Starting phenix.real_space_refine on Mon Mar 11 00:17:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fks_29255/03_2024/8fks_29255_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fks_29255/03_2024/8fks_29255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fks_29255/03_2024/8fks_29255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fks_29255/03_2024/8fks_29255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fks_29255/03_2024/8fks_29255_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fks_29255/03_2024/8fks_29255_neut_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.041 sd= 0.152 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 2 6.06 5 P 2049 5.49 5 Mg 61 5.21 5 S 276 5.16 5 C 60609 2.51 5 N 20266 2.21 5 O 25429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA ASP 45": "OD1" <-> "OD2" Residue "BA ASP 150": "OD1" <-> "OD2" Residue "L6 GLU 108": "OE1" <-> "OE2" Residue "L6 GLU 119": "OE1" <-> "OE2" Residue "L7 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 GLU 144": "OE1" <-> "OE2" Residue "L7 GLU 194": "OE1" <-> "OE2" Residue "L8 ASP 29": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L8 ASP 106": "OD1" <-> "OD2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 9": "OE1" <-> "OE2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 GLU 123": "OE1" <-> "OE2" Residue "L9 ASP 147": "OD1" <-> "OD2" Residue "LA GLU 31": "OE1" <-> "OE2" Residue "LA TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 89": "OE1" <-> "OE2" Residue "LA GLU 103": "OE1" <-> "OE2" Residue "LB GLU 17": "OE1" <-> "OE2" Residue "LB ASP 22": "OD1" <-> "OD2" Residue "LB ASP 89": "OD1" <-> "OD2" Residue "LB ASP 129": "OD1" <-> "OD2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LC ASP 147": "OD1" <-> "OD2" Residue "LE GLU 147": "OE1" <-> "OE2" Residue "LE GLU 149": "OE1" <-> "OE2" Residue "LE GLU 152": "OE1" <-> "OE2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI GLU 37": "OE1" <-> "OE2" Residue "LI TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI GLU 120": "OE1" <-> "OE2" Residue "LL GLU 52": "OE1" <-> "OE2" Residue "LL ASP 105": "OD1" <-> "OD2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ASP 26": "OD1" <-> "OD2" Residue "LQ ASP 42": "OD1" <-> "OD2" Residue "LQ PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 84": "OE1" <-> "OE2" Residue "LS ASP 8": "OD1" <-> "OD2" Residue "LS GLU 15": "OE1" <-> "OE2" Residue "LS GLU 27": "OE1" <-> "OE2" Residue "LS GLU 67": "OE1" <-> "OE2" Residue "LT GLU 38": "OE1" <-> "OE2" Residue "LU GLU 46": "OE1" <-> "OE2" Residue "LU GLU 89": "OE1" <-> "OE2" Residue "NE ASP 284": "OD1" <-> "OD2" Residue "NF GLU 22": "OE1" <-> "OE2" Residue "NF GLU 69": "OE1" <-> "OE2" Residue "NF PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NG GLU 143": "OE1" <-> "OE2" Residue "NG GLU 157": "OE1" <-> "OE2" Residue "NG GLU 159": "OE1" <-> "OE2" Residue "NG GLU 190": "OE1" <-> "OE2" Residue "NN ASP 72": "OD1" <-> "OD2" Residue "NN PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN ASP 184": "OD1" <-> "OD2" Residue "NN TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 191": "OE1" <-> "OE2" Residue "NN TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 56": "OE1" <-> "OE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ASP 261": "OD1" <-> "OD2" Residue "SC TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC ASP 254": "OD1" <-> "OD2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 137": "OE1" <-> "OE2" Residue "SD ASP 171": "OD1" <-> "OD2" Residue "SD GLU 229": "OE1" <-> "OE2" Residue "SD ASP 232": "OD1" <-> "OD2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE ASP 88": "OD1" <-> "OD2" Residue "SE GLU 105": "OE1" <-> "OE2" Residue "SE GLU 109": "OE1" <-> "OE2" Residue "SE ASP 162": "OD1" <-> "OD2" Residue "SE GLU 220": "OE1" <-> "OE2" Residue "SE ASP 228": "OD1" <-> "OD2" Residue "SG GLU 14": "OE1" <-> "OE2" Residue "SG GLU 44": "OE1" <-> "OE2" Residue "SG GLU 107": "OE1" <-> "OE2" Residue "SG GLU 120": "OE1" <-> "OE2" Residue "SG ASP 142": "OD1" <-> "OD2" Residue "SG GLU 143": "OE1" <-> "OE2" Residue "SG ASP 150": "OD1" <-> "OD2" Residue "SG ASP 177": "OD1" <-> "OD2" Residue "SH ASP 57": "OD1" <-> "OD2" Residue "SH PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 97": "OD1" <-> "OD2" Residue "SH GLU 104": "OE1" <-> "OE2" Residue "SH GLU 162": "OE1" <-> "OE2" Residue "SH GLU 163": "OE1" <-> "OE2" Residue "SI GLU 89": "OE1" <-> "OE2" Residue "SI ASP 92": "OD1" <-> "OD2" Residue "SI PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 666": "OE1" <-> "OE2" Residue "SJ ASP 683": "OD1" <-> "OD2" Residue "SJ ASP 686": "OD1" <-> "OD2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SJ GLU 708": "OE1" <-> "OE2" Residue "SJ TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 39": "OE1" <-> "OE2" Residue "SK GLU 127": "OE1" <-> "OE2" Residue "SK PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 41": "OD1" <-> "OD2" Residue "SL GLU 77": "OE1" <-> "OE2" Residue "SL ASP 94": "OD1" <-> "OD2" Residue "SL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 246": "OE1" <-> "OE2" Residue "SM TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 65": "OE1" <-> "OE2" Residue "SN ASP 101": "OD1" <-> "OD2" Residue "SN GLU 139": "OE1" <-> "OE2" Residue "SN GLU 162": "OE1" <-> "OE2" Residue "SN GLU 191": "OE1" <-> "OE2" Residue "SN TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 183": "OE1" <-> "OE2" Residue "SO TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 293": "OE1" <-> "OE2" Residue "SQ PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 55": "OD1" <-> "OD2" Residue "SQ ASP 172": "OD1" <-> "OD2" Residue "SQ ASP 180": "OD1" <-> "OD2" Residue "SR TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 81": "OD1" <-> "OD2" Residue "SR ASP 211": "OD1" <-> "OD2" Residue "SR TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 227": "OD1" <-> "OD2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 298": "OE1" <-> "OE2" Residue "SR ASP 427": "OD1" <-> "OD2" Residue "SR ASP 443": "OD1" <-> "OD2" Residue "SR GLU 452": "OE1" <-> "OE2" Residue "SS GLU 124": "OE1" <-> "OE2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 70": "OE1" <-> "OE2" Residue "SV GLU 77": "OE1" <-> "OE2" Residue "SV GLU 84": "OE1" <-> "OE2" Residue "SV PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 126": "OE1" <-> "OE2" Residue "SW PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 493": "OE1" <-> "OE2" Residue "SW ASP 552": "OD1" <-> "OD2" Residue "SW PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW ASP 622": "OD1" <-> "OD2" Residue "SZ GLU 98": "OE1" <-> "OE2" Residue "SZ ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 108693 Number of models: 1 Model: "" Number of chains: 58 Chain: "BA" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1176 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain: "L1" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3234 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 61, 'rna3p_pyr': 66} Link IDs: {'rna2p': 24, 'rna3p': 127} Chain breaks: 1 Chain: "L2" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1468 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 21, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 52} Chain breaks: 3 Chain: "L3" Number of atoms: 39106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1824, 39106 Classifications: {'RNA': 1824} Modifications used: {'rna2p_pur': 177, 'rna2p_pyr': 108, 'rna3p_pur': 818, 'rna3p_pyr': 721} Link IDs: {'rna2p': 285, 'rna3p': 1538} Chain breaks: 35 Chain: "L6" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 104} Chain: "L7" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1507 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "LA" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 981 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain breaks: 2 Chain: "LB" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1223 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LE" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 702 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "LG" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 844 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "LH" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 284 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain breaks: 1 Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LK" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 642 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "LL" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "LN" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3044 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "LQ" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 834 Chain: "LW" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "NE" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1331 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "NF" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1588 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 3 Chain: "NG" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 738 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "NN" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1950 Classifications: {'peptide': 244} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 230} Chain breaks: 2 Chain: "SA" Number of atoms: 2645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2645 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "SC" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Chain: "SD" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1755 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain: "SE" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 175} Chain: "SG" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} bond proxies already assigned to first conformer: 1528 Chain: "SH" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SI" Number of atoms: 1732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 bond proxies already assigned to first conformer: 1742 Chain: "SJ" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 609 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "SK" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1721 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "SL" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1960 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "SM" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 90 Chain: "SN" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1350 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "SO" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2460 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 274} Chain breaks: 1 Chain: "SQ" Number of atoms: 1778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} bond proxies already assigned to first conformer: 1797 Chain: "SR" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3524 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 19, 'TRANS': 408} Chain breaks: 2 Chain: "SS" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1955 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 25, 'TRANS': 209} Chain breaks: 2 Chain: "ST" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 323 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "SV" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1171 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "SW" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3560 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 19, 'TRANS': 425} Chain breaks: 1 Chain: "SZ" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1338 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Chain: "L1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L3" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "L9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' K': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 65191 SG CYSLW 19 96.245 127.449 146.412 1.00 63.34 S ATOM 65219 SG CYSLW 22 96.901 124.706 148.965 1.00 56.10 S ATOM 65310 SG CYSLW 34 98.971 127.799 149.084 1.00 61.39 S ATOM 65329 SG CYSLW 37 99.438 125.461 146.176 1.00 56.31 S ATOM A01ZR SG CYSSV 6 62.430 190.813 247.783 1.00 33.91 S ATOM A020K SG CYSSV 9 58.833 189.395 247.681 1.00 36.64 S ATOM A025O SG CYSSV 32 61.649 187.069 247.240 1.00 33.85 S ATOM A026I SG CYSSV 36 60.852 189.579 244.523 1.00 36.07 S Time building chain proxies: 42.44, per 1000 atoms: 0.39 Number of scatterers: 108693 At special positions: 0 Unit cell: (213.328, 236.912, 333.