 3.751A pdb=" N LEUHL 74 " --> pdb=" O ASPHL 70 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THRHL 75 " --> pdb=" O ILEHL 71 " (cutoff:3.500A) Processing helix chain 'HL' and resid 76 through 89 removed outlier: 3.937A pdb=" N THRHL 89 " --> pdb=" O LEUHL 85 " (cutoff:3.500A) Processing helix chain 'LL' and resid 141 through 154 removed outlier: 3.808A pdb=" N GLNLL 154 " --> pdb=" O LYSLL 150 " (cutoff:3.500A) Processing helix chain 'LL' and resid 157 through 168 removed outlier: 3.760A pdb=" N LEULL 168 " --> pdb=" O LEULL 164 " (cutoff:3.500A) Processing helix chain 'LL' and resid 177 through 192 removed outlier: 3.575A pdb=" N VALLL 191 " --> pdb=" O ALALL 187 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLYLL 192 " --> pdb=" O LEULL 188 " (cutoff:3.500A) Processing helix chain 'B2' and resid 72 through 77 removed outlier: 3.600A pdb=" N TRPB2 76 " --> pdb=" O ASPB2 72 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLYB2 77 " --> pdb=" O PROB2 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 72 through 77' Processing helix chain 'B2' and resid 88 through 96 removed outlier: 3.871A pdb=" N LYSB2 95 " --> pdb=" O GLNB2 91 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SERB2 96 " --> pdb=" O LEUB2 92 " (cutoff:3.500A) Processing helix chain 'B2' and resid 97 through 125 removed outlier: 3.733A pdb=" N TYRB2 105 " --> pdb=" O HISB2 101 " (cutoff:3.500A) Processing helix chain 'B2' and resid 131 through 160 removed outlier: 3.946A pdb=" N GLUB2 135 " --> pdb=" O PROB2 131 " (cutoff:3.500A) Processing helix chain 'B2' and resid 193 through 199 removed outlier: 3.672A pdb=" N ARGB2 198 " --> pdb=" O LYSB2 194 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYSB2 199 " --> pdb=" O LYSB2 195 " (cutoff:3.500A) Processing helix chain 'B2' and resid 206 through 241 removed outlier: 4.517A pdb=" N PHEB2 210 " --> pdb=" O TYRB2 206 " (cutoff:3.500A) Proline residue: B2 241 - end of helix Processing helix chain 'B2' and resid 65 through 70 removed outlier: 3.950A pdb=" N GLUB2 68 " --> pdb=" O GLYB2 65 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHEB2 69 " --> pdb=" O LEUB2 66 " (cutoff:3.500A) Processing helix chain 'B3' and resid 42 through 48 removed outlier: 4.363A pdb=" N PHEB3 46 " --> pdb=" O PROB3 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLNB3 47 " --> pdb=" O ASPB3 43 " (cutoff:3.500A) Proline residue: B3 48 - end of helix No H-bonds generated for 'chain 'B3' and resid 42 through 48' Processing helix chain 'B3' and resid 49 through 57 removed outlier: 3.870A pdb=" N HISB3 53 " --> pdb=" O SERB3 49 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLUB3 54 " --> pdb=" O PROB3 50 " (cutoff:3.500A) Processing helix chain 'B3' and resid 79 through 90 removed outlier: 4.015A pdb=" N GLYB3 90 " --> pdb=" O ILEB3 86 " (cutoff:3.500A) Processing helix chain 'B3' and resid 103 through 114 removed outlier: 3.947A pdb=" N LYSB3 109 " --> pdb=" O SERB3 105 " (cutoff:3.500A) Processing helix chain 'B3' and resid 130 through 135 removed outlier: 3.565A pdb=" N METB3 134 " --> pdb=" O THRB3 130 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALAB3 135 " --> pdb=" O GLUB3 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 130 through 135' Processing helix chain 'B4' and resid 85 through 96 Processing helix chain 'B5' and resid 86 through 96 removed outlier: 4.282A pdb=" N ASNB5 96 " --> pdb=" O CYSB5 92 " (cutoff:3.500A) Processing helix chain 'B5' and resid 123 through 146 removed outlier: 3.621A pdb=" N GLUB5 145 " --> pdb=" O METB5 141 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLYB5 146 " --> pdb=" O GLYB5 142 " (cutoff:3.500A) Processing helix chain 'B7' and resid 59 through 67 Processing helix chain 'B7' and resid 68 through 76 removed outlier: 4.184A pdb=" N THRB7 75 " --> pdb=" O ARGB7 71 " (cutoff:3.500A) Proline residue: B7 76 - end of helix Processing helix chain 'B7' and resid 77 through 89 Processing helix chain 'B8' and resid 107 through 114 removed outlier: 4.164A pdb=" N ILEB8 111 " --> pdb=" O VALB8 107 " (cutoff:3.500A) Processing helix chain 'B8' and resid 132 through 137 removed outlier: 3.879A pdb=" N LYSB8 136 " --> pdb=" O LYSB8 132 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THRB8 137 " --> pdb=" O LEUB8 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B8' and resid 132 through 137' Processing helix chain 'B8' and resid 138 through 147 removed outlier: 5.622A pdb=" N PHEB8 147 " --> pdb=" O ARGB8 143 " (cutoff:3.500A) Processing helix chain 'B8' and resid 151 through 163 removed outlier: 5.080A pdb=" N THRB8 163 " --> pdb=" O ASPB8 159 " (cutoff:3.500A) Processing helix chain 'B8' and resid 177 through 182 removed outlier: 4.802A pdb=" N ASPB8 182 " --> pdb=" O GLNB8 178 " (cutoff:3.500A) Processing helix chain 'BC' and resid 42 through 47 removed outlier: 4.123A pdb=" N ILEBC 46 " --> pdb=" O PROBC 42 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARGBC 47 " --> pdb=" O ASNBC 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 42 through 47' Processing helix chain 'BC' and resid 58 through 71 removed outlier: 3.930A pdb=" N GLYBC 71 " --> pdb=" O LEUBC 67 " (cutoff:3.500A) Processing helix chain 'BC' and resid 92 through 99 Processing helix chain 'BC' and resid 127 through 139 removed outlier: 4.012A pdb=" N VALBC 137 " --> pdb=" O ARGBC 133 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEUBC 138 " --> pdb=" O ALABC 134 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASPBC 139 " --> pdb=" O LEUBC 135 " (cutoff:3.500A) Processing helix chain 'BC' and resid 152 through 166 removed outlier: 3.649A pdb=" N METBC 156 " --> pdb=" O GLNBC 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYRBC 165 " --> pdb=" O GLNBC 161 " (cutoff:3.500A) Processing helix chain 'BC' and resid 182 through 193 Processing helix chain 'BC' and resid 239 through 261 removed outlier: 4.293A pdb=" N ALABC 244 " --> pdb=" O ALABC 240 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALABC 245 " --> pdb=" O GLUBC 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASNBC 259 " --> pdb=" O GLUBC 255 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SERBC 260 " --> pdb=" O CYSBC 256 " (cutoff:3.500A) Processing helix chain 'BC' and resid 262 through 271 removed outlier: 4.109A pdb=" N GLUBC 270 " --> pdb=" O GLUBC 266 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLUBC 271 " --> pdb=" O METBC 267 " (cutoff:3.500A) Processing helix chain 'BC' and resid 275 through 290 Processing helix chain 'BC' and resid 305 through 316 removed outlier: 4.176A pdb=" N LEUBC 309 " --> pdb=" O GLYBC 305 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEUBC 314 " --> pdb=" O LEUBC 310 " (cutoff:3.500A) Processing helix chain 'BC' and resid 319 through 324 removed outlier: 3.927A pdb=" N VALBC 323 " --> pdb=" O ASNBC 319 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLNBC 324 " --> pdb=" O PROBC 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 319 through 324' Processing helix chain 'BC' and resid 462 through 478 removed outlier: 3.770A pdb=" N ARGBC 475 " --> pdb=" O GLYBC 471 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLUBC 476 " --> pdb=" O ARGBC 472 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASPBC 477 " --> pdb=" O PHEBC 473 " (cutoff:3.500A) Proline residue: BC 478 - end of helix Processing helix chain 'BC' and resid 497 through 512 Processing helix chain 'BC' and resid 579 through 595 removed outlier: 3.688A pdb=" N VALBC 583 " --> pdb=" O PROBC 579 " (cutoff:3.500A) Proline residue: BC 584 - end of helix removed outlier: 3.513A pdb=" N CYSBC 594 " --> pdb=" O PHEBC 590 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLUBC 595 " --> pdb=" O LEUBC 591 " (cutoff:3.500A) Processing helix chain 'BC' and resid 622 through 641 removed outlier: 3.626A pdb=" N ALABC 637 " --> pdb=" O ALABC 633 " (cutoff:3.500A) Processing helix chain 'BC' and resid 657 through 672 removed outlier: 3.906A pdb=" N GLNBC 661 " --> pdb=" O PROBC 657 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLYBC 662 " --> pdb=" O ASNBC 658 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLNBC 663 " --> pdb=" O GLUBC 659 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HISBC 672 " --> pdb=" O ILEBC 668 " (cutoff:3.500A) Processing helix chain 'BC' and resid 692 through 697 removed outlier: 3.867A pdb=" N PHEBC 697 " --> pdb=" O LEUBC 693 " (cutoff:3.500A) Processing helix chain 'BC' and resid 698 through 708 removed outlier: 4.074A pdb=" N GLUBC 702 " --> pdb=" O GLYBC 698 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARGBC 704 " --> pdb=" O SERBC 700 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SERBC 705 " --> pdb=" O THRBC 701 " (cutoff:3.500A) Processing helix chain 'BC' and resid 724 through 740 Processing helix chain 'BD' and resid 184 through 189 removed outlier: 3.698A pdb=" N LEUBD 188 " --> pdb=" O PROBD 184 " (cutoff:3.500A) Proline residue: BD 189 - end of helix No H-bonds generated for 'chain 'BD' and resid 184 through 189' Processing helix chain 'BD' and resid 260 through 268 removed outlier: 4.378A pdb=" N ASNBD 264 " --> pdb=" O LYSBD 260 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARGBD 265 " --> pdb=" O ALABD 261 " (cutoff:3.500A) Processing helix chain 'BE' and resid 48 through 53 removed outlier: 4.571A pdb=" N HISBE 52 " --> pdb=" O TRPBE 48 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEUBE 53 " --> pdb=" O TRPBE 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 48 through 53' Processing helix chain 'BE' and resid 54 through 83 Proline residue: BE 59 - end of helix removed outlier: 3.512A pdb=" N GLUBE 68 " --> pdb=" O LEUBE 64 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYSBE 78 " --> pdb=" O ALABE 74 " (cutoff:3.500A) Proline residue: BE 79 - end of helix removed outlier: 4.050A pdb=" N ASPBE 82 " --> pdb=" O CYSBE 78 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLUBE 83 " --> pdb=" O PROBE 79 " (cutoff:3.500A) Processing helix chain 'BE' and resid 134 through 139 Processing helix chain 'BE' and resid 153 through 158 removed outlier: 4.352A pdb=" N LYSBE 157 " --> pdb=" O SERBE 153 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SERBE 158 " --> pdb=" O HISBE 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 153 through 158' Processing helix chain 'BE' and resid 159 through 169 Processing helix chain 'BE' and resid 217 through 222 Processing helix chain 'BE' and resid 320 through 325 removed outlier: 4.141A pdb=" N ASPBE 324 " --> pdb=" O PHEBE 320 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLUBE 325 " --> pdb=" O PROBE 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 320 through 325' Processing helix chain 'BE' and resid 194 through 199 removed outlier: 3.735A pdb=" N PHEBE 198 " --> pdb=" O ALABE 195 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARGBE 199 " --> pdb=" O ALABE 196 " (cutoff:3.500A) Processing helix chain 'BF' and resid 92 through 109 removed outlier: 4.912A pdb=" N LYSBF 107 " --> pdb=" O GLNBF 103 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARGBF 108 " --> pdb=" O LYSBF 104 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILEBF 109 " --> pdb=" O ASNBF 105 " (cutoff:3.500A) Processing helix chain 'BF' and resid 166 through 185 removed outlier: 3.584A pdb=" N GLNBF 172 " --> pdb=" O LYSBF 168 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASPBF 185 " --> pdb=" O LYSBF 181 " (cutoff:3.500A) Processing helix chain 'BF' and resid 199 through 211 removed outlier: 3.943A pdb=" N LEUBF 203 " --> pdb=" O ASPBF 199 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILEBF 204 " --> pdb=" O PROBF 200 " (cutoff:3.500A) Processing helix chain 'BF' and resid 227 through 238 removed outlier: 4.175A pdb=" N GLYBF 236 " --> pdb=" O ALABF 232 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEUBF 237 " --> pdb=" O ALABF 233 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYSBF 238 " --> pdb=" O THRBF 234 " (cutoff:3.500A) Processing helix chain 'BF' and resid 249 through 257 removed outlier: 5.081A pdb=" N GLNBF 257 " --> pdb=" O METBF 253 " (cutoff:3.500A) Processing helix chain 'BF' and resid 262 through 279 removed outlier: 3.557A pdb=" N TRPBF 275 " --> pdb=" O GLUBF 271 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HISBF 276 " --> pdb=" O LYSBF 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASNBF 277 " --> pdb=" O LEUBF 273 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SERBF 278 " --> pdb=" O LEUBF 274 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARGBF 279 " --> pdb=" O TRPBF 275 " (cutoff:3.500A) Processing helix chain 'BF' and resid 84 through 89 Processing helix chain 'BI' and resid 74 through 79 removed outlier: 4.136A pdb=" N ARGBI 78 " --> pdb=" O HISBI 74 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VALBI 79 " --> pdb=" O ARGBI 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'BI' and resid 74 through 79' Processing helix chain 'BI' and resid 85 through 90 removed outlier: 3.511A pdb=" N ARGBI 89 " --> pdb=" O ASPBI 85 " (cutoff:3.500A) Proline residue: BI 90 - end of helix No H-bonds generated for 'chain 'BI' and resid 85 through 90' Processing helix chain 'BI' and resid 115 through 122 Processing helix chain 'BI' and resid 133 through 150 removed outlier: 4.071A pdb=" N LEUBI 139 " --> pdb=" O GLUBI 135 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLUBI 149 " --> pdb=" O LEUBI 145 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLYBI 150 " --> pdb=" O LEUBI 146 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 41 through 52 Processing helix chain 'BJ' and resid 76 through 92 Processing helix chain 'BJ' and resid 105 through 120 removed outlier: 3.989A pdb=" N HISBJ 119 " --> pdb=" O GLNBJ 115 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 127 through 139 Proline residue: BJ 133 - end of helix removed outlier: 4.662A pdb=" N LYSBJ 139 " --> pdb=" O LEUBJ 135 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 143 through 148 removed outlier: 3.666A pdb=" N PHEBJ 147 " --> pdb=" O LEUBJ 143 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VALBJ 148 " --> pdb=" O LEUBJ 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 143 through 148' Processing helix chain 'BJ' and resid 160 through 172 removed outlier: 4.024A pdb=" N METBJ 164 " --> pdb=" O LYSBJ 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLYBJ 170 " --> pdb=" O ARGBJ 166 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILEBJ 171 " --> pdb=" O ILEBJ 167 " (cutoff:3.500A) Proline residue: BJ 172 - end of helix Processing helix chain 'BJ' and resid 187 through 198 Proline residue: BJ 198 - end of helix Processing helix chain 'BJ' and resid 199 through 225 removed outlier: 3.729A pdb=" N VALBJ 208 " --> pdb=" O GLNBJ 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLYBJ 209 " --> pdb=" O GLYBJ 205 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEUBJ 214 " --> pdb=" O GLYBJ 210 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THRBJ 215 " --> pdb=" O LEUBJ 211 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLNBJ 225 " --> pdb=" O METBJ 221 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 226 through 240 removed outlier: 3.605A pdb=" N THRBJ 230 " --> pdb=" O PROBJ 226 " (cutoff:3.500A) Processing helix chain 'BK' and resid 33 through 43 Proline residue: BK 37 - end of helix Processing helix chain 'BK' and resid 45 through 58 removed outlier: 3.680A pdb=" N PHEBK 49 " --> pdb=" O SERBK 45 " (cutoff:3.500A) Processing helix chain 'BK' and resid 86 through 96 Processing helix chain 'BK' and resid 113 through 126 removed outlier: 4.710A pdb=" N GLNBK 126 " --> pdb=" O ARGBK 122 " (cutoff:3.500A) Processing helix chain 'BK' and resid 127 through 134 removed outlier: 4.914A pdb=" N ASPBK 134 " --> pdb=" O PHEBK 130 " (cutoff:3.500A) Processing helix chain 'BK' and resid 136 through 152 removed outlier: 3.855A pdb=" N VALBK 140 " --> pdb=" O PROBK 136 " (cutoff:3.500A) Processing helix chain 'BK' and resid 162 through 192 removed outlier: 3.895A pdb=" N GLUBK 170 " --> pdb=" O ALABK 166 " (cutoff:3.500A) Processing helix chain 'BN' and resid 5 through 15 Processing helix chain 'BN' and resid 27 through 41 removed outlier: 3.773A pdb=" N METBN 34 " --> pdb=" O LYSBN 30 " (cutoff:3.500A) Processing helix chain 'BN' and resid 70 through 75 Processing helix chain 'BN' and resid 91 through 99 Processing helix chain 'BN' and resid 100 through 113 removed outlier: 4.786A pdb=" N VALBN 104 " --> pdb=" O PROBN 100 " (cutoff:3.500A) Proline residue: BN 113 - end of helix Processing helix chain 'BN' and resid 115 through 126 removed outlier: 4.908A pdb=" N ARGBN 119 " --> pdb=" O ASNBN 115 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THRBN 120 " --> pdb=" O LEUBN 116 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARGBN 124 " --> pdb=" O THRBN 120 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEUBN 125 " --> pdb=" O METBN 121 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HISBN 126 " --> pdb=" O METBN 122 " (cutoff:3.500A) Processing helix chain 'BN' and resid 134 through 141 removed outlier: 4.353A pdb=" N ASNBN 140 " --> pdb=" O ASPBN 136 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEUBN 141 " --> pdb=" O ILEBN 137 " (cutoff:3.500A) Processing helix chain 'BN' and resid 159 through 167 Proline residue: BN 167 - end of helix Processing helix chain 'BO' and resid 44 through 49 Processing helix chain 'BO' and resid 124 through 131 removed outlier: 4.731A pdb=" N ARGBO 128 " --> pdb=" O PROBO 124 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLNBO 129 " --> pdb=" O SERBO 125 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARGBO 130 " --> pdb=" O SERBO 126 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLUBO 131 " --> pdb=" O LEUBO 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'BO' and resid 124 through 131' Processing helix chain 'BO' and resid 134 through 142 removed outlier: 3.852A pdb=" N ILEBO 140 " --> pdb=" O LYSBO 136 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALABO 141 " --> pdb=" O VALBO 137 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLNBO 142 " --> pdb=" O LEUBO 138 " (cutoff:3.500A) Processing helix chain 'BP' and resid 10 through 20 removed outlier: 4.059A pdb=" N ASPBP 14 " --> pdb=" O PROBP 10 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARGBP 17 " --> pdb=" O LEUBP 13 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALABP 18 " --> pdb=" O ASPBP 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEUBP 19 " --> pdb=" O LEUBP 15 " (cutoff:3.500A) Proline residue: BP 20 - end of helix Processing helix chain 'BP' and resid 55 through 60 Processing helix chain 'BP' and resid 73 through 78 removed outlier: 3.705A pdb=" N ILEBP 78 " --> pdb=" O PHEBP 74 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 108 Processing helix chain 'BP' and resid 117 through 125 Processing helix chain 'BP' and resid 160 through 171 removed outlier: 3.645A pdb=" N ASNBP 170 " --> pdb=" O ALABP 166 " (cutoff:3.500A) Processing helix chain 'BP' and resid 180 through 190 Proline residue: BP 190 - end of helix Processing helix chain 'BP' and resid 191 through 197 removed outlier: 3.611A pdb=" N ARGBP 196 " --> pdb=" O PROBP 192 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLYBP 197 " --> pdb=" O PHEBP 193 " (cutoff:3.500A) Processing helix chain 'BP' and resid 207 through 216 Proline residue: BP 212 - end of helix removed outlier: 3.504A pdb=" N ASPBP 216 " --> pdb=" O PROBP 212 " (cutoff:3.500A) Processing helix chain 'BP' and resid 225 through 241 removed outlier: 3.965A pdb=" N PHEBP 229 " --> pdb=" O ASPBP 225 " (cutoff:3.500A) Proline residue: BP 230 - end of helix Processing helix chain 'BP' and resid 246 through 251 removed outlier: 4.142A pdb=" N ASPBP 250 " --> pdb=" O ASPBP 246 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLUBP 251 " --> pdb=" O ILEBP 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 246 through 251' Processing helix chain 'BP' and resid 252 through 258 Processing helix chain 'BP' and resid 287 through 296 Processing helix chain 'BQ' and resid 69 through 74 removed outlier: 5.466A pdb=" N GLYBQ 74 " --> pdb=" O SERBQ 70 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 98 through 113 Processing helix chain 'BQ' and resid 170 through 184 removed outlier: 4.461A pdb=" N LEUBQ 178 " --> pdb=" O GLYBQ 174 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VALBQ 179 " --> pdb=" O PHEBQ 175 " (cutoff:3.500A) Proline residue: BQ 184 - end of helix Processing helix chain 'BQ' and resid 191 through 209 Processing helix chain 'BQ' and resid 214 through 222 Processing helix chain 'BQ' and resid 225 through 231 removed outlier: 4.697A pdb=" N VALBQ 229 " --> pdb=" O GLYBQ 225 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SERBQ 231 " --> pdb=" O ARGBQ 227 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 232 through 238 removed outlier: 4.486A pdb=" N THRBQ 236 " --> pdb=" O PROBQ 232 " (cutoff:3.500A) Processing helix chain 'BR' and resid 21 through 40 Processing helix chain 'BR' and resid 46 through 66 removed outlier: 4.397A pdb=" N GLYBR 54 " --> pdb=" O ASPBR 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYRBR 55 " --> pdb=" O GLUBR 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEUBR 65 " --> pdb=" O ASPBR 61 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLYBR 66 " --> pdb=" O TYRBR 62 " (cutoff:3.500A) Processing helix chain 'BR' and resid 69 through 80 Processing helix chain 'BR' and resid 82 through 98 removed outlier: 4.434A pdb=" N ILEBR 86 " --> pdb=" O GLUBR 82 " (cutoff:3.500A) Proline residue: BR 87 - end of helix removed outlier: 3.849A pdb=" N LEUBR 93 " --> pdb=" O LEUBR 89 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALABR 94 " --> pdb=" O PHEBR 90 " (cutoff:3.500A) Proline residue: BR 95 - end of helix removed outlier: 4.311A pdb=" N GLNBR 98 " --> pdb=" O ALABR 94 " (cutoff:3.500A) Processing helix chain 'BR' and resid 144 through 161 removed outlier: 3.642A pdb=" N SERBR 161 " --> pdb=" O GLNBR 157 " (cutoff:3.500A) Processing helix chain 'BS' and resid 52 through 60 removed outlier: 4.681A pdb=" N LEUBS 56 " --> pdb=" O ASNBS 52 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLUBS 57 " --> pdb=" O PROBS 53 " (cutoff:3.500A) Processing helix chain 'BS' and resid 109 through 116 removed outlier: 3.532A pdb=" N HISBS 115 " --> pdb=" O ALABS 111 " (cutoff:3.500A) Processing helix chain 'BS' and resid 121 through 140 Processing helix chain 'BS' and resid 149 through 156 removed outlier: 4.156A pdb=" N ALABS 154 " --> pdb=" O PROBS 150 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SERBS 155 " --> pdb=" O TRPBS 151 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASPBS 156 " --> pdb=" O GLUBS 152 " (cutoff:3.500A) Processing helix chain 'BS' and resid 157 through 169 removed outlier: 3.727A pdb=" N GLYBS 169 " --> pdb=" O METBS 165 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'AI' and resid 270 through 276 removed outlier: 3.941A pdb=" N HISAI 327 " --> pdb=" O SERAI 291 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARGAI 293 " --> pdb=" O HISAI 327 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BT' and resid 129 through 135 removed outlier: 4.653A pdb=" N LYSBT 129 " --> pdb=" O ASPBT 123 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILEBT 116 " --> pdb=" O VALBT 177 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLUBT 173 " --> pdb=" O THRBT 120 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'BT' and resid 139 through 142 removed outlier: 3.906A pdb=" N GLNBT 139 " --> pdb=" O ILEBT 150 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALABT 147 " --> pdb=" O LEUBT 166 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'BV' and resid 109 through 113 removed outlier: 7.256A pdb=" N LEUBV 138 " --> pdb=" O GLYBV 149 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHEBV 145 " --> pdb=" O ALABV 142 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'BV' and resid 115 through 121 removed outlier: 6.515A pdb=" N VALBV 196 " --> pdb=" O ILEBV 165 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLUBV 161 " --> pdb=" O ASNBV 200 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VALBV 160 " --> pdb=" O LEUBV 134 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLUBV 130 " --> pdb=" O VALBV 164 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'BV' and resid 166 through 169 removed outlier: 3.801A pdb=" N GLUBV 166 " --> pdb=" O VALBV 196 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'BV' and resid 172 through 179 removed outlier: 4.569A pdb=" N TYRBV 184 " --> pdb=" O GLNBV 179 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'BW' and resid 69 through 76 removed outlier: 4.629A pdb=" N ALABW 69 " --> pdb=" O GLUBW 178 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYSBW 175 " --> pdb=" O ALABW 141 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'BW' and resid 142 through 148 removed outlier: 3.653A pdb=" N GLUBW 142 " --> pdb=" O LYSBW 175 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHEBW 169 " --> pdb=" O GLYBW 148 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'BW' and resid 150 through 157 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'BX' and resid 26 through 29 removed outlier: 4.420A pdb=" N GLNBX 41 " --> pdb=" O VALBX 29 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYSBX 93 " --> pdb=" O ILEBX 44 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYSBX 88 " --> pdb=" O ASNBX 77 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASNBX 77 " --> pdb=" O LYSBX 88 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLYBX 75 " --> pdb=" O PROBX 90 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'BY' and resid 61 through 64 removed outlier: 4.401A pdb=" N LYSBY 72 " --> pdb=" O ILEBY 64 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'BY' and resid 92 through 97 removed outlier: 5.574A pdb=" N ASNBY 92 " --> pdb=" O ALABY 113 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'Ba' and resid 126 through 130 removed outlier: 5.201A pdb=" N LEUBa 351 " --> pdb=" O ASPBa 348 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ARGBa 200 " --> pdb=" O LYSBa 233 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'Ba' and resid 208 through 214 removed outlier: 5.129A pdb=" N LEUBa 219 " --> pdb=" O ALABa 103 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Ba' and resid 230 through 233 removed outlier: 6.885A pdb=" N LEUBa 230 " --> pdb=" O HISBa 289 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Bb' and resid 183 through 187 removed outlier: 6.091A pdb=" N ASPBb 183 " --> pdb=" O VALBb 179 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VALBb 175 " --> pdb=" O VALBb 187 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'Bb' and resid 231 through 234 removed outlier: 6.665A pdb=" N LEUBb 218 " --> pdb=" O HISBb 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRPBb 235 " --> pdb=" O LEUBb 218 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Bb' and resid 311 through 314 removed outlier: 6.594A pdb=" N LEUBb 272 " --> pdb=" O ALABb 314 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Bb' and resid 213 through 221 removed outlier: 3.569A pdb=" N LEUBb 213 " --> pdb=" O GLNBb 275 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARGBb 267 " --> pdb=" O LEUBb 221 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Bc' and resid 74 through 80 removed outlier: 4.352A pdb=" N THRBc 74 " --> pdb=" O HISBc 66 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLUBc 60 " --> pdb=" O LYSBc 80 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYSBc 120 " --> pdb=" O GLUBc 63 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHEBc 124 " --> pdb=" O VALBc 67 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Bc' and resid 160 through 164 removed outlier: 7.006A pdb=" N VALBc 160 " --> pdb=" O ASPBc 183 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASPBc 179 " --> pdb=" O VALBc 164 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLNBc 294 " --> pdb=" O SERBc 278 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Bc' and resid 214 through 218 Processing sheet with id= 24, first strand: chain 'Bc' and resid 279 through 284 removed outlier: 3.543A pdb=" N ALABc 279 " --> pdb=" O GLNBc 294 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Be' and resid 40 through 43 removed outlier: 5.602A pdb=" N LYSBe 47 " --> pdb=" O GLYBe 43 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Bf' and resid 44 through 52 removed outlier: 4.774A pdb=" N ASNBf 44 " --> pdb=" O VALBf 65 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THRBf 57 " --> pdb=" O THRBf 52 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Bg' and resid 61 through 68 removed outlier: 4.309A pdb=" N ALABg 83 " --> pdb=" O TYRBg 79 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Bh' and resid 254 through 257 removed outlier: 3.561A pdb=" N VALBh 269 " --> pdb=" O SERBh 261 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARGBh 259 " --> pdb=" O PHEBh 271 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Bh' and resid 269 through 275 removed outlier: 3.778A pdb=" N ALABh 282 " --> pdb=" O LEUBh 274 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Bi' and resid 192 through 195 removed outlier: 6.869A pdb=" N THRBi 213 " --> pdb=" O VALBi 195 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLNBi 196 " --> pdb=" O THRBi 213 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Bi' and resid 262 through 266 Processing sheet with id= 32, first strand: chain 'Bi' and resid 208 through 219 removed outlier: 6.907A pdb=" N ILEBi 208 " --> pdb=" O LEUBi 252 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Bj' and resid 174 through 177 removed outlier: 3.825A pdb=" N GLYBj 49 " --> pdb=" O SERBj 176 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N LEUBj 51 " --> pdb=" O VALBj 161 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VALBj 161 " --> pdb=" O LEUBj 51 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEUBj 53 " --> pdb=" O LEUBj 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUBj 159 " --> pdb=" O LEUBj 53 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARGBj 155 " --> pdb=" O PROBj 57 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N HISBj 251 " --> pdb=" O ARGBj 162 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Bj' and resid 211 through 217 removed outlier: 5.455A pdb=" N LEUBj 227 " --> pdb=" O PHEBj 217 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASNBj 199 " --> pdb=" O ASPBj 242 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASPBj 242 " --> pdb=" O ASNBj 199 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Bj' and resid 44 through 55 Processing sheet with id= 36, first strand: chain 'Bk' and resid 78 through 82 removed outlier: 7.385A pdb=" N ARGBk 78 " --> pdb=" O GLYBk 89 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLYBk 89 " --> pdb=" O ARGBk 78 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEUBk 82 " --> pdb=" O ASPBk 85 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASPBk 85 " --> pdb=" O LEUBk 82 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THRBk 152 " --> pdb=" O THRBk 129 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THRBk 129 " --> pdb=" O THRBk 152 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLUBk 154 " --> pdb=" O METBk 127 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Bk' and resid 91 through 97 Processing sheet with id= 38, first strand: chain 'Bl' and resid 95 through 101 removed outlier: 5.277A pdb=" N VALBl 137 " --> pdb=" O LYSBl 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Bp' and resid 49 through 56 Processing sheet with id= 40, first strand: chain 'Bu' and resid 78 through 85 removed outlier: 3.646A pdb=" N GLYBu 85 " --> pdb=" O LYSBu 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSBu 93 " --> pdb=" O GLYBu 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B0' and resid 75 through 78 removed outlier: 6.300A pdb=" N VALB0 133 " --> pdb=" O GLYB0 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B0' and resid 80 through 84 removed outlier: 7.907A pdb=" N HISB0 80 " --> pdb=" O LEUB0 92 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYSB0 88 " --> pdb=" O GLYB0 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Bw' and resid 90 through 93 removed outlier: 4.184A pdb=" N ASNBw 228 " --> pdb=" O VALBw 93 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARGBw 219 " --> pdb=" O ILEBw 210 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILEBw 210 " --> pdb=" O ARGBw 219 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASPBw 221 " --> pdb=" O GLUBw 208 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLUBw 208 " --> pdb=" O ASPBw 221 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEUBw 223 " --> pdb=" O ARGBw 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGBw 198 " --> pdb=" O PROBw 231 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Bw' and resid 112 through 116 Processing sheet with id= 45, first strand: chain 'Bw' and resid 291 through 296 removed outlier: 4.376A pdb=" N TYRBw 360 " --> pdb=" O ASPBw 357 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Bx' and resid 35 through 42 removed outlier: 3.592A pdb=" N PHEBx 35 " --> pdb=" O THRBx 54 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'AB' and resid 163 through 167 removed outlier: 3.817A pdb=" N LEUAB 195 " --> pdb=" O VALAB 144 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'AC' and resid 69 through 72 removed outlier: 5.634A pdb=" N LEUAC 69 " --> pdb=" O LEUAC 108 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'AE' and resid 219 through 223 removed outlier: 6.433A pdb=" N LEUAE 244 " --> pdb=" O LEUAE 223 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'AE' and resid 293 through 297 removed outlier: 3.644A pdb=" N TYRAE 333 " --> pdb=" O LYSAE 306 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'AE' and resid 240 through 248 Processing sheet with id= 52, first strand: chain 'AF' and resid 38 through 42 removed outlier: 3.636A pdb=" N ASPAF 67 " --> pdb=" O ASNAF 38 