Starting phenix.real_space_refine on Sun Feb 18 04:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkz_29262/02_2024/8fkz_29262_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkz_29262/02_2024/8fkz_29262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkz_29262/02_2024/8fkz_29262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkz_29262/02_2024/8fkz_29262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkz_29262/02_2024/8fkz_29262_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkz_29262/02_2024/8fkz_29262_neut_updated.pdb" } resolution = 3.04 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= 0.035 sd= 0.132 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 4 6.06 5 P 3057 5.49 5 Mg 64 5.21 5 S 260 5.16 5 C 69871 2.51 5 N 24372 2.21 5 O 32382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L6 GLU 108": "OE1" <-> "OE2" Residue "L6 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 ASP 113": "OD1" <-> "OD2" Residue "L7 GLU 144": "OE1" <-> "OE2" Residue "L7 GLU 158": "OE1" <-> "OE2" Residue "L7 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 194": "OE1" <-> "OE2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 29": "OD1" <-> "OD2" Residue "L8 ASP 32": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L8 GLU 99": "OE1" <-> "OE2" Residue "L9 GLU 9": "OE1" <-> "OE2" Residue "L9 GLU 123": "OE1" <-> "OE2" Residue "LA TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 7": "OD1" <-> "OD2" Residue "LA ASP 50": "OD1" <-> "OD2" Residue "LA GLU 115": "OE1" <-> "OE2" Residue "LA TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 152": "OE1" <-> "OE2" Residue "LB GLU 17": "OE1" <-> "OE2" Residue "LB GLU 76": "OE1" <-> "OE2" Residue "LB ASP 88": "OD1" <-> "OD2" Residue "LC GLU 9": "OE1" <-> "OE2" Residue "LC TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 96": "OE1" <-> "OE2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LD GLU 111": "OE1" <-> "OE2" Residue "LD TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 137": "OE1" <-> "OE2" Residue "LE GLU 147": "OE1" <-> "OE2" Residue "LF PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 108": "OE1" <-> "OE2" Residue "LG GLU 71": "OE1" <-> "OE2" Residue "LG PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 84": "OE1" <-> "OE2" Residue "LH GLU 91": "OE1" <-> "OE2" Residue "LH ASP 118": "OD1" <-> "OD2" Residue "LI ASP 10": "OD1" <-> "OD2" Residue "LI TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ASP 112": "OD1" <-> "OD2" Residue "LJ TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ GLU 119": "OE1" <-> "OE2" Residue "LK ASP 76": "OD1" <-> "OD2" Residue "LK GLU 84": "OE1" <-> "OE2" Residue "LK ASP 102": "OD1" <-> "OD2" Residue "LK GLU 134": "OE1" <-> "OE2" Residue "LL TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 61": "OD1" <-> "OD2" Residue "LN GLU 71": "OE1" <-> "OE2" Residue "LN PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 279": "OE1" <-> "OE2" Residue "LN TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 61": "OE1" <-> "OE2" Residue "LP GLU 19": "OE1" <-> "OE2" Residue "LQ GLU 86": "OE1" <-> "OE2" Residue "LR TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR ASP 89": "OD1" <-> "OD2" Residue "LR GLU 98": "OE1" <-> "OE2" Residue "LS ASP 22": "OD1" <-> "OD2" Residue "LS ASP 23": "OD1" <-> "OD2" Residue "LS GLU 27": "OE1" <-> "OE2" Residue "LS ASP 82": "OD1" <-> "OD2" Residue "LS GLU 100": "OE1" <-> "OE2" Residue "LT GLU 31": "OE1" <-> "OE2" Residue "LT ASP 37": "OD1" <-> "OD2" Residue "LT GLU 38": "OE1" <-> "OE2" Residue "LU GLU 46": "OE1" <-> "OE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 59": "OE1" <-> "OE2" Residue "LU ASP 66": "OD1" <-> "OD2" Residue "LU GLU 89": "OE1" <-> "OE2" Residue "LW TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY GLU 7": "OE1" <-> "OE2" Residue "LY ASP 30": "OD1" <-> "OD2" Residue "LY TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY GLU 54": "OE1" <-> "OE2" Residue "NB GLU 65": "OE1" <-> "OE2" Residue "NF TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 22": "OE1" <-> "OE2" Residue "NF GLU 34": "OE1" <-> "OE2" Residue "NK GLU 16": "OE1" <-> "OE2" Residue "NK ASP 88": "OD1" <-> "OD2" Residue "NL PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NL GLU 273": "OE1" <-> "OE2" Residue "NL GLU 367": "OE1" <-> "OE2" Residue "NL ASP 417": "OD1" <-> "OD2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 146": "OE1" <-> "OE2" Residue "SA GLU 155": "OE1" <-> "OE2" Residue "SA ASP 179": "OD1" <-> "OD2" Residue "SA TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 238": "OE1" <-> "OE2" Residue "SD PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 152": "OE1" <-> "OE2" Residue "SE PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 44": "OD1" <-> "OD2" Residue "SE PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 211": "OD1" <-> "OD2" Residue "SE GLU 220": "OE1" <-> "OE2" Residue "SE GLU 232": "OE1" <-> "OE2" Residue "SF GLU 36": "OE1" <-> "OE2" Residue "SF PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF ASP 65": "OD1" <-> "OD2" Residue "SF GLU 74": "OE1" <-> "OE2" Residue "SF GLU 109": "OE1" <-> "OE2" Residue "SF ASP 176": "OD1" <-> "OD2" Residue "SG GLU 14": "OE1" <-> "OE2" Residue "SG ASP 17": "OD1" <-> "OD2" Residue "SG ASP 37": "OD1" <-> "OD2" Residue "SG GLU 66": "OE1" <-> "OE2" Residue "SG TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 143": "OE1" <-> "OE2" Residue "SG ASP 150": "OD1" <-> "OD2" Residue "SG ASP 177": "OD1" <-> "OD2" Residue "SH ASP 97": "OD1" <-> "OD2" Residue "SI ASP 67": "OD1" <-> "OD2" Residue "SI ASP 178": "OD1" <-> "OD2" Residue "SI PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 32": "OE1" <-> "OE2" Residue "SK GLU 124": "OE1" <-> "OE2" Residue "SL PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 