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 1 19.00 S 276 16.00 P 2049 15.00 Mg 61 11.99 O 25429 8.00 N 20266 7.00 C 60609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.58 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15186 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 297 helices and 75 sheets defined 49.4% alpha, 13.5% beta 661 base pairs and 1010 stacking pairs defined. Time for finding SS restraints: 64.57 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 36 Proline residue: BA 30 - end of helix Proline residue: BA 34 - end of helix Processing helix chain 'BA' and resid 38 through 51 removed outlier: 3.620A pdb=" N GLYBA 51 " --> pdb=" O ALABA 47 " (cutoff:3.500A) Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.623A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 91 through 96 removed outlier: 4.874A pdb=" N LYSBA 96 " --> pdb=" O ARGBA 92 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.019A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.620A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 removed outlier: 3.660A pdb=" N ILEBA 151 " --> pdb=" O HISBA 147 " (cutoff:3.500A) Processing helix chain 'L6' and resid 27 through 47 removed outlier: 3.544A pdb=" N ALAL6 47 " --> pdb=" O ALAL6 43 " (cutoff:3.500A) Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.400A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.732A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 Processing helix chain 'L7' and resid 46 through 56 removed outlier: 3.986A pdb=" N ALAL7 56 " --> pdb=" O LEUL7 52 " (cutoff:3.500A) Processing helix chain 'L7' and resid 75 through 89 Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.572A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.765A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 149 through 190 removed outlier: 3.649A pdb=" N THRL7 153 " --> pdb=" O TYRL7 149 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASPL7 190 " --> pdb=" O GLUL7 186 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 Processing helix chain 'L8' and resid 51 through 56 removed outlier: 4.069A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.573A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.999A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 Processing helix chain 'L9' and resid 2 through 14 removed outlier: 4.002A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 5.022A pdb=" N SERL9 34 " --> pdb=" O TYRL9 30 " (cutoff:3.500A) Processing helix chain 'L9' and resid 44 through 52 Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.665A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 4.022A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 147 through 153 removed outlier: 6.521A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.225A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 removed outlier: 3.548A pdb=" N GLULA 31 " --> pdb=" O LYSLA 27 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LA' and resid 108 through 113 removed outlier: 3.834A pdb=" N LEULA 112 " --> pdb=" O ASPLA 108 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VALLA 113 " --> pdb=" O VALLA 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 108 through 113' Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.128A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.675A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.666A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.323A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.620A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.464A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.861A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 100 through 121 removed outlier: 3.901A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 3.824A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALALG 136 " --> pdb=" O ILELG 132 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 131 through 137' Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.807A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SERLI 31 " --> pdb=" O ARGLI 27 " (cutoff:3.500A) Processing helix chain 'LI' and resid 35 through 43 Processing helix chain 'LI' and resid 100 through 105 removed outlier: 4.082A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 Processing helix chain 'LK' and resid 2 through 7 removed outlier: 4.020A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYSLK 7 " --> pdb=" O SERLK 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 2 through 7' Processing helix chain 'LK' and resid 60 through 67 removed outlier: 5.396A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.766A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.600A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LL' and resid 2 through 13 removed outlier: 5.636A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 72 through 77 removed outlier: 3.509A pdb=" N SERLL 76 " --> pdb=" O LYSLL 72 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYRLL 77 " --> pdb=" O PROLL 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 72 through 77' Processing helix chain 'LL' and resid 85 through 101 removed outlier: 4.120A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 122 removed outlier: 3.958A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.307A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 3.758A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 156 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 3.959A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.989A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 244 through 251 removed outlier: 3.881A pdb=" N VALLN 251 " --> pdb=" O GLYLN 247 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.370A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLULN 361 " --> pdb=" O ARGLN 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 356 through 361' Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 393 through 403 removed outlier: 3.991A pdb=" N ILELN 397 " --> pdb=" O LYSLN 393 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.531A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 3.962A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.846A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.532A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 4.132A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 4.043A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 94 Processing helix chain 'LS' and resid 96 through 102 Processing helix chain 'LS' and resid 104 through 115 Proline residue: LS 115 - end of helix Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.902A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLULT 40 " --> pdb=" O ARGLT 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 35 through 40' Processing helix chain 'LU' and resid 25 through 30 removed outlier: 4.064A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 removed outlier: 3.551A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLYLU 49 " --> pdb=" O ARGLU 45 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 51 through 58 removed outlier: 3.545A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 3.892A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'NE' and resid 212 through 224 removed outlier: 3.542A pdb=" N GLNNE 222 " --> pdb=" O LYSNE 218 " (cutoff:3.500A) Processing helix chain 'NE' and resid 235 through 257 removed outlier: 3.528A pdb=" N GLYNE 255 " --> pdb=" O ASPNE 251 " (cutoff:3.500A) Processing helix chain 'NE' and resid 258 through 279 Processing helix chain 'NE' and resid 285 through 348 Processing helix chain 'NE' and resid 351 through 357 Processing helix chain 'NF' and resid 5 through 14 Processing helix chain 'NF' and resid 19 through 42 removed outlier: 4.548A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SERNF 36 " --> pdb=" O ALANF 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N METNF 42 " --> pdb=" O LYSNF 38 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NF' and resid 97 through 115 Processing helix chain 'NF' and resid 205 through 212 removed outlier: 3.579A pdb=" N THRNF 209 " --> pdb=" O SERNF 205 " (cutoff:3.500A) Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NG' and resid 127 through 145 removed outlier: 4.355A pdb=" N METNG 144 " --> pdb=" O LEUNG 140 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N METNG 145 " --> pdb=" O GLUNG 141 " (cutoff:3.500A) Processing helix chain 'NG' and resid 151 through 192 removed outlier: 5.736A pdb=" N GLUNG 157 " --> pdb=" O VALNG 153 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THRNG 158 " --> pdb=" O GLNNG 154 " (cutoff:3.500A) Processing helix chain 'NG' and resid 194 through 206 removed outlier: 3.540A pdb=" N ARGNG 198 " --> pdb=" O SERNG 194 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SERNG 206 " --> pdb=" O ILENG 202 " (cutoff:3.500A) Processing helix chain 'NG' and resid 207 through 215 Processing helix chain 'NN' and resid 7 through 29 removed outlier: 3.555A pdb=" N ALANN 26 " --> pdb=" O LEUNN 22 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALANN 27 " --> pdb=" O GLUNN 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASNNN 28 " --> pdb=" O ALANN 24 " (cutoff:3.500A) Proline residue: NN 29 - end of helix Processing helix chain 'NN' and resid 40 through 55 removed outlier: 3.515A pdb=" N GLUNN 55 " --> pdb=" O ARGNN 51 " (cutoff:3.500A) Processing helix chain 'NN' and resid 69 through 81 removed outlier: 3.783A pdb=" N CYSNN 73 " --> pdb=" O SERNN 69 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLYNN 78 " --> pdb=" O VALNN 74 " (cutoff:3.500A) Proline residue: NN 79 - end of helix Processing helix chain 'NN' and resid 117 through 126 removed outlier: 5.074A pdb=" N ARGNN 126 " --> pdb=" O VALNN 122 " (cutoff:3.500A) Processing helix chain 'NN' and resid 131 through 137 removed outlier: 4.377A pdb=" N PHENN 135 " --> pdb=" O HISNN 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALANN 136 " --> pdb=" O GLUNN 132 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HISNN 137 " --> pdb=" O GLNNN 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 131 through 137' Processing helix chain 'NN' and resid 150 through 165 removed outlier: 3.652A pdb=" N METNN 156 " --> pdb=" O HISNN 152 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHENN 164 " --> pdb=" O PHENN 160 " (cutoff:3.500A) Proline residue: NN 165 - end of helix Processing helix chain 'NN' and resid 173 through 178 removed