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYRAF 63 " --> pdb=" O LEUAF 42 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHEAF 68 " --> pdb=" O TYRAF 4 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILEAF 9 " --> pdb=" O ARGAF 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARGAF 90 " --> pdb=" O ILEAF 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'AG' and resid 156 through 162 Processing sheet with id= 54, first strand: chain 'AJ' and resid 110 through 121 removed outlier: 5.568A pdb=" N GLUAJ 110 " --> pdb=" O CYSAJ 142 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYSAJ 142 " --> pdb=" O GLUAJ 110 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYRAJ 140 " --> pdb=" O PROAJ 112 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARGAJ 75 " --> pdb=" O THRAJ 175 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'AK' and resid 97 through 103 Processing sheet with id= 56, first strand: chain 'AL' and resid 57 through 61 Processing sheet with id= 57, first strand: chain 'AL' and resid 63 through 69 removed outlier: 5.051A pdb=" N LYSAL 79 " --> pdb=" O ILEAL 95 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'AP' and resid 19 through 25 removed outlier: 4.440A pdb=" N PHEAP 31 " --> pdb=" O GLYAP 24 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYRAP 32 " --> pdb=" O SERAP 53 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SERAP 53 " --> pdb=" O TYRAP 32 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILEAP 34 " --> pdb=" O LEUAP 51 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'AQ' and resid 12 through 16 Processing sheet with id= 60, first strand: chain 'AQ' and resid 24 through 36 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'Aa' and resid 177 through 182 removed outlier: 3.531A pdb=" N ASPAa 182 " --> pdb=" O PHEAa 193 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHEAa 193 " --> pdb=" O ASPAa 182 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THRAa 202 " --> pdb=" O GLUAa 198 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Ac' and resid 62 through 68 removed outlier: 3.510A pdb=" N VALAc 29 " --> pdb=" O TYRAc 79 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'B1' and resid 49 through 53 removed outlier: 5.166A pdb=" N LYSB1 49 " --> pdb=" O VALB1 62 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLNB1 58 " --> pdb=" O ASNB1 53 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'B1' and resid 85 through 91 Processing sheet with id= 65, first strand: chain 'Af' and resid 100 through 105 removed outlier: 4.293A pdb=" N THRAf 139 " --> pdb=" O ILEAf 105 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Af' and resid 112 through 116 Processing sheet with id= 67, first strand: chain 'Af' and resid 150 through 153 removed outlier: 6.904A pdb=" N LEUAf 150 " --> pdb=" O ILEAf 163 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SERAf 152 " --> pdb=" O THRAf 161 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Ag' and resid 122 through 127 Processing sheet with id= 69, first strand: chain 'Ag' and resid 149 through 154 removed outlier: 3.900A pdb=" N ASPAg 262 " --> pdb=" O ILEAg 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VALAg 261 " --> pdb=" O VALAg 306 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THRAg 308 " --> pdb=" O VALAg 261 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Ag' and resid 168 through 171 removed outlier: 4.096A pdb=" N LEUAg 168 " --> pdb=" O ASPAg 178 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASPAg 178 " --> pdb=" O LEUAg 168 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Aj' and resid 41 through 44 removed outlier: 7.254A pdb=" N METAj 41 " --> pdb=" O LEUAj 50 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASNAj 48 " --> pdb=" O ARGAj 43 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Aj' and resid 77 through 81 removed outlier: 4.102A pdb=" N ARGAj 78 " --> pdb=" O LEUAj 97 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Aj' and resid 99 through 103 removed outlier: 4.060A pdb=" N ARGAj 99 " --> pdb=" O TRPAj 115 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N HISAj 111 " --> pdb=" O ASPAj 103 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Aj' and resid 162 through 165 removed outlier: 6.588A pdb=" N LEUAj 162 " --> pdb=" O LEUAj 193 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Ak' and resid 151 through 155 removed outlier: 5.418A pdb=" N ARGAk 199 " --> pdb=" O THRAk 208 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LL' and resid 169 through 172 removed outlier: 7.054A pdb=" N VALLL 132 " --> pdb=" O ILELL 172 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THRLL 194 " --> pdb=" O THRLL 135 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'B2' and resid 167 through 172 Processing sheet with id= 78, first strand: chain 'B3' and resid 97 through 101 removed outlier: 5.212A pdb=" N LEUB3 66 " --> pdb=" O LEUB3 122 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEUB3 116 " --> pdb=" O ILEB3 72 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'B3' and resid 137 through 140 removed outlier: 4.106A pdb=" N GLUB3 144 " --> pdb=" O LYSB3 140 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'B4' and resid 64 through 68 Processing sheet with id= 81, first strand: chain 'B5' and resid 155 through 160 Processing sheet with id= 82, first strand: chain 'B6' and resid 28 through 33 removed outlier: 6.036A pdb=" N PHEB6 28 " --> pdb=" O SERB6 22 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEUB6 17 " --> pdb=" O ILEB6 62 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'B6' and resid 41 through 46 removed outlier: 6.389A pdb=" N LEUB6 41 " --> pdb=" O GLUB6 58 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'B9' and resid 63 through 67 removed outlier: 5.910A pdb=" N HISB9 95 " --> pdb=" O CYSB9 89 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N CYSB9 89 " --> pdb=" O HISB9 95 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRPB9 85 " --> pdb=" O GLNB9 99 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'BC' and resid 104 through 110 removed outlier: 5.640A pdb=" N ALABC 53 " --> pdb=" O THRBC 121 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLYBC 140 " --> pdb=" O ASNBC 48 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'BC' and resid 201 through 205 removed outlier: 8.017A pdb=" N METBC 201 " --> pdb=" O LEUBC 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLYBC 213 " --> pdb=" O METBC 205 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARGBC 221 " --> pdb=" O ASPBC 216 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILEBC 232 " --> pdb=" O ASPBC 226 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'BC' and resid 359 through 362 removed outlier: 3.760A pdb=" N LYSBC 359 " --> pdb=" O TYRBC 370 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYRBC 370 " --> pdb=" O PHEBC 358 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHEBC 353 " --> pdb=" O ASPBC 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASPBC 433 " --> pdb=" O PHEBC 353 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASPBC 429 " --> pdb=" O ALABC 357 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THRBC 430 " --> pdb=" O THRBC 387 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASPBC 382 " --> pdb=" O LEUBC 395 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYSBC 391 " --> pdb=" O ASNBC 386 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'BC' and resid 480 through 486 removed outlier: 3.946A pdb=" N GLUBC 490 " --> pdb=" O ASPBC 485 " (cutoff:3.500A) removed outlier: 15.317A pdb=" N LYSBC 489 " --> pdb=" O PROBC 457 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THRBC 491 " --> pdb=" O METBC 455 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N METBC 455 " --> pdb=" O THRBC 491 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'BC' and resid 532 through 542 removed outlier: 4.760A pdb=" N GLNBC 548 " --> pdb=" O LYSBC 541 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'BC' and resid 566 through 572 removed outlier: 3.898A pdb=" N LEUBC 607 " --> pdb=" O LYSBC 566 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'BC' and resid 677 through 681 removed outlier: 3.583A pdb=" N GLYBC 677 " --> pdb=" O TYRBC 688 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N THRBC 686 " --> pdb=" O ASPBC 679 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYRBC 684 " --> pdb=" O VALBC 681 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'BC' and resid 369 through 372 Processing sheet with id= 93, first strand: chain 'BD' and resid 129 through 132 removed outlier: 3.629A pdb=" N ALABD 129 " --> pdb=" O LEUBD 142 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEUBD 142 " --> pdb=" O ILEBD 128 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASPBD 162 " --> pdb=" O VALBD 127 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLYBD 180 " --> pdb=" O THRBD 163 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEUBD 165 " --> pdb=" O GLYBD 180 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'BD' and resid 192 through 195 removed outlier: 4.291A pdb=" N THRBD 192 " --> pdb=" O LEUBD 217 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILEBD 226 " --> pdb=" O LEUBD 218 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARGBD 233 " --> pdb=" O LEUBD 229 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEUBD 238 " --> pdb=" O TYRBD 296 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'BD' and resid 140 through 145 Processing sheet with id= 96, first strand: chain 'BE' and resid 98 through 101 Processing sheet with id= 97, first strand: chain 'BE' and resid 105 through 111 removed outlier: 3.839A pdb=" N GLYBE 105 " --> pdb=" O LEUBE 121 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLNBE 115 " --> pdb=" O THRBE 111 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASNBE 281 " --> pdb=" O VALBE 124 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'BE' and resid 126 through 130 removed outlier: 6.750A pdb=" N ASPBE 126 " --> pdb=" O LYSBE 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYSBE 150 " --> pdb=" O ASPBE 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HISBE 128 " --> pdb=" O GLYBE 148 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THRBE 146 " --> pdb=" O LEUBE 130 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYSBE 175 " --> pdb=" O GLYBE 149 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'BE' and resid 201 through 205 removed outlier: 4.017A pdb=" N GLNBE 202 " --> pdb=" O VALBE 273 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'BF' and resid 47 through 50 removed outlier: 3.870A pdb=" N VALBF 47 " --> pdb=" O VALBF 77 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'BF' and resid 186 through 189 Processing sheet with id=102, first strand: chain 'BI' and resid 55 through 58 removed outlier: 7.141A pdb=" N ILEBI 55 " --> pdb=" O VALBI 83 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'BI' and resid 94 through 98 removed outlier: 4.204A pdb=" N ASPBI 110 " --> pdb=" O LEUBI 98 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'BJ' and resid 121 through 125 removed outlier: 5.470A pdb=" N HISBJ 150 " --> pdb=" O HISBJ 101 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HISBJ 101 " --> pdb=" O HISBJ 150 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'BK' and resid 18 through 23 removed outlier: 3.978A pdb=" N THRBK 77 " --> pdb=" O LYSBK 73 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'BN' and resid 55 through 60 removed outlier: 3.772A pdb=" N GLUBN 143 " --> pdb=" O TRPBN 18 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASPBN 22 " --> pdb=" O LEUBN 145 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'BN' and resid 77 through 81 removed outlier: 7.324A pdb=" N GLYBN 86 " --> pdb=" O THRBN 81 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'BO' and resid 38 through 41 Processing sheet with id=109, first strand: chain 'BO' and resid 72 through 76 Processing sheet with id=110, first strand: chain 'BP' and resid 93 through 96 Processing sheet with id=111, first strand: chain 'BP' and resid 273 through 277 Processing sheet with id=112, first strand: chain 'BQ' and resid 93 through 96 No H-bonds generated for sheet with id=112 Processing sheet with id=113, first strand: chain 'BQ' and resid 118 through 122 removed outlier: 4.329A pdb=" N VALBQ 161 " --> pdb=" O ILEBQ 89 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILEBQ 89 " --> pdb=" O ILEBQ 160 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARGBQ 158 " --> pdb=" O ALABQ 91 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'BQ' and resid 131 through 134 removed outlier: 6.862A pdb=" N ILEBQ 131 " --> pdb=" O ASPBQ 148 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'BQ' and resid 88 through 92 Processing sheet with id=116, first strand: chain 'BR' and resid 41 through 45 removed outlier: 4.637A pdb=" N METBR 121 " --> pdb=" O ILEBR 110 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYRBR 104 " --> pdb=" O LYSBR 127 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'BS' and resid 80 through 85 removed outlier: 6.377A pdb=" N ILEBS 90 " --> pdb=" O THRBS 107 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VALBS 103 " --> pdb=" O VALBS 94 " (cutoff:3.500A) 4909 hydrogen bonds defined for protein. 14613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1803 hydrogen bonds 3152 hydrogen bond angles 0 basepair planarities 742 basepair parallelities 1311 stacking parallelities Total time for adding SS restraints: 122.26 Time building geometry restraints manager: 65.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 49463 1.34 - 1.46: 58466 1.46 - 1.59: 76019 1.59 - 1.71: 5437 1.71 - 1.83: 819 Bond restraints: 190204 Sorted by residual: bond pdb=" N3B GNPBC 802 " pdb=" PG GNPBC 802 " ideal model delta sigma weight residual 1.801 1.707 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O5' GNPBC 802 " pdb=" PA GNPBC 802 " ideal model delta sigma weight residual 1.660 1.574 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" SD FMEAV 101 " pdb=" CE FMEAV 101 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" CG FMEAV 101 " pdb=" SD FMEAV 101 " ideal model delta sigma weight residual 1.817 1.772 0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" O3A GNPBC 802 " pdb=" PB GNPBC 802 " ideal model delta sigma weight residual 1.687 1.643 0.044 2.00e-02 2.50e+03 4.78e+00 ... (remaining 190199 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.66: 20504 106.66 - 113.51: 106623 113.51 - 120.37: 72804 120.37 - 127.22: 62856 127.22 - 134.07: 7396 Bond angle restraints: 270183 Sorted by residual: angle pdb=" N PROBf 80 " pdb=" CA PROBf 80 " pdb=" CB PROBf 80 " ideal model delta sigma weight residual 103.25 111.14 -7.89 1.05e+00 9.07e-01 5.65e+01 angle pdb=" N PROAe 342 " pdb=" CA PROAe 342 " pdb=" CB PROAe 342 " ideal model delta sigma weight residual 103.25 111.08 -7.83 1.05e+00 9.07e-01 5.57e+01 angle pdb=" N PROBf 78 " pdb=" CA PROBf 78 " pdb=" CB PROBf 78 " ideal model delta sigma weight residual 103.25 110.98 -7.73 1.05e+00 9.07e-01 5.41e+01 angle pdb=" N PROBu 167 " pdb=" CA PROBu 167 " pdb=" CB PROBu 167 " ideal model delta sigma weight residual 103.25 110.97 -7.72 1.05e+00 9.07e-01 5.40e+01 angle pdb=" N PROBq 59 " pdb=" CA PROBq 59 " pdb=" CB PROBq 59 " ideal model delta sigma weight residual 103.25 110.29 -7.04 1.05e+00 9.07e-01 4.50e+01 ... (remaining 270178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 107151 35.94 - 71.88: 2131 71.88 - 107.82: 252 107.82 - 143.77: 20 143.77 - 179.71: 38 Dihedral angle restraints: 109592 sinusoidal: 65404 harmonic: 44188 Sorted by residual: dihedral pdb=" O4' UBA1536 " pdb=" C1' UBA1536 " pdb=" N1 UBA1536 " pdb=" C2 UBA1536 " ideal model delta sinusoidal sigma weight residual 200.00 26.90 173.10 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' UBA 831 " pdb=" C1' UBA 831 " pdb=" N1 UBA 831 " pdb=" C2 UBA 831 " ideal model delta sinusoidal sigma weight residual 200.00 30.52 169.48 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' CBA 238 " pdb=" C1' CBA 238 " pdb=" N1 CBA 238 " pdb=" C2 CBA 238 " ideal model delta sinusoidal sigma weight residual 200.00 34.97 165.03 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 109589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 28308 0.050 - 0.099: 2973 0.099 - 0.149: 530 0.149 - 0.199: 20 0.199 - 0.249: 3 Chirality restraints: 31834 Sorted by residual: chirality pdb=" CA PROBu 167 " pdb=" N PROBu 167 " pdb=" C PROBu 167 " pdb=" CB PROBu 167 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PROB4 87 " pdb=" N PROB4 87 " pdb=" C PROB4 87 " pdb=" CB PROB4 87 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' AAY 14 " pdb=" O4' AAY 14 " pdb=" C2' AAY 14 " pdb=" N9 AAY 14 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 31831 not shown) Planarity restraints: 24650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ABA 130 " -0.035 2.00e-02 2.50e+03 1.60e-02 7.05e+00 pdb=" N9 ABA 130 " 0.038 2.00e-02 2.50e+03 pdb=" C8 ABA 130 " 0.005 2.00e-02 2.50e+03 pdb=" N7 ABA 130 " -0.003 2.00e-02 2.50e+03 pdb=" C5 ABA 130 " -0.002 2.00e-02 2.50e+03 pdb=" C6 ABA 130 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ABA 130 " -0.008 2.00e-02 2.50e+03 pdb=" N1 ABA 130 " -0.000 2.00e-02 2.50e+03 pdb=" C2 ABA 130 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ABA 130 " 0.005 2.00e-02 2.50e+03 pdb=" C4 ABA 130 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ABA 50 " -0.034 2.00e-02 2.50e+03 1.53e-02 6.44e+00 pdb=" N9 ABA 50 " 0.035 2.00e-02 2.50e+03 pdb=" C8 ABA 50 " 0.005 2.00e-02 2.50e+03 pdb=" N7 ABA 50 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ABA 50 " -0.002 2.00e-02 2.50e+03 pdb=" C6 ABA 50 " -0.004 2.00e-02 2.50e+03 pdb=" N6 ABA 50 " -0.009 2.00e-02 2.50e+03 pdb=" N1 ABA 50 " -0.002 2.00e-02 2.50e+03 pdb=" C2 ABA 50 " 0.004 2.00e-02 2.50e+03 pdb=" N3 ABA 50 " 0.004 2.00e-02 2.50e+03 pdb=" C4 ABA 50 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ABA1463 " -0.032 2.00e-02 2.50e+03 1.50e-02 6.20e+00 pdb=" N9 ABA1463 " 0.036 2.00e-02 2.50e+03 pdb=" C8 ABA1463 " 0.002 2.00e-02 2.50e+03 pdb=" N7 ABA1463 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ABA1463 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ABA1463 " -0.000 2.00e-02 2.50e+03 pdb=" N6 ABA1463 " -0.007 2.00e-02 2.50e+03 pdb=" N1 ABA1463 " -0.003 2.00e-02 2.50e+03 pdb=" C2 ABA1463 " 0.002 2.00e-02 2.50e+03 pdb=" N3 ABA1463 " 0.006 2.00e-02 2.50e+03 pdb=" C4 ABA1463 " 0.005 2.00e-02 2.50e+03 ... (remaining 24647 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 4 1.97 - 2.70: 8202 2.70 - 3.43: 246159 3.43 - 4.17: 487839 4.17 - 4.90: 772660 Nonbonded interactions: 1514864 Sorted by model distance: nonbonded pdb="MG MGBAA4EZ " pdb="MG MGBAA4GZ " model vdw 1.232 1.300 nonbonded pdb="MG MGBAA4EY " pdb="MG MGBAA4F2 " model vdw 1.238 1.300 nonbonded pdb="MG MGAAA594 " pdb="MG MGAAA5AU " model vdw 1.250 1.300 nonbonded pdb="MG MGBAA4GN " pdb="MG MGBAA4JE " model vdw 1.273 1.300 nonbonded pdb=" OP1 GBA1399 " pdb="MG MGBAA4EU " model vdw 1.969 2.170 ... (remaining 1514859 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 'AV' and resid 1 through 71) selection = chain 'AY' } ncs_group { reference = (chain 'DL' and resid 64 through 89) selection = (chain 'EL' and resid 64 through 89) selection = (chain 'FL' and resid 64 through 89) selection = (chain 'GL' and resid 64 through 89) selection = chain 'HL' } 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 6 6.06 5 P 2724 5.49 5 Mg 325 5.21 5 S 513 5.16 5 C 103941 2.51 5 N 32857 2.21 5 O 40470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 20.040 Check model and map are aligned: 1.980 Convert atoms to be neutral: 1.200 Process input model: 479.600 Find NCS groups from input model: 5.810 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 512.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 0.002 0.094 190204 Z= 0.119 Angle : 0.471 10.150 270183 Z= 0.267 Chirality : 0.032 0.249 31834 Planarity : 0.003 0.051 24650 Dihedral : 13.306 179.708 80956 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: -1.95 (0.06), residues: 14964 helix: -0.37 (0.06), residues: 5806 sheet: -1.20 (0.11), residues: 1801 loop : -2.09 (0.06), residues: 7357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5644 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 5394 time to evaluate : 13.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 250 outliers final: 53 residues processed: 5554 average time/residue: 1.5840 time to fit residues: 15096.8925 Evaluate side-chains 2967 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 2914 time to evaluate : 11.060 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.2749 time to fit residues: 141.7584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1472 optimal weight: 3.9990 chunk 1321 optimal weight: 10.0000 chunk 733 optimal weight: 8.9990 chunk 451 optimal weight: 8.9990 chunk 891 optimal weight: 0.4980 chunk 706 optimal weight: 2.9990 chunk 1366 optimal weight: 10.0000 chunk 528 optimal weight: 4.9990 chunk 831 optimal weight: 0.9980 chunk 1017 optimal weight: 20.0000 chunk 1583 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 139 GLN AI 156 GLN AI 252 GLN ** AI 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 319 HIS BT 175 GLN ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 239 ASN BU 94 GLN BV 109 GLN BV 183 ASN BW 77 GLN BW 113 GLN BW 131 ASN BW 208 HIS ** BY 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 73 GLN BY 84 ASN BY 92 ASN Ba 108 HIS Ba 146 HIS Ba 223 HIS Ba 266 GLN ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 360 ASN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 307 HIS Bb 308 GLN Bb 332 HIS Bb 354 GLN ** Bc 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 301 HIS Bd 99 GLN ** Bd 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 137 ASN ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 42 GLN Bh 69 HIS ** Bh 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 106 GLN Bh 128 GLN Bh 222 GLN ** Bi 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 59 HIS Bi 161 HIS Bi 235 GLN Bj 199 ASN Bj 251 HIS Bk 54 HIS Bk 177 ASN Bm 74 HIS Bm 96 HIS Bm 115 ASN Bm 120 GLN Bm 132 ASN Bo 69 GLN Bo 100 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 19 GLN Bq 129 HIS Bu 67 GLN Bu 95 ASN ** Bv 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 112 GLN Bv 138 GLN ** B0 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B0 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B0 86 ASN B0 107 ASN Bw 65 GLN ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 201 HIS Bw 226 GLN Bw 234 GLN ** Bw 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 381 ASN ** Bw 