outlier: 4.154A pdb=" N ILENN 177 " --> pdb=" O ASNNN 173 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYSNN 178 " --> pdb=" O LEUNN 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 173 through 178' Processing helix chain 'NN' and resid 246 through 251 removed outlier: 4.707A pdb=" N THRNN 251 " --> pdb=" O ASPNN 247 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.415A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 4.061A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.616A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.627A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 155 through 161 removed outlier: 4.884A pdb=" N GLUSA 159 " --> pdb=" O GLUSA 155 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 155 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.979A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLNSA 187 " --> pdb=" O VALSA 183 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.565A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 263 removed outlier: 3.745A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.569A pdb=" N ARGSA 300 " --> pdb=" O PROSA 296 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.401A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.279A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 132 through 137 removed outlier: 6.053A pdb=" N VALSC 137 " --> pdb=" O PHESC 133 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.878A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.833A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.154A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.491A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 37 through 79 removed outlier: 3.633A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.649A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 157 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.142A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.795A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 3.561A pdb=" N LEUSD 208 " --> pdb=" O ALASD 204 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.697A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.738A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.599A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.646A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 169 through 178 Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.646A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.948A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLUSE 220 " --> pdb=" O ALASE 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASNSE 227 " --> pdb=" O ARGSE 223 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.059A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRPSE 237 " --> pdb=" O ILESE 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'SE' and resid 232 through 237' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.615A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.598A pdb=" N ILESG 161 " --> pdb=" O SERSG 157 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.696A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.638A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 6.001A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 removed outlier: 3.534A pdb=" N LYSSH 147 " --> pdb=" O TYRSH 143 " (cutoff:3.500A) Processing helix chain 'SH' and resid 154 through 180 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.673A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.739A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.532A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 3.974A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ARGSI 230 " --> pdb=" O ALASI 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 225 through 230' Processing helix chain 'SI' and resid 231 through 237 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.430A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 removed outlier: 3.658A pdb=" N SERSJ 677 " --> pdb=" O VALSJ 673 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 3.916A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.605A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 removed outlier: 3.613A pdb=" N VALSJ 724 " --> pdb=" O GLYSJ 720 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.889A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 43 removed outlier: 3.625A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 64 removed outlier: 3.892A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VALSK 64 " --> pdb=" O GLYSK 60 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 89 Proline residue: SK 89 - end of helix Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.690A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.367A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SL' and resid 32 through 50 removed outlier: 3.516A pdb=" N LYSSL 38 " --> pdb=" O GLUSL 34 " (cutoff:3.500A) Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.677A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 3.613A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 3.956A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 removed outlier: 3.658A pdb=" N GLUSL 193 " --> pdb=" O ASNSL 189 " (cutoff:3.500A) Processing helix chain 'SL' and resid 222 through 241 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.699A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 removed outlier: 3.599A pdb=" N LEUSM 40 " --> pdb=" O ARGSM 36 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 4.152A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Proline residue: SM 77 - end of helix Processing helix chain 'SM' and resid 78 through 99 removed outlier: 3.609A pdb=" N LYSSM 86 " --> pdb=" O PHESM 82 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 removed outlier: 3.611A pdb=" N LYSSM 121 " --> pdb=" O ASPSM 117 " (cutoff:3.500A) Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 148 removed outlier: 4.912A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHESM 147 " --> pdb=" O LEUSM 143 " (cutoff:3.500A) Proline residue: SM 148 - end of helix Processing helix chain 'SM' and resid 154 through 176 Processing helix chain 'SM' and resid 216 through 243 removed outlier: 3.513A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.913A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.592A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.585A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.491A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.859A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SM' and resid 436 through 448 Processing helix chain 'SM' and resid 541 through 586 Processing helix chain 'SN' and resid 19 through 30 Processing helix chain 'SN' and resid 49 through 61 Processing helix chain 'SN' and resid 65 through 70 Processing helix chain 'SN' and resid 100 through 127 Proline residue: SN 121 - end of helix Processing helix chain 'SN' and resid 143 through 177 removed outlier: 3.593A pdb=" N ALASN 172 " --> pdb=" O LYSSN 168 " (cutoff:3.500A) Processing helix chain 'SN' and resid 178 through 205 Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.311A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 175 removed outlier: 4.592A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 169 through 175' Processing helix chain 'SO' and resid 176 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.566A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 328 through 333 removed outlier: 5.648A pdb=" N LYSSO 333 " --> pdb=" O LEUSO 329 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.056A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THRSQ 36 " --> pdb=" O LYSSQ 32 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.632A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILESQ 56 " --> pdb=" O LYSSQ 52 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.981A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 3.526A pdb=" N VALSQ 112 " --> pdb=" O THRSQ 108 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 removed outlier: 3.589A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.899A pdb=" N LEUSR 94 " --> pdb=" O ASPSR 90 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASNSR 108 " --> pdb=" O ASNSR 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 146 removed outlier: 3.600A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) Processing helix chain 'SR' and resid 147 through 161 removed outlier: 3.532A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Processing helix chain 'SR' and resid 180 through 189 Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.641A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 3.519A pdb=" N GLNSR 239 " --> pdb=" O THRSR 235 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 4.565A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.731A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.540A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLYSR 314 " --> pdb=" O LEUSR 310 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 345 Processing helix chain 'SR' and resid 412 through 417 removed outlier: 4.796A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 3.968A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.550A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLYSR 464 " --> pdb=" O ARGSR 460 " (cutoff:3.500A) Processing helix chain 'SR' and resid 422 through 427 removed outlier: 3.639A pdb=" N LYSSR 425 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HISSR 426 " --> pdb=" O SERSR 423 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASPSR 427 " --> pdb=" O GLUSR 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 422 through 427' Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.551A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASPSS 146 " --> pdb=" O GLUSS 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 146' Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 4.119A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILESS 247 " --> pdb=" O LYSSS 243 " (cutoff:3.500A) Proline residue: SS 248 - end of helix No H-bonds generated for 'chain 'SS' and resid 242 through 248' Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.500A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLUSS 254 " --> pdb=" O LEUSS 250 " (cutoff:3.500A) Processing helix chain 'SS' and resid 323 through 334 removed outlier: 3.672A pdb=" N LEUSS 328 " --> pdb=" O GLUSS 324 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.534A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 3.550A pdb=" N GLNST 223 " --> pdb=" O GLYST 219 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.412A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.459A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 136 removed outlier: 3.750A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILESV 108 " --> pdb=" O GLNSV 104 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALASV 136 " --> pdb=" O HISSV 132 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 4.269A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASNSW 184 " --> pdb=" O ALASW 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'SW' and resid 178 through 184' Processing helix chain 'SW' and resid 187 through 198 removed outlier: 3.534A pdb=" N LEUSW 191 " --> pdb=" O ASNSW 187 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYSSW 192 " --> pdb=" O GLUSW 188 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALASW 193 " --> pdb=" O ASNSW 189 " (cutoff:3.500A) Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.690A pdb=" N ARGSW 211 " --> pdb=" O HISSW 207 " (cutoff:3.500A) Proline residue: SW 212 - end of helix Processing helix chain 'SW' and resid 228 through 245 removed outlier: 3.627A pdb=" N PHESW 233 " --> pdb=" O LYSSW 229 " (cutoff:3.500A) Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 removed outlier: 3.820A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 290 through 301 removed outlier: 3.506A pdb=" N GLUSW 294 " --> pdb=" O ASNSW 290 " (cutoff:3.500A) Processing helix chain 'SW' and resid 308 through 318 removed outlier: 3.540A pdb=" N LEUSW 312 " --> pdb=" O THRSW 308 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.704A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) Processing helix chain 'SW' and resid 343 through 355 removed outlier: 3.610A pdb=" N GLNSW 349 " --> pdb=" O GLUSW 345 " (cutoff:3.500A) Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 Processing helix chain 'SW' and resid 408 through 424 removed outlier: 5.146A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEUSW 414 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) Processing helix chain 'SW' and resid 434 through 449 removed outlier: 4.483A pdb=" N ASPSW 449 " --> pdb=" O LEUSW 445 " (cutoff:3.500A) Processing helix chain 'SW' and resid 460 through 475 removed outlier: 5.515A pdb=" N ASPSW 475 " --> pdb=" O PHESW 471 " (cutoff:3.500A) Processing helix chain 'SW' and resid 482 through 487 Processing helix chain 'SW' and resid 505 through 516 removed outlier: 3.639A pdb=" N GLYSW 514 " --> pdb=" O ILESW 510 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THRSW 516 " --> pdb=" O ARGSW 512 " (cutoff:3.500A) Processing helix chain 'SW' and resid 534 through 545 removed outlier: 4.654A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SERSW 544 " --> pdb=" O TYRSW 540 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 573 removed outlier: 5.051A pdb=" N TYRSW 573 " --> pdb=" O ILESW 569 " (cutoff:3.500A) Processing helix chain 'SW' and resid 574 through 593 Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 removed outlier: 3.673A pdb=" N LEUSW 611 " --> pdb=" O PROSW 607 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SERSW 612 " --> pdb=" O GLNSW 608 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.921A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 18 through 32 Proline residue: SZ 32 - end of helix Processing helix chain 'SZ' and resid 36 through 43 Processing helix chain 'SZ' and resid 48 through 57 Processing helix chain 'SZ' and resid 61 through 67 Proline residue: SZ 67 - end of helix Processing helix chain 'SZ' and resid 90 through 104 removed outlier: 4.677A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASNSZ 95 " --> pdb=" O PROSZ 91 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEUSZ 103 " --> pdb=" O ALASZ 99 " (cutoff:3.500A) Proline residue: SZ 104 - end of helix Processing helix chain 'SZ' and resid 112 through 126 Processing helix chain 'SZ' and resid 129 through 136 removed outlier: 3.523A pdb=" N ARGSZ 135 " --> pdb=" O LYSSZ 131 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 144 through 159 Processing helix chain 'SZ' and resid 160 through 178 Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 3.934A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 3, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.405A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.539A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.412A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.758A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.326A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILELA 146 " --> pdb=" O GLYLA 19 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'LB' and resid 118 through 121 removed outlier: 3.559A pdb=" N ALALB 102 " --> pdb=" O LEULB 121 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.621A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.302A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.887A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LE' and resid 39 through 42 removed outlier: 4.320A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 14, first strand: chain 'LG' and resid 24 through 27 removed outlier: 5.110A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LG' and resid 60 through 63 removed outlier: 6.948A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.268A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.771A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LI' and resid 71 through 75 removed outlier: 3.573A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.708A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 21, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.472A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYSLL 65 " --> pdb=" O THRLL 48 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LN' and resid 41 through 44 removed outlier: 6.006A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N METLN 84 " --> pdb=" O VALLN 205 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LN' and resid 53 through 60 removed outlier: 6.780A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLYLN 225 " --> pdb=" O GLYLN 273 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLYLN 273 " --> pdb=" O GLYLN 225 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.714A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LN' and resid 286 through 289 removed outlier: 3.566A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 27, first strand: chain 'LN' and resid 88 through 93 Processing sheet with id= 28, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.269A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 30, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.920A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LT' and resid 8 through 12 removed outlier: 6.095A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 33, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.232A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ALALW 26 " --> pdb=" O GLYLW 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THRLW 33 " --> pdb=" O HISLW 28 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'NF' and resid 147 through 150 removed outlier: 3.701A pdb=" N ARGNF 148 " --> pdb=" O ARGNF 169 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.599A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'NN' and resid 30 through 35 removed outlier: 4.851A pdb=" N VALNN 95 " --> pdb=" O VALNN 112 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THRNN 109 " --> pdb=" O ILENN 284 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THRNN 280 " --> pdb=" O LYSNN 113 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEUNN 283 " --> pdb=" O GLNNN 190 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLNNN 190 " --> pdb=" O LEUNN 283 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'NN' and resid 106 through 109 removed outlier: 3.685A pdb=" N LYSNN 285 " --> pdb=" O THRNN 109 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'NN' and resid 197 through 203 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'SA' and resid 6 through 10 removed outlier: 4.964A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.470A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'SC' and resid 90 through 95 removed outlier: 8.787A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.421A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 44, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.212A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 46, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.923A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 48, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.336A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.654A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SG' and resid 88 through 92 removed outlier: 3.511A pdb=" N ARGSG 89 " --> pdb=" O GLYSG 185 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SH' and resid 72 through 76 removed outlier: 3.560A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.566A pdb=" N GLYSI 150 " --> pdb=" O PHESI 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SK' and resid 2 through 5 removed outlier: 3.506A pdb=" N CYSSK 206 " --> pdb=" O VALSK 3 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 55, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 56, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 57, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 58, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.249A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 60, first strand: chain 'SL' and resid 210 through 216 removed outlier: 6.155A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.512A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 63, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.184A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.506A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.020A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THRSQ 105 " --> pdb=" O TYRSQ 39 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.821A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 68, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.646A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.374A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SR' and resid 205 through 211 removed outlier: 5.238A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.517A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUSS 196 " --> pdb=" O ARGSS 183 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.598A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SV' and resid 18 through 23 removed outlier: 4.425A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SW' and resid 281 through 285 removed outlier: 3.561A pdb=" N ASPSW 333 " --> pdb=" O LEUSW 257 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEUSW 219 " --> pdb=" O THRSW 360 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALASW 223 " --> pdb=" O SERSW 364 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VALSW 386 " --> pdb=" O LEUSW 220 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALASW 222 " --> pdb=" O VALSW 386 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VALSW 388 " --> pdb=" O ALASW 222 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SW' and resid 452 through 455 removed outlier: 3.590A pdb=" N GLYSW 477 " --> pdb=" O LYSSW 426 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILESW 529 " --> pdb=" O GLNSW 499 " (cutoff:3.500A) 2975 hydrogen bonds defined for protein. 8855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1750 hydrogen bonds 3054 hydrogen bond angles 0 basepair planarities 661 basepair parallelities 1010 stacking parallelities Total time for adding SS restraints: 76.59 Time building geometry restraints manager: 38.