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN Bx 167 HIS ** Bx 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 126 GLN AE 175 GLN AE 292 HIS ** AE 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 317 HIS AE 356 GLN AE 360 GLN ** AG 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 122 GLN AG 127 HIS AG 196 HIS AG 215 ASN AG 224 HIS AJ 51 HIS AJ 109 HIS AJ 163 ASN AK 107 GLN AL 34 ASN AL 35 GLN AL 74 ASN AL 134 HIS AN 55 ASN AN 113 HIS AN 117 HIS AO 84 HIS AO 147 HIS ** AO 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 236 HIS AP 28 ASN AP 38 HIS ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 HIS AQ 57 GLN AQ 79 HIS AR 72 HIS ** AR 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 105 GLN Aa 189 HIS ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 369 GLN Aa 372 GLN Ab 66 HIS Ac 33 ASN Ac 35 ASN Ac 51 ASN Ac 59 ASN Ac 63 GLN Ac 69 ASN ** Ac 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 101 HIS Ac 128 HIS ** Ac 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 62 GLN Ad 109 ASN Ad 131 GLN Ad 135 GLN Ad 159 GLN ** Ae 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 181 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 422 GLN B1 4 HIS ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 HIS Ag 61 GLN Ag 62 HIS Ag 68 ASN Ag 200 GLN Ag 298 ASN ** Ag 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 366 GLN Ag 371 HIS Ag 386 ASN Ag 389 GLN Ah 288 ASN Ah 309 ASN Ah 321 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 40 GLN ** Ai 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 45 HIS Aj 89 HIS Aj 108 ASN Aj 137 HIS Aj 177 GLN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 263 ASN Ak 270 GLN Am 15 ASN Am 92 ASN An 141 HIS ** Ao 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 GLN Ao 260 HIS Ao 288 ASN Ao 336 GLN Ao 473 GLN Ao 629 GLN Ap 152 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DL 83 ASN FL 65 GLN FL 83 ASN B2 90 GLN ** B2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 95 HIS ** B4 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 83 ASN ** B5 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 118 GLN B5 120 HIS B6 23 GLN ** B7 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 87 HIS B8 118 HIS BC 124 HIS BC 154 GLN BC 159 ASN ** BC 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 197 ASN BC 330 ASN BC 349 ASN ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 617 HIS BC 694 ASN BD 228 GLN BE 128 HIS BE 174 GLN BE 216 GLN BE 281 ASN BE 313 ASN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 97 HIS ** BF 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 201 GLN ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 88 HIS BI 121 ASN BI 126 GLN BI 136 ASN BJ 41 HIS BJ 114 HIS BJ 189 GLN ** BJ 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 41 GLN BK 133 GLN BK 168 GLN BN 40 GLN BN 74 GLN BO 33 GLN BO 52 HIS BO 89 HIS BO 103 ASN BO 104 ASN BO 113 ASN BO 142 GLN ** BP 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 153 ASN BQ 68 ASN BQ 98 HIS BQ 117 ASN BQ 210 GLN ** BR 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 89 HIS ** BS 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 142 ASN BS 163 HIS Total number of N/Q/H flips: 199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 190204 Z= 0.190 Angle : 0.569 11.991 270183 Z= 0.282 Chirality : 0.036 0.250 31834 Planarity : 0.005 0.118 24650 Dihedral : 14.273 179.994 49456 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: -1.06 (0.07), residues: 14964 helix: 0.40 (0.07), residues: 5868 sheet: -0.72 (0.12), residues: 1756 loop : -1.63 (0.07), residues: 7340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3714 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 3693 time to evaluate : 11.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 3702 average time/residue: 1.3742 time to fit residues: 8846.4538 Evaluate side-chains 2655 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2653 time to evaluate : 12.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.3448 time to fit residues: 20.1132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 880 optimal weight: 20.0000 chunk 491 optimal weight: 10.0000 chunk 1318 optimal weight: 10.0000 chunk 1078 optimal weight: 9.9990 chunk 436 optimal weight: 5.9990 chunk 1586 optimal weight: 5.9990 chunk 1713 optimal weight: 2.9990 chunk 1413 optimal weight: 10.0000 chunk 1573 optimal weight: 3.9990 chunk 540 optimal weight: 20.0000 chunk 1272 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AI 256 GLN ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 77 GLN BW 103 GLN BW 130 HIS ** BX 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 82 GLN BY 92 ASN ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 119 GLN Ba 160 HIS ** Ba 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 174 HIS ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 332 HIS ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 301 HIS Bd 99 GLN Bg 24 GLN ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 66 ASN ** Bg 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 135 ASN Bh 106 GLN Bh 128 GLN ** Bi 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 153 ASN Bi 161 HIS ** Bj 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 199 ASN ** Bk 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 158 GLN Bo 69 GLN Bp 93 HIS Bt 21 HIS ** Bv 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B0 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B0 86 ASN ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN Bw 385 ASN Bw 414 GLN Bx 164 ASN ** Bx 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 125 GLN AB 133 HIS ** AB 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 238 ASN AB 253 GLN AC 72 HIS AC 75 ASN AE 127 ASN AE 280 HIS ** AF 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 72 GLN AK 73 ASN AK 107 GLN AK 121 ASN AL 37 HIS AL 105 HIS ** AN 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 38 HIS ** AP 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 HIS ** Aa 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 35 ASN Ac 101 HIS Ad 109 ASN ** Ae 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 404 GLN ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 42 HIS B1 89 HIS B1 177 HIS Af 87 HIS Ag 89 GLN Ag 189 ASN Ag 311 GLN Ag 320 ASN Ag 325 GLN Ag 371 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 55 HIS Aj 108 ASN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 105 ASN An 141 HIS ** Ao 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 458 ASN Ap 152 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 90 ASN B5 106 ASN B5 187 GLN ** B7 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 197 ASN ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 542 GLN BD 87 HIS BD 116 HIS BD 147 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 216 GLN ** BE 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 100 GLN BJ 204 GLN BN 61 ASN BO 33 GLN BO 59 HIS BO 103 ASN BP 84 ASN ** BP 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 117 ASN BR 112 ASN ** BR 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 88 HIS ** BS 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 142 ASN BS 162 GLN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 190204 Z= 0.297 Angle : 0.663 14.732 270183 Z= 0.333 Chirality : 0.039 0.301 31834 Planarity : 0.006 0.100 24650 Dihedral : 14.602 179.737 49456 Min Nonbonded Distance : 0.967 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.07 % Favored : 94.91 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.84 (0.07), residues: 14964 helix: 0.51 (0.07), residues: 5844 sheet: -0.60 (0.12), residues: 1767 loop : -1.43 (0.07), residues: 7353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3372 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 3355 time to evaluate : 12.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 3365 average time/residue: 1.3700 time to fit residues: 8062.4755 Evaluate side-chains 2488 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2485 time to evaluate : 11.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.1810 time to fit residues: 20.9842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1567 optimal weight: 0.8980 chunk 1192 optimal weight: 0.0970 chunk 823 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 757 optimal weight: 0.9990 chunk 1065 optimal weight: 20.0000 chunk 1592 optimal weight: 7.9990 chunk 1685 optimal weight: 7.9990 chunk 831 optimal weight: 2.9990 chunk 1509 optimal weight: 5.9990 chunk 454 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 313 GLN ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 27 HIS BW 208 HIS ** BX 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 18 ASN BY 92 ASN Ba 65 HIS ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 119 GLN Ba 146 HIS Ba 353 GLN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 85 HIS Bf 105 GLN ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 106 GLN Bh 128 GLN ** Bi 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 161 HIS ** Bk 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 158 GLN Bo 69 GLN Bp 72 HIS Bp 93 HIS ** Bt 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 67 GLN Bv 60 GLN B0 76 HIS ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN Bw 402 ASN Bx 164 ASN Bx 196 HIS ** AB 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 215 ASN AE 175 GLN AE 280 HIS ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 45 GLN AJ 125 HIS AK 107 GLN AK 121 ASN AL 37 HIS AN 113 HIS AN 117 HIS ** AP 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 HIS Aa 251 ASN ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 66 HIS ** Ac 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 35 ASN ** Ac 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 59 ASN Ac 101 HIS Ad 109 ASN ** Ae 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 56 ASN B1 177 HIS Ag 66 HIS Ag 163 ASN Ag 290 HIS Ag 320 ASN ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 55 HIS Aj 88 GLN Aj 108 ASN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 183 ASN ** Ak 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 105 ASN An 141 HIS ** Ao 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 GLN Ao 380 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 37 ASN B5 106 ASN ** B7 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 65 HIS B7 87 HIS ** BC 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 488 ASN BC 542 GLN BD 116 HIS BD 147 ASN BD 166 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 234 GLN ** BE 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 140 ASN BO 33 GLN BO 103 ASN BO 142 GLN BP 84 ASN ** BP 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 117 ASN BR 30 GLN BR 114 ASN BR 155 GLN BS 79 HIS BS 89 HIS ** BS 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.100 190204 Z= 0.159 Angle : 0.557 12.620 270183 Z= 0.278 Chirality : 0.036 0.239 31834 Planarity : 0.004 0.076 24650 Dihedral : 14.536 179.995 49456 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.03 % Favored : 95.96 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % 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: -0.51 (0.07), residues: 14964 helix: 0.82 (0.07), residues: 5825 sheet: -0.47 (0.12), residues: 1768 loop : -1.25 (0.07), residues: 7371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3340 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 3329 time to evaluate : 12.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 3334 average time/residue: 1.3619 time to fit residues: 7950.3299 Evaluate side-chains 2520 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2518 time to evaluate : 11.141 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1405 time to fit residues: 18.4043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1403 optimal weight: 10.0000 chunk 956 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 1255 optimal weight: 4.9990 chunk 695 optimal weight: 6.9990 chunk 1438 optimal weight: 10.0000 chunk 1165 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 860 optimal weight: 2.9990 chunk 1513 optimal weight: 8.9990 chunk 425 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AI 127 HIS AI 252 GLN ** AI 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 82 GLN BY 92 ASN ** BY 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 231 ASN ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 102 GLN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 332 HIS Bc 197 HIS ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 85 HIS ** Bd 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 135 ASN Bh 106 GLN Bh 128 GLN ** Bi 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 77 HIS Bi 161 HIS ** Bj 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 251 HIS ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 92 HIS Bm 115 ASN Bo 69 GLN Bo 89 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS ** Bq 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B0 107 ASN ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 68 HIS AB 227 ASN AE 280 HIS AF 38 ASN ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 125 HIS AK 107 GLN AK 121 ASN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 37 HIS AN 55 ASN ** AN 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 84 HIS ** AP 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 HIS AQ 76 HIS AR 72 HIS ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 66 HIS Ac 101 HIS Ad 109 ASN Ae 185 ASN ** Ae 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 56 ASN B1 177 HIS ** Ag 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 113 ASN ** Ag 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 320 ASN ** Ah 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 55 HIS Aj 108 ASN Aj 133 GLN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 124 HIS Ak 183 ASN ** Ak 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 59 ASN ** Am 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 141 HIS Ao 129 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 152 HIS B3 115 HIS B5 106 ASN B7 65 HIS ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 542 GLN BC 548 GLN BD 147 ASN BD 234 GLN BE 197 HIS BE 216 GLN BF 74 GLN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 184 GLN ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 100 GLN BN 61 ASN BO 33 GLN BO 103 ASN BP 84 ASN BP 87 HIS BQ 117 ASN BR 147 ASN ** BS 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.136 190204 Z= 0.347 Angle : 0.706 15.845 270183 Z= 0.355 Chirality : 0.041 0.265 31834 Planarity : 0.006 0.106 24650 Dihedral : 14.864 179.849 49456 Min Nonbonded Distance : 0.979 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.87 % Favored : 94.12 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.71 (0.07), residues: 14964 helix: 0.56 (0.07), residues: 5840 sheet: -0.61 (0.12), residues: 1807 loop : -1.28 (0.07), residues: 7317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3094 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 3079 time to evaluate : 11.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 3088 average time/residue: 1.3393 time to fit residues: 7268.8175 Evaluate side-chains 2355 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2352 time to evaluate : 11.146 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 1.1172 time to fit residues: 20.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 567 optimal weight: 20.0000 chunk 1518 optimal weight: 0.1980 chunk 333 optimal weight: 9.9990 chunk 989 optimal weight: 6.9990 chunk 416 optimal weight: 7.9990 chunk 1687 optimal weight: 5.9990 chunk 1400 optimal weight: 10.9990 chunk 781 optimal weight: 3.9990 chunk 140 optimal weight: 0.0980 chunk 558 optimal weight: 10.0000 chunk 885 optimal weight: 0.0980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AI 252 GLN ** AI 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 60 GLN BW 130 HIS BW 208 HIS ** BX 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 92 ASN ** BY 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 119 GLN Ba 146 HIS ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 359 HIS ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 85 HIS Bd 99 GLN ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 107 GLN ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 106 GLN Bi 77 HIS ** Bi 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 132 ASN Bo 69 GLN Bo 89 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS Bq 124 HIS B0 107 ASN Bw 148 HIS Bw 173 GLN ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN AB 125 GLN AE 280 HIS ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 121 ASN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 37 HIS ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 109 ASN ** Ae 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 HIS ** Ag 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 320 ASN Ag 371 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 55 HIS Aj 88 GLN Aj 108 ASN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 183 ASN An 141 HIS An 178 GLN Ao 129 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 59 GLN ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 488 ASN BC 542 GLN ** BC 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 147 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 234 GLN ** BE 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 184 GLN ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 121 ASN BJ 100 GLN BP 84 ASN BQ 117 ASN BR 114 ASN BR 116 GLN ** BS 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN BS 163 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.158 190204 Z= 0.184 Angle : 0.587 14.894 270183 Z= 0.295 Chirality : 0.037 0.232 31834 Planarity : 0.005 0.099 24650 Dihedral : 14.808 179.641 49456 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.52 % Favored : 95.47 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.47 (0.07), residues: 14964 helix: 0.78 (0.07), residues: 5829 sheet: -0.54 (0.12), residues: 1783 loop : -1.14 (0.07), residues: 7352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3150 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 3143 time to evaluate : 11.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 3146 average time/residue: 1.3444 time to fit residues: 7436.5887 Evaluate side-chains 2412 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2410 time to evaluate : 11.067 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1162 time to fit residues: 18.3024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1626 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 961 optimal weight: 8.9990 chunk 1232 optimal weight: 6.9990 chunk 954 optimal weight: 5.9990 chunk 1420 optimal weight: 10.0000 chunk 942 optimal weight: 0.0770 chunk 1680 optimal weight: 3.9990 chunk 1051 optimal weight: 20.0000 chunk 1024 optimal weight: 0.0270 chunk 776 optimal weight: 4.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AI 87 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 252 GLN ** AI 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 82 GLN BY 92 ASN ** BY 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 119 GLN Ba 146 HIS ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 231 ASN ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 380 GLN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 332 HIS ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 135 ASN Bi 77 HIS Bi 161 HIS ** Bj 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 251 HIS ** Bk 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 158 GLN Bo 69 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS B0 132 HIS Bw 148 HIS Bw 173 GLN ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN AB 125 GLN AB 227 ASN AE 280 HIS ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 121 ASN AL 37 HIS ** AN 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 72 HIS ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 59 ASN Ac 101 HIS Ad 109 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 314 GLN ** Ae 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 HIS ** Ag 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 320 ASN Ag 371 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 55 HIS Aj 88 GLN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 183 ASN ** Ak 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 59 ASN Ao 129 GLN Ao 287 ASN Ao 376 HIS Ap 152 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 197 ASN ** B5 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 23 GLN B7 65 HIS ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 542 GLN ** BC 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 147 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 234 GLN ** BE 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 121 ASN BK 103 HIS BN 61 ASN BN 140 ASN BO 33 GLN BP 84 ASN BQ 117 ASN ** BR 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 142 ASN BS 162 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.216 190204 Z= 0.185 Angle : 0.590 22.418 270183 Z= 0.297 Chirality : 0.037 0.431 31834 Planarity : 0.005 0.089 24650 Dihedral : 14.767 179.974 49456 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.19 % Favored : 94.80 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.37 (0.07), residues: 14964 helix: 0.87 (0.07), residues: 5815 sheet: -0.52 (0.12), residues: 1799 loop : -1.07 (0.07), residues: 7350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3078 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 3069 time to evaluate : 11.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 3074 average time/residue: 1.3904 time to fit residues: 7537.2833 Evaluate side-chains 2402 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2398 time to evaluate : 11.079 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.1316 time to fit residues: 22.