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22518 1.33 - 1.45: 36105 1.45 - 1.58: 51859 1.58 - 1.70: 4059 1.70 - 1.82: 448 Bond restraints: 114989 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.517 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.397 -0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.405 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1' GDPSR1001 " pdb=" N9 GDPSR1001 " ideal model delta sigma weight residual 1.485 1.423 0.062 2.00e-02 2.50e+03 9.72e+00 ... (remaining 114984 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.81: 13745 106.81 - 114.95: 72566 114.95 - 123.09: 65007 123.09 - 131.22: 13052 131.22 - 139.36: 542 Bond angle restraints: 164912 Sorted by residual: angle pdb=" C LYSLS 87 " pdb=" CA LYSLS 87 " pdb=" CB LYSLS 87 " ideal model delta sigma weight residual 116.54 111.38 5.16 1.15e+00 7.56e-01 2.02e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 121.21 -13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" N ILELG 40 " pdb=" CA ILELG 40 " pdb=" C ILELG 40 " ideal model delta sigma weight residual 112.12 109.00 3.12 8.40e-01 1.42e+00 1.38e+01 angle pdb=" CA PROLG 70 " pdb=" N PROLG 70 " pdb=" CD PROLG 70 " ideal model delta sigma weight residual 112.00 107.21 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" N LEUSQ 20 " pdb=" CA LEUSQ 20 " pdb=" CB LEUSQ 20 " ideal model delta sigma weight residual 114.17 110.55 3.62 1.14e+00 7.69e-01 1.01e+01 ... (remaining 164907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 67701 35.94 - 71.88: 4989 71.88 - 107.81: 711 107.81 - 143.75: 10 143.75 - 179.69: 8 Dihedral angle restraints: 73419 sinusoidal: 50028 harmonic: 23391 Sorted by residual: dihedral pdb=" O4' CL33869 " pdb=" C1' CL33869 " pdb=" N1 CL33869 " pdb=" C2 CL33869 " ideal model delta sinusoidal sigma weight residual -160.00 18.94 -178.94 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CL35008 " pdb=" C1' CL35008 " pdb=" N1 CL35008 " pdb=" C2 CL35008 " ideal model delta sinusoidal sigma weight residual -160.00 10.93 -170.93 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 30.74 169.26 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 73416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 18966 0.079 - 0.159: 931 0.159 - 0.238: 10 0.238 - 0.318: 0 0.318 - 0.397: 1 Chirality restraints: 19908 Sorted by residual: chirality pdb=" CB VALL7 185 " pdb=" CA VALL7 185 " pdb=" CG1 VALL7 185 " pdb=" CG2 VALL7 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1' GL31854 " pdb=" O4' GL31854 " pdb=" C2' GL31854 " pdb=" N9 GL31854 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C1' AL3 746 " pdb=" O4' AL3 746 " pdb=" C2' AL3 746 " pdb=" N9 AL3 746 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 19905 not shown) Planarity restraints: 13332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.049 2.00e-02 2.50e+03 2.00e-02 1.20e+01 pdb=" N9 GL1 39 " 0.043 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " 0.009 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.007 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.015 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.005 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.004 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.008 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERBA 38 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PROBA 39 " 0.143 5.00e-02 4.00e+02 pdb=" CA PROBA 39 " -0.043 5.00e-02 4.00e+02 pdb=" CD PROBA 39 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHESI 151 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PROSI 152 " -0.141 5.00e-02 4.00e+02 pdb=" CA PROSI 152 " 0.042 5.00e-02 4.00e+02 pdb=" CD PROSI 152 " 0.045 5.00e-02 4.00e+02 ... (remaining 13329 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 492 2.54 - 3.19: 89580 3.19 - 3.84: 225446 3.84 - 4.49: 323839 4.49 - 5.14: 462687 Nonbonded interactions: 1102044 Sorted by model distance: nonbonded pdb=" OP2 GL32280 " pdb="MG MGL36017 " model vdw 1.885 2.170 nonbonded pdb=" O6 GL3 356 " pdb="MG MGL36010 " model vdw 1.919 2.170 nonbonded pdb=" O5' GL34975 " pdb="MG MGL36021 " model vdw 1.937 2.170 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36030 " model vdw 1.972 2.170 nonbonded pdb=" OG SERLN 304 " pdb=" O SERLN 310 " model vdw 1.989 2.440 ... (remaining 1102039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.060 Extract box with map and model: 23.850 Check model and map are aligned: 1.160 Set scattering table: 0.700 Process input model: 316.580 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 360.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.004 0.167 114989 Z= 0.223 Angle : 0.568 13.208 164912 Z= 0.298 Chirality : 0.036 0.397 19908 Planarity : 0.005 0.082 13332 Dihedral : 20.514 179.688 58233 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.01 % Allowed : 0.07 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.20 (0.09), residues: 7869 helix: 1.68 (0.09), residues: 3285 sheet: 0.48 (0.15), residues: 1099 loop : 0.14 (0.10), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPSE 237 HIS 0.010 0.001 HISLA 25 PHE 0.020 0.001 PHESR 69 TYR 0.030 0.001 TYRLC 84 ARG 0.012 0.001 ARGL6 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 876 time to evaluate : 6.776 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: BA 46 ILE cc_start: 0.8527 (mt) cc_final: 0.8239 (mt) REVERT: LA 111 SER cc_start: 0.7257 (m) cc_final: 0.6827 (m) REVERT: LC 30 MET cc_start: 0.8146 (ttm) cc_final: 0.7917 (ttm) REVERT: NN 193 ASP cc_start: 0.6903 (m-30) cc_final: 0.6113 (m-30) REVERT: SC 56 ARG cc_start: 0.5473 (ttt90) cc_final: 0.4949 (tmt170) REVERT: SC 205 ASN cc_start: 0.6963 (p0) cc_final: 0.6728 (p0) REVERT: SC 254 ASP cc_start: 0.6245 (m-30) cc_final: 0.5882 (m-30) REVERT: SN 161 MET cc_start: 0.7695 (mmm) cc_final: 0.7491 (mtm) REVERT: SN 191 GLU cc_start: 0.6695 (tt0) cc_final: 0.6489 (tt0) REVERT: SO 83 MET cc_start: 0.8047 (tpp) cc_final: 0.7782 (tpp) REVERT: ST 216 GLU cc_start: 0.7933 (pm20) cc_final: 0.7655 (mp0) REVERT: SV 70 GLU cc_start: 0.6952 (mp0) cc_final: 0.6529 (mp0) outliers start: 1 outliers final: 2 residues processed: 877 average time/residue: 1.7200 time to fit residues: 2101.2423 Evaluate side-chains 665 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 663 time to evaluate : 6.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 67 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 830 optimal weight: 7.9990 chunk 745 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 503 optimal weight: 3.9990 chunk 398 optimal weight: 0.0010 chunk 771 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 468 optimal weight: 9.9990 chunk 574 optimal weight: 3.9990 chunk 893 optimal weight: 7.9990 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 142 ASN L6 104 ASN L7 90 HIS L8 69 HIS ** LA 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 28 ASN LA 54 GLN LA 93 HIS LE 112 ASN LE 144 ASN LG 77 HIS LH 57 GLN LI 43 ASN LK 62 HIS LN 109 HIS LS 30 GLN LS 63 GLN LS 65 GLN LS 107 GLN LW 66 HIS NE 235 ASN NF 68 HIS NF 104 ASN NG 161 ASN NG 181 GLN NN 10 GLN NN 131 HIS NN 175 ASN SC 136 HIS SC 190 HIS ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SE 236 HIS ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 156 ASN SH 51 HIS SH 60 GLN SH 67 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 68 HIS SK 79 GLN SL 46 HIS SL 218 HIS SM 211 HIS SO 340 GLN SR 35 HIS SR 37 HIS SR 157 HIS SR 209 HIS SR 239 GLN ** SS 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 213 GLN SV 17 HIS SV 101 GLN SV 115 ASN SW 593 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 114989 Z= 0.246 Angle : 0.550 12.202 164912 Z= 0.286 Chirality : 0.037 0.231 19908 Planarity : 0.004 0.066 13332 Dihedral : 22.072 178.921 41392 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.59 % Allowed : 6.55 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.53 (0.09), residues: 7869 helix: 2.15 (0.09), residues: 3336 sheet: 0.46 (0.15), residues: 1090 loop : 0.15 (0.10), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPNE 307 HIS 0.011 0.001 HISLA 25 PHE 0.022 0.002 PHESH 165 TYR 0.030 0.002 TYRSK 113 ARG 0.008 0.001 ARGBA 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 687 time to evaluate : 6.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 173 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.7038 (mt0) REVERT: LA 40 HIS cc_start: 0.5801 (t-90) cc_final: 0.5582 (t-90) REVERT: LA 42 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8328 (mmp80) REVERT: LN 168 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7554 (mmt) REVERT: LN 397 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7352 (mp) REVERT: NE 284 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7241 (p0) REVERT: NG 165 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7925 (tp) REVERT: SC 56 ARG cc_start: 0.5594 (ttt90) cc_final: 0.5062 (tmt170) REVERT: SC 205 ASN cc_start: 0.7024 (p0) cc_final: 0.6800 (p0) REVERT: SC 250 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: SH 42 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7763 (mp) REVERT: SL 271 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6369 (t60) REVERT: SM 414 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: SO 85 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7264 (mtt) REVERT: SO 154 MET cc_start: 0.8087 (mtm) cc_final: 0.7795 (mtt) REVERT: SS 138 ASN cc_start: 0.7540 (p0) cc_final: 0.7331 (p0) REVERT: ST 216 GLU cc_start: 0.7826 (pm20) cc_final: 0.7564 (mp0) REVERT: SV 70 GLU cc_start: 0.7148 (mp0) cc_final: 0.6795 (mp0) outliers start: 109 outliers final: 39 residues processed: 734 average time/residue: 1.7569 time to fit residues: 1788.1672 Evaluate side-chains 673 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 624 time to evaluate : 6.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain L6 residue 130 LYS Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LG residue 20 LEU Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LN residue 157 CYS Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 397 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 49 VAL Chi-restraints excluded: chain LU residue 32 ARG Chi-restraints excluded: chain LW residue 29 LEU Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 284 ASP Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SC residue 250 GLN Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SH residue 42 LEU Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 414 PHE Chi-restraints excluded: chain SN residue 209 LYS Chi-restraints excluded: chain SO residue 85 MET Chi-restraints excluded: chain SQ residue 30 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SW residue 286 MET Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SZ residue 114 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 496 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 743 optimal weight: 4.9990 chunk 608 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 895 optimal weight: 3.9990 chunk 967 optimal weight: 2.9990 chunk 797 optimal weight: 9.9990 chunk 887 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 718 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 93 HIS LC 125 GLN LN 109 HIS LS 30 GLN LS 65 GLN LS 107 GLN LT 21 GLN NE 235 ASN NE 353 GLN ** NF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NG 181 GLN SG 98 HIS ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN SK 82 GLN SK 86 ASN SL 189 ASN SM 253 GLN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 361 GLN SV 101 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 114989 Z= 0.269 Angle : 0.540 10.245 164912 Z= 0.280 Chirality : 0.037 0.238 19908 Planarity : 0.004 0.073 13332 Dihedral : 21.975 178.835 41389 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.01 % Allowed : 8.63 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.48 (0.09), residues: 7869 helix: 2.18 (0.09), residues: 3347 sheet: 0.34 (0.15), residues: 1078 loop : 0.06 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPNE 307 HIS 0.011 0.001 HISL6 67 PHE 0.026 0.002 PHESO 65 TYR 0.022 0.002 TYRSK 113 ARG 0.009 0.001 ARGSM 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 671 time to evaluate : 6.748 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: BA 103 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.7107 (m-40) REVERT: L6 130 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6016 (mmmm) REVERT: LA 42 ARG cc_start: 0.8677 (tpp-160) cc_final: 0.8339 (mmp80) REVERT: LB 93 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: LU 32 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6638 (mmt90) REVERT: NF 60 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7630 (tp-100) REVERT: SC 56 ARG cc_start: 0.5717 (ttt90) cc_final: 0.5104 (tmt170) REVERT: SH 42 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7808 (mp) REVERT: SJ 666 GLU cc_start: 0.7749 (mp0) cc_final: 0.7283 (mp0) REVERT: SL 271 TRP cc_start: 0.7046 (OUTLIER) cc_final: 0.6358 (t60) REVERT: SO 83 MET cc_start: 0.8169 (tpp) cc_final: 0.7885 (tpp) REVERT: SO 85 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7270 (mtt) REVERT: SO 347 MET cc_start: 0.6679 (mmt) cc_final: 0.6239 (mmt) REVERT: SV 104 GLN cc_start: 0.7869 (mt0) cc_final: 0.7656 (mt0) REVERT: SW 265 MET cc_start: 0.6687 (mpp) cc_final: 0.6119 (mmm) outliers start: 138 outliers final: 52 residues processed: 730 average time/residue: 1.7834 time to fit residues: 1809.3803 Evaluate side-chains 681 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 621 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 103 ASN Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 130 LYS Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain LA residue 149 ILE Chi-restraints excluded: chain LB residue 93 GLN Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LN residue 157 CYS Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LU residue 32 ARG Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 60 GLN Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 196 ILE Chi-restraints excluded: chain NG residue 146 CYS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 20 LYS Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SC residue 112 MET Chi-restraints excluded: chain SH residue 42 LEU Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SN residue 209 LYS Chi-restraints excluded: chain SO residue 85 MET Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SR residue 447 MET Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 296 HIS Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 435 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 884 optimal weight: 0.2980 chunk 673 optimal weight: 0.5980 chunk 464 optimal weight: 4.9990 chunk 99 optimal weight: 40.0000 chunk 427 optimal weight: 5.9990 chunk 601 optimal weight: 6.9990 chunk 898 optimal weight: 0.9990 chunk 951 optimal weight: 3.9990 chunk 469 optimal weight: 30.0000 chunk 851 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN LA 56 GLN LA 93 HIS LN 109 HIS LS 30 GLN LS 65 GLN LS 107 GLN NE 235 ASN ** NF 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NG 161 ASN NG 180 HIS ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 114989 Z= 0.157 Angle : 0.482 10.028 164912 Z= 0.251 Chirality : 0.034 0.211 19908 Planarity : 0.004 0.056 13332 Dihedral : 21.921 179.345 41389 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.65 % Allowed : 10.30 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.63 (0.09), residues: 7869 helix: 2.35 (0.09), residues: 3345 sheet: 0.41 (0.15), residues: 1077 loop : 0.09 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.009 0.001 HISSJ 726 PHE 0.028 0.001 PHELK 69 TYR 0.023 0.001 TYRSK 23 ARG 0.008 0.000 ARGBA 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 653 time to evaluate : 7.014 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: L7 173 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: LA 42 ARG cc_start: 0.8460 (tpp-160) cc_final: 0.8228 (mmp80) REVERT: LB 82 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9031 (p) REVERT: LG 72 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7754 (mm) REVERT: NF 243 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7529 (tm-30) REVERT: SA 95 MET cc_start: 0.8551 (pmm) cc_final: 0.8276 (mpp) REVERT: SC 56 ARG cc_start: 0.5623 (ttt90) cc_final: 0.5065 (tmt170) REVERT: SK 140 GLN cc_start: 0.6172 (mm-40) cc_final: 0.5965 (mm110) REVERT: SL 271 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.6353 (t60) REVERT: SO 83 MET cc_start: 0.8111 (tpp) cc_final: 0.7897 (tpp) REVERT: SQ 107 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6805 (mtt180) REVERT: SQ 119 TYR cc_start: 0.4893 (t80) cc_final: 0.4586 (t80) REVERT: SV 26 CYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6435 (t) REVERT: SW 247 MET cc_start: 0.7678 (tpt) cc_final: 0.7417 (tpp) outliers start: 113 outliers final: 46 residues processed: 712 average time/residue: 1.7817 time to fit residues: 1770.9621 Evaluate side-chains 666 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 615 time to evaluate : 6.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 130 LYS Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L8 residue 104 MET Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 141 VAL Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LN residue 157 CYS Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 49 VAL Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 196 ILE Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SR residue 447 MET Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 213 LEU Chi-restraints excluded: chain SW residue 286 MET Chi-restraints excluded: chain SW residue 435 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 792 optimal weight: 9.9990 chunk 539 optimal weight: 0.0030 chunk 13 optimal weight: 0.8980 chunk 708 optimal weight: 5.9990 chunk 392 optimal weight: 7.9990 chunk 811 optimal weight: 7.9990 chunk 657 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 485 optimal weight: 4.9990 chunk 853 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 93 HIS LN 109 HIS LQ 80 HIS LS 30 GLN LS 65 GLN LS 107 GLN NE 353 GLN ** NF 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NG 161 ASN NG 180 HIS SD 63 GLN ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SG 189 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 225 HIS SM 209 HIS SM 403 ASN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN SZ 18 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 114989 Z= 0.237 Angle : 0.511 9.576 164912 Z= 0.264 Chirality : 0.036 0.237 19908 Planarity : 0.004 0.073 13332 Dihedral : 21.859 179.539 41389 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.74 % Favored : 98.25 % Rotamer: Outliers : 2.10 % Allowed : 10.79 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.56 (0.09), residues: 7869 helix: 2.31 (0.09), residues: 3338 sheet: 0.35 (0.15), residues: 1069 loop : 0.05 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPNE 307 HIS 0.010 0.001 HISL6 67 PHE 0.021 0.002 PHESO 65 TYR 0.025 0.001 TYRSK 113 ARG 0.008 0.000 ARGBA 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 635 time to evaluate : 6.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 130 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5911 (mmmm) REVERT: L7 173 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: L8 70 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6783 (tt0) REVERT: LA 42 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.8213 (mmp80) REVERT: LB 82 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9001 (p) REVERT: LB 93 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: LG 72 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8157 (mt) REVERT: LQ 113 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: LU 32 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6763 (mmt90) REVERT: NF 60 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7617 (tp-100) REVERT: SA 95 MET cc_start: 0.8532 (pmm) cc_final: 0.8249 (mpp) REVERT: SL 271 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.6360 (t60) REVERT: SO 83 MET cc_start: 0.8074 (tpp) cc_final: 0.7852 (tpp) REVERT: SO 85 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6616 (mpp) REVERT: SQ 60 TRP cc_start: 0.7668 (m100) cc_final: 0.7441 (m100) REVERT: SQ 107 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6878 (mtt180) REVERT: SS 361 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: SV 26 CYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6486 (t) REVERT: SW 247 MET cc_start: 0.7778 (tpt) cc_final: 0.7485 (tpp) REVERT: SW 323 MET cc_start: 0.6816 (ptp) cc_final: 0.6571 (ptp) outliers start: 144 outliers final: 64 residues processed: 715 average time/residue: 1.7264 time to fit residues: 1718.2348 Evaluate side-chains 691 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 614 time to evaluate : 6.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 125 LEU Chi-restraints excluded: chain BA residue 138 SER Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 130 LYS Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 104 MET Chi-restraints excluded: chain L9 residue 189 ARG Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 93 GLN Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 141 VAL Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LN residue 157 CYS Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LU residue 32 ARG Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 60 GLN Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 196 ILE Chi-restraints excluded: chain NG residue 145 MET Chi-restraints excluded: chain NN residue 180 CYS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 20 LYS Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 26 LEU Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SN residue 209 LYS Chi-restraints excluded: chain SO residue 85 MET Chi-restraints excluded: chain SQ residue 35 ASP Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SR residue 447 MET Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 249 SER Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 361 GLN Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SZ residue 168 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 320 optimal weight: 8.9990 chunk 856 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 558 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 952 optimal weight: 5.9990 chunk 790 optimal weight: 20.0000 chunk 440 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 314 optimal weight: 7.9990 chunk 499 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L9 8 GLN LA 54 GLN LA 56 GLN LA 93 HIS LC 125 GLN LH 33 HIS LN 109 HIS LS 65 GLN LS 107 GLN NE 353 GLN ** NF 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NG 161 ASN NG 178 GLN NN 68 ASN SD 151 ASN ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SG 189 GLN SI 171 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN ** SK 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 140 GLN ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 129 ASN SR 5 ASN SR 91 HIS ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN SV 129 GLN SW 206 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 114989 Z= 0.358 Angle : 0.585 9.493 164912 Z= 0.301 Chirality : 0.039 0.210 19908 Planarity : 0.005 0.078 13332 Dihedral : 21.872 178.644 41389 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.09 % Favored : 97.90 % Rotamer: Outliers : 2.43 % Allowed : 11.48 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.28 (0.09), residues: 7869 helix: 2.08 (0.09), residues: 3334 sheet: 0.18 (0.15), residues: 1071 loop : -0.08 (0.10), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPNE 307 HIS 0.010 0.001 HISSH 51 PHE 0.033 0.002 PHENG 174 TYR 0.026 0.002 TYRSK 113 ARG 0.013 0.001 ARGNG 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 638 time to evaluate : 6.790 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: BA 103 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7185 (m-40) REVERT: L6 130 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6071 (mmmm) REVERT: L7 87 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7812 (mtt) REVERT: L7 173 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: LA 82 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6297 (mtt90) REVERT: LB 82 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8992 (p) REVERT: LB 93 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: LC 138 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7185 (mtm180) REVERT: LG 72 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8378 (mt) REVERT: LN 53 MET cc_start: 0.7810 (mtt) cc_final: 0.7497 (mtt) REVERT: LN 208 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6708 (m-40) REVERT: LQ 113 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: LU 32 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6708 (mmt90) REVERT: NN 174 LEU cc_start: 0.7942 (tp) cc_final: 0.7730 (tp) REVERT: SH 42 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7959 (mp) REVERT: SK 1 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5390 (mtt) REVERT: SL 271 TRP cc_start: 0.7141 (OUTLIER) cc_final: 0.6452 (t60) REVERT: SO 65 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8774 (p90) REVERT: SO 83 MET cc_start: 0.8092 (tpp) cc_final: 0.7830 (tpp) REVERT: SO 85 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6813 (mpp) REVERT: SQ 60 TRP cc_start: 0.7776 (m100) cc_final: 0.7558 (m100) REVERT: SQ 107 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6857 (mtt180) REVERT: SS 361 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: SV 26 CYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6511 (t) REVERT: SW 247 MET cc_start: 0.7880 (tpt) cc_final: 0.7547 (tpp) REVERT: SW 265 MET cc_start: 0.7095 (mmm) cc_final: 0.6515 (mmt) outliers start: 167 outliers final: 80 residues processed: 731 average time/residue: 1.7140 time to fit residues: 1752.9284 Evaluate side-chains 705 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 606 time to evaluate : 7.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 103 ASN Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 125 LEU Chi-restraints excluded: chain BA residue 138 SER Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 130 LYS Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 189 ARG Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LA residue 82 ARG Chi-restraints excluded: chain LA residue 149 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 93 GLN Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 138 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 141 VAL Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LN residue 77 THR Chi-restraints excluded: chain LN residue 157 CYS Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 23 ASP Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LU residue 32 ARG Chi-restraints excluded: chain LW residue 33 THR Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 192 PHE Chi-restraints excluded: chain NF residue 196 ILE Chi-restraints excluded: chain NG residue 139 ARG Chi-restraints excluded: chain NG residue 146 CYS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain NN residue 284 ILE Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SD residue 189 ASP Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SG residue 183 GLU Chi-restraints excluded: chain SH residue 42 LEU Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 26 LEU Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SM residue 393 VAL Chi-restraints excluded: chain SN residue 209 LYS Chi-restraints excluded: chain SO residue 65 PHE Chi-restraints excluded: chain SO residue 85 MET Chi-restraints excluded: chain SQ residue 115 TRP Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 225 ILE Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SS residue 189 MET Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 249 SER Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 361 GLN Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 52 THR Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SZ residue 168 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 917 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 542 optimal weight: 2.9990 chunk 695 optimal weight: 5.9990 chunk 538 optimal weight: 0.9980 chunk 801 optimal weight: 0.8980 chunk 531 optimal weight: 2.9990 chunk 948 optimal weight: 0.7980 chunk 593 optimal weight: 0.9980 chunk 578 optimal weight: 0.9990 chunk 437 optimal weight: 0.0050 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L9 32 GLN LA 54 GLN LA 56 GLN LA 93 HIS LN 109 HIS LS 30 GLN LS 65 GLN LS 107 GLN NE 353 GLN ** NF 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NG 161 ASN NG 178 GLN NG 180 HIS ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SI 171 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN SK 86 ASN ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 5 ASN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 114989 Z= 0.127 Angle : 0.484 11.574 164912 Z= 0.250 Chirality : 0.033 0.214 19908 Planarity : 0.004 0.048 13332 Dihedral : 21.845 179.119 41389 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 13.09 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.55 (0.09), residues: 7869 helix: 2.34 (0.09), residues: 3336 sheet: 0.26 (0.15), residues: 1067 loop : 0.04 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPL9 120 HIS 0.011 0.001 HISSJ 726 PHE 0.015 0.001 PHESL 267 TYR 0.023 0.001 TYRLG 38 ARG 0.014 0.000 ARGNG 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 649 time to evaluate : 6.930 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: L7 173 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: LA 50 ASP cc_start: 0.6914 (t0) cc_final: 0.6295 (t0) REVERT: LB 82 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.9008 (p) REVERT: LE 152 GLU cc_start: 0.6300 (tp30) cc_final: 0.5365 (tp30) REVERT: LG 72 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8209 (mt) REVERT: LN 97 ARG cc_start: 0.6613 (tmm160) cc_final: 0.5774 (tpt170) REVERT: LN 332 MET cc_start: 0.7348 (ttp) cc_final: 0.6958 (ttp) REVERT: LQ 113 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: SJ 725 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6365 (mm-30) REVERT: SL 268 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7547 (m) REVERT: SQ 60 TRP cc_start: 0.7645 (m100) cc_final: 0.7436 (m100) REVERT: SR 4 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.5624 (m-10) REVERT: SV 26 CYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6522 (t) REVERT: SV 77 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6864 (mm-30) REVERT: SW 247 MET cc_start: 0.7851 (tpt) cc_final: 0.7516 (tpp) REVERT: SW 265 MET cc_start: 0.7094 (mmm) cc_final: 0.6637 (mmm) outliers start: 96 outliers final: 50 residues processed: 700 average time/residue: 1.7109 time to fit residues: 1672.1573 Evaluate side-chains 671 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 614 time to evaluate : 6.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 23 ASP Chi-restraints excluded: chain LS residue 113 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 192 PHE Chi-restraints excluded: chain NG residue 139 ARG Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SG residue 66 GLU Chi-restraints excluded: chain SI residue 26 LEU Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SQ residue 115 TRP Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 5 ASN Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SR residue 447 MET Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SZ residue 168 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 586 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 chunk 566 optimal weight: 0.0020 chunk 285 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 602 optimal weight: 5.9990 chunk 646 optimal weight: 5.9990 chunk 468 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 745 optimal weight: 5.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 54 GLN LA 93 HIS LN 109 HIS LS 107 GLN NE 353 GLN NF 68 HIS NF 72 ASN NG 161 ASN NG 178 GLN NG 180 HIS ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SI 171 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN ** SK 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 114989 Z= 0.364 Angle : 0.576 12.204 164912 Z= 0.295 Chirality : 0.039 0.268 19908 Planarity : 0.005 0.068 13332 Dihedral : 21.795 178.939 41389 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.84 % Allowed : 13.13 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.32 (0.09), residues: 7869 helix: 2.14 (0.09), residues: 3332 sheet: 0.15 (0.15), residues: 1079 loop : -0.08 (0.10), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPNE 307 HIS 0.010 0.001 HISSH 51 PHE 0.024 0.002 PHESR 18 TYR 0.031 0.002 TYRSK 113 ARG 0.016 0.001 ARGNG 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 619 time to evaluate : 6.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 130 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6256 (mmtm) REVERT: L7 173 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: LB 82 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8999 (p) REVERT: LC 138 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7180 (mtm180) REVERT: LN 97 ARG cc_start: 0.6657 (tmm160) cc_final: 0.5602 (tpt170) REVERT: LN 208 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.6841 (m-40) REVERT: LQ 113 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: LU 32 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6704 (mmt90) REVERT: NG 195 MET cc_start: 0.4394 (tpt) cc_final: 0.3866 (tpt) REVERT: SG 128 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.6292 (mpt) REVERT: SK 1 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5437 (mtt) REVERT: SL 268 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7597 (m) REVERT: SL 271 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.6363 (t60) REVERT: SN 106 MET cc_start: 0.7125 (mmm) cc_final: 0.6886 (mmm) REVERT: SO 83 MET cc_start: 0.8185 (tpp) cc_final: 0.7955 (tpt) REVERT: SO 85 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6799 (mpp) REVERT: SR 4 TYR cc_start: 0.5903 (OUTLIER) cc_final: 0.5652 (m-10) REVERT: SR 137 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8489 (mtt) REVERT: SV 26 CYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6732 (t) REVERT: SV 77 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6927 (mm-30) REVERT: SW 247 MET cc_start: 0.7883 (tpt) cc_final: 0.7528 (tpp) REVERT: SW 265 MET cc_start: 0.7064 (mmm) cc_final: 0.6632 (mmm) outliers start: 126 outliers final: 70 residues processed: 693 average time/residue: 1.7277 time to fit residues: 1679.4011 Evaluate side-chains 693 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 608 time to evaluate : 6.