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1039 optimal weight: 4.9990 chunk 671 optimal weight: 3.9990 chunk 1003 optimal weight: 7.9990 chunk 506 optimal weight: 0.9980 chunk 330 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 1068 optimal weight: 2.9990 chunk 1145 optimal weight: 1.9990 chunk 831 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 1321 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AI 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 262 GLN ** BW 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 208 HIS ** BY 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 92 ASN ** BY 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 119 GLN Ba 146 HIS ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 380 GLN ** Bb 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 77 HIS Bi 161 HIS ** Bj 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 251 HIS Bn 65 ASN Bo 69 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS Bt 62 HIS Bt 78 GLN ** Bv 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 148 HIS ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN ** AE 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 280 HIS ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 121 ASN AL 37 HIS AL 136 GLN ** AO 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 72 HIS ** AR 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 337 GLN ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 35 ASN Ac 59 ASN Ad 109 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 HIS ** Ag 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 320 ASN Ag 371 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 55 HIS Aj 88 GLN Aj 108 ASN ** Aj 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 183 ASN ** Ak 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 GLN Ap 152 GLN ** Ap 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 106 ASN B5 115 HIS B7 65 HIS B7 87 HIS ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 542 GLN ** BC 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 147 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 61 ASN ** BN 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 103 ASN BP 84 ASN BQ 117 ASN ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 142 ASN BS 162 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.841 190204 Z= 0.303 Angle : 0.649 106.100 270183 Z= 0.318 Chirality : 0.038 0.542 31834 Planarity : 0.005 0.151 24650 Dihedral : 14.768 179.969 49456 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.04 % Favored : 94.95 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.38 (0.07), residues: 14964 helix: 0.85 (0.07), residues: 5830 sheet: -0.53 (0.12), residues: 1807 loop : -1.08 (0.07), residues: 7327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2954 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2950 time to evaluate : 11.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 2951 average time/residue: 1.3800 time to fit residues: 7195.3938 Evaluate side-chains 2362 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2362 time to evaluate : 11.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 14.1951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1529 optimal weight: 4.9990 chunk 1610 optimal weight: 0.6980 chunk 1469 optimal weight: 5.9990 chunk 1566 optimal weight: 10.0000 chunk 1609 optimal weight: 0.0000 chunk 942 optimal weight: 5.9990 chunk 682 optimal weight: 4.9990 chunk 1230 optimal weight: 0.8980 chunk 480 optimal weight: 3.9990 chunk 1415 optimal weight: 10.0000 chunk 1481 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AI 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 103 GLN BW 208 HIS BX 82 HIS ** BY 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 82 GLN ** BY 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 HIS Ba 165 HIS ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 380 GLN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 99 GLN ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 251 HIS Bo 69 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS Bt 78 GLN Bw 148 HIS ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN AE 280 HIS ** AF 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 121 ASN AK 131 GLN AL 37 HIS AL 136 GLN ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 72 HIS ** AR 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 110 GLN ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 310 GLN ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 35 ASN Ac 59 ASN Ac 101 HIS Ad 109 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 56 ASN B1 177 HIS ** Ag 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 371 HIS ** Ah 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN Aj 108 ASN Aj 179 GLN Ak 183 ASN Am 59 ASN Ao 129 GLN Ap 181 HIS ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 106 ASN B7 65 HIS B7 87 HIS ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 488 ASN ** BC 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 100 GLN BK 103 HIS BN 61 ASN BN 140 ASN BN 160 GLN BO 33 GLN BO 103 ASN BP 84 ASN BQ 117 ASN BS 88 HIS ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 142 ASN BS 162 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.810 190204 Z= 0.255 Angle : 0.603 80.822 270183 Z= 0.297 Chirality : 0.036 0.326 31834 Planarity : 0.005 0.117 24650 Dihedral : 14.709 179.982 49456 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.65 % Favored : 95.34 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.30 (0.07), residues: 14964 helix: 0.92 (0.07), residues: 5838 sheet: -0.46 (0.12), residues: 1801 loop : -1.03 (0.07), residues: 7325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3059 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3053 time to evaluate : 12.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 6 outliers final: 3 residues processed: 3057 average time/residue: 1.4103 time to fit residues: 7616.0518 Evaluate side-chains 2394 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2391 time to evaluate : 11.089 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.2424 time to fit residues: 21.0510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 1560 optimal weight: 10.0000 chunk 1028 optimal weight: 3.9990 chunk 1656 optimal weight: 0.8980 chunk 1010 optimal weight: 7.9990 chunk 785 optimal weight: 0.8980 chunk 1151 optimal weight: 5.9990 chunk 1737 optimal weight: 4.9990 chunk 1599 optimal weight: 0.3980 chunk 1383 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 1068 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 82 HIS ** BY 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 119 GLN Ba 146 HIS ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 380 GLN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 118 ASN Bh 172 ASN Bi 161 HIS ** Bj 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 251 HIS Bk 177 ASN Bo 69 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS ** Bt 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 148 HIS ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN AB 227 ASN AE 280 HIS AE 415 GLN AK 121 ASN AL 37 HIS ** AO 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 35 ASN Ac 56 GLN Ac 59 ASN Ad 109 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 418 GLN ** Ae 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 66 HIS Ag 366 GLN Ag 371 HIS Ah 321 HIS Ah 364 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN Aj 108 ASN Aj 179 GLN An 141 HIS Ao 129 GLN ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 106 ASN B7 87 HIS ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 622 ASN ** BC 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 147 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 234 GLN ** BE 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN BF 98 GLN ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 103 HIS BN 140 ASN BO 103 ASN BQ 117 ASN ** BR 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 142 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.758 190204 Z= 0.254 Angle : 0.616 77.983 270183 Z= 0.306 Chirality : 0.036 0.270 31834 Planarity : 0.005 0.109 24650 Dihedral : 14.685 179.927 49456 Min Nonbonded Distance : 1.064 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.87 % Favored : 95.12 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.26 (0.07), residues: 14964 helix: 0.93 (0.07), residues: 5843 sheet: -0.38 (0.12), residues: 1799 loop : -1.00 (0.07), residues: 7322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29928 Ramachandran restraints generated. 14964 Oldfield, 0 Emsley, 14964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2999 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2994 time to evaluate : 11.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 2997 average time/residue: 1.3753 time to fit residues: 7288.4163 Evaluate side-chains 2406 residues out of total 13263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2404 time to evaluate : 11.197 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.0798 time to fit residues: 18.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1744 random chunks: chunk 848 optimal weight: 30.0000 chunk 1098 optimal weight: 4.9990 chunk 1473 optimal weight: 10.0000 chunk 423 optimal weight: 8.9990 chunk 1275 optimal weight: 0.9990 chunk 204 optimal weight: 0.0970 chunk 384 optimal weight: 0.9990 chunk 1385 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 1422 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 262 GLN BV 86 GLN ** BW 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 208 HIS BX 82 HIS BY 82 GLN ** BY 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 380 GLN ** Bb 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 99 GLN ** Bg 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 135 ASN Bi 161 HIS ** Bj 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 207 ASN Bk 175 HIS Bk 177 ASN Bo 69 GLN ** Bp 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 93 HIS ** Bp 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B0 107 ASN Bw 148 HIS ** Bw 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 321 ASN ** Bw 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 125 GLN AE 280 HIS ** AG 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 121 ASN AK 185 HIS AL 37 HIS ** AN 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 72 HIS ** Aa 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 101 HIS Ad 109 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 286 ASN ** Ae 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 56 ASN Ag 371 HIS ** Ah 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 ASN Aj 88 GLN Aj 108 ASN An 141 HIS Ao 129 GLN ** CL 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 106 ASN ** BC 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 542 GLN ** BC 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 147 ASN ** BD 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 234 GLN BD 264 ASN ** BE 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 100 GLN BK 103 HIS BN 61 ASN BN 140 ASN BO 33 GLN BO 103 ASN BP 84 ASN BQ 98 HIS BQ 117 ASN BS 100 GLN ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.146311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122617 restraints weight = 423942.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124305 restraints weight = 249658.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124658 restraints weight = 155763.041| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.746 190204 Z= 0.291 Angle : 0.654 77.394 270183 Z= 0.325 Chirality : 0.038 0.316 31834 Planarity : 0.005 0.097 24650 Dihedral : 14.790 179.710 49456 Min Nonbonded Distance : 1.010 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.46 % Favored : 94.53 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.32 (0.07), residues: 14964 helix: 0.86 (0.07), residues: 5833 sheet: -0.46 (0.12), residues: 1822 loop : -1.01 (0.07), residues: 7309 =============================================================================== Job complete usr+sys time: 93694.10 seconds wall clock time: 1603 minutes 36.41 seconds (96216.41 seconds total)