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 76 SER Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 125 LEU Chi-restraints excluded: chain BA residue 138 SER Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 130 LYS Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 138 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LN residue 77 THR Chi-restraints excluded: chain LN residue 157 CYS Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LU residue 32 ARG Chi-restraints excluded: chain LU residue 37 THR Chi-restraints excluded: chain LW residue 33 THR Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 192 PHE Chi-restraints excluded: chain NG residue 139 ARG Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 193 LEU Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SG residue 66 GLU Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 26 LEU Chi-restraints excluded: chain SI residue 193 CYS Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 711 GLN Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SM residue 393 VAL Chi-restraints excluded: chain SO residue 85 MET Chi-restraints excluded: chain SO residue 347 MET Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 137 MET Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SR residue 447 MET Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 435 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 862 optimal weight: 2.9990 chunk 908 optimal weight: 0.9980 chunk 828 optimal weight: 0.9980 chunk 883 optimal weight: 9.9990 chunk 531 optimal weight: 7.9990 chunk 385 optimal weight: 0.2980 chunk 693 optimal weight: 1.9990 chunk 271 optimal weight: 0.8980 chunk 798 optimal weight: 2.9990 chunk 835 optimal weight: 0.0060 chunk 880 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 93 HIS LN 109 HIS LS 30 GLN LS 107 GLN NE 353 GLN NG 178 GLN NG 180 HIS ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SI 171 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 121 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 5 ASN SV 101 GLN SW 278 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 114989 Z= 0.127 Angle : 0.481 12.428 164912 Z= 0.249 Chirality : 0.033 0.259 19908 Planarity : 0.004 0.054 13332 Dihedral : 21.788 179.505 41389 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.27 % Allowed : 14.05 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.55 (0.09), residues: 7869 helix: 2.37 (0.09), residues: 3337 sheet: 0.23 (0.15), residues: 1064 loop : 0.01 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPBA 53 HIS 0.014 0.001 HISSJ 726 PHE 0.014 0.001 PHESL 267 TYR 0.025 0.001 TYRLG 38 ARG 0.018 0.000 ARGNG 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 632 time to evaluate : 6.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 173 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: LB 82 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8979 (p) REVERT: LI 117 LYS cc_start: 0.7307 (tptp) cc_final: 0.7106 (pttt) REVERT: LN 53 MET cc_start: 0.7540 (mtt) cc_final: 0.7103 (mtt) REVERT: LN 97 ARG cc_start: 0.6571 (tmm160) cc_final: 0.5595 (tpt170) REVERT: LQ 113 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: NG 195 MET cc_start: 0.4209 (tpt) cc_final: 0.3638 (tpt) REVERT: SD 247 MET cc_start: 0.8108 (mmm) cc_final: 0.7860 (mtp) REVERT: SI 26 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6811 (mt) REVERT: SK 1 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5384 (mtt) REVERT: SL 268 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7551 (m) REVERT: SL 271 TRP cc_start: 0.6989 (OUTLIER) cc_final: 0.6410 (t60) REVERT: SN 106 MET cc_start: 0.7025 (mmm) cc_final: 0.6819 (mmm) REVERT: SN 170 LEU cc_start: 0.8741 (mm) cc_final: 0.8496 (tp) REVERT: SO 83 MET cc_start: 0.8127 (tpp) cc_final: 0.7901 (tpp) REVERT: SO 347 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6367 (mmt) REVERT: SR 422 LEU cc_start: 0.7890 (mt) cc_final: 0.7682 (pp) REVERT: SV 26 CYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6546 (t) REVERT: SW 247 MET cc_start: 0.7854 (tpt) cc_final: 0.7516 (tpp) REVERT: SW 265 MET cc_start: 0.7106 (mmm) cc_final: 0.6527 (mmm) REVERT: SW 361 MET cc_start: 0.6938 (mpp) cc_final: 0.6403 (mpp) outliers start: 87 outliers final: 55 residues processed: 682 average time/residue: 1.7671 time to fit residues: 1681.1876 Evaluate side-chains 682 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 618 time to evaluate : 7.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 76 SER Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 125 LEU Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 192 PHE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 180 CYS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SG residue 66 GLU Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SI residue 26 LEU Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SO residue 347 MET Chi-restraints excluded: chain SQ residue 207 MET Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 435 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 580 optimal weight: 10.0000 chunk 934 optimal weight: 30.0000 chunk 570 optimal weight: 4.9990 chunk 443 optimal weight: 4.9990 chunk 649 optimal weight: 1.9990 chunk 980 optimal weight: 0.9990 chunk 902 optimal weight: 20.0000 chunk 780 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 602 optimal weight: 0.7980 chunk 478 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS LA 93 HIS LN 109 HIS LS 65 GLN LS 107 GLN NE 353 GLN NG 161 ASN NG 178 GLN NG 180 HIS ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SI 171 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 79 GLN ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 217 GLN ** SR 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 114989 Z= 0.191 Angle : 0.495 13.012 164912 Z= 0.255 Chirality : 0.034 0.262 19908 Planarity : 0.004 0.054 13332 Dihedral : 21.732 179.730 41389 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.93 % Favored : 98.05 % Rotamer: Outliers : 1.27 % Allowed : 14.22 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.55 (0.09), residues: 7869 helix: 2.36 (0.09), residues: 3335 sheet: 0.23 (0.15), residues: 1068 loop : 0.02 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRPBA 53 HIS 0.010 0.001 HISBA 147 PHE 0.022 0.001 PHEL7 47 TYR 0.025 0.001 TYRSK 113 ARG 0.020 0.000 ARGNG 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15738 Ramachandran restraints generated. 7869 Oldfield, 0 Emsley, 7869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 628 time to evaluate : 7.102 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: BA 70 GLN cc_start: 0.6184 (tp-100) cc_final: 0.5165 (tp-100) REVERT: L7 173 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: LB 82 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8977 (p) REVERT: LC 138 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7162 (mtm180) REVERT: LI 117 LYS cc_start: 0.7336 (tptp) cc_final: 0.7115 (pttt) REVERT: LN 97 ARG cc_start: 0.6625 (tmm160) cc_final: 0.5892 (tpt170) REVERT: LN 208 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6762 (m-40) REVERT: LQ 113 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: NF 205 SER cc_start: 0.6577 (m) cc_final: 0.6300 (p) REVERT: NG 195 MET cc_start: 0.4078 (tpt) cc_final: 0.3473 (tpt) REVERT: SI 26 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6838 (mt) REVERT: SK 1 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5407 (mtt) REVERT: SL 268 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7541 (m) REVERT: SL 271 TRP cc_start: 0.6995 (OUTLIER) cc_final: 0.6407 (t60) REVERT: SN 106 MET cc_start: 0.7070 (mmm) cc_final: 0.6862 (mmm) REVERT: SN 170 LEU cc_start: 0.8744 (mm) cc_final: 0.8502 (tp) REVERT: SO 347 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.6265 (mmt) REVERT: SS 377 ARG cc_start: 0.7195 (ptt180) cc_final: 0.6911 (ptt180) REVERT: SV 26 CYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6704 (t) REVERT: SW 247 MET cc_start: 0.7857 (tpt) cc_final: 0.7524 (tpp) REVERT: SW 265 MET cc_start: 0.7138 (mmm) cc_final: 0.6479 (mmm) REVERT: SW 361 MET cc_start: 0.6896 (mpp) cc_final: 0.6387 (mpp) outliers start: 87 outliers final: 62 residues processed: 676 average time/residue: 1.8009 time to fit residues: 1699.5561 Evaluate side-chains 690 residues out of total 7068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 617 time to evaluate : 6.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 76 SER Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 125 LEU Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L7 residue 158 GLU Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 138 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 23 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 113 GLU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LU residue 37 THR Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 154 CYS Chi-restraints excluded: chain NF residue 192 PHE Chi-restraints excluded: chain NG residue 139 ARG Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 180 CYS Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SD residue 41 MET Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 235 ARG Chi-restraints excluded: chain SG residue 66 GLU Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 77 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 26 LEU Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SM residue 393 VAL Chi-restraints excluded: chain SO residue 347 MET Chi-restraints excluded: chain SQ residue 207 MET Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 340 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 373 CYS Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 26 CYS Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SW residue 324 TYR Chi-restraints excluded: chain SW residue 435 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 984 random chunks: chunk 620 optimal weight: 6.9990 chunk 831 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 719 optimal weight: 0.9980 chunk 115 optimal weight: 40.0000 chunk 216 optimal weight: 10.0000 chunk 781 optimal weight: 9.9990 chunk 327 optimal weight: 30.0000 chunk 802 optimal weight: 0.7980 chunk 98 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS LA 93 HIS LN 109 HIS LS 65 GLN LS 107 GLN NE 353 GLN NF 72 ASN NG 178 GLN NG 180 HIS ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SI 171 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 140 GLN ** SK 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 310 HIS SV 101 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.086349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063306 restraints weight = 346918.471| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.73 r_work: 0.3161 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 114989 Z= 0.218 Angle : 0.512 17.095 164912 Z= 0.263 Chirality : 0.035 0.258 19908 Planarity : 0.004 0.056 13332 Dihedral : 21.724 179.532 41389 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.39 % Allowed : 14.13 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 1.51 (0.09), residues: 7869 helix: 2.33 (0.09), residues: 3329 sheet: 0.22 (0.15), residues: 1062 loop : 0.00 (0.10), residues: 3478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRPBA 53 HIS 0.010 0.001 HISBA 147 PHE 0.019 0.001 PHESR 18 TYR 0.026 0.001 TYRLG 38 ARG 0.022 0.000 ARGNG 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30331.50 seconds wall clock time: 528 minutes 11.54 seconds (31691.54 seconds total)