138": "OE1" <-> "OE2" Residue "SL GLU 143": "OE1" <-> "OE2" Residue "SM ASP 214": "OD1" <-> "OD2" Residue "SM ASP 268": "OD1" <-> "OD2" Residue "SM GLU 270": "OE1" <-> "OE2" Residue "SM TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ GLU 110": "OE1" <-> "OE2" Residue "SQ ASP 172": "OD1" <-> "OD2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 355": "OE1" <-> "OE2" Residue "SR ASP 427": "OD1" <-> "OD2" Residue "SR TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ASP 25": "OD1" <-> "OD2" Residue "SV PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 62": "OE1" <-> "OE2" Residue "SV GLU 77": "OE1" <-> "OE2" Residue "SV TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 97": "OE1" <-> "OE2" Residue "SV PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 130011 Number of models: 1 Model: "" Number of chains: 63 Chain: "BA" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 954 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 9, 'TRANS': 150} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 102 Chain: "L1" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3277 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 25, 'rna3p': 128} Chain breaks: 1 Chain: "L2" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1445 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 21, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 53} Chain breaks: 3 Chain: "L3" Number of atoms: 60779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2833, 60779 Classifications: {'RNA': 2833} Modifications used: {'rna2p_pur': 263, 'rna2p_pyr': 181, 'rna3p_pur': 1288, 'rna3p_pyr': 1101} Link IDs: {'rna2p': 443, 'rna3p': 2389} Chain breaks: 35 Chain: "L6" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1539 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 178} Chain: "L7" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 191} 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: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} 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: "LD" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1078 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "LE" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 690 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 99} 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: "LF" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 842 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "LG" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 934 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Chain: "LH" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1156 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 134} 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: "LJ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "LK" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 852 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "LL" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LN" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2877 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 344} Chain breaks: 1 Chain: "LO" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "LP" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 879 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: "LR" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} 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: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "LW" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 642 Classifications: {'peptide': 77} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 73} Chain: "LX" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "LY" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "LZ" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "NB" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 603 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain breaks: 1 Chain: "NC" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 350 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "NF" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1136 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 125 Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NL" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2574 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 294} Chain breaks: 2 Chain: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SC" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1684 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "SD" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "SE" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1741 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "SF" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1184 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain: "SG" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "SH" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1120 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 141} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "SI" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1919 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "SL" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1520 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Chain: "SM" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3278 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 380} Chain breaks: 2 Chain: "SQ" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "SR" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4808 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 23, 'TRANS': 562} Chain breaks: 2 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: "L1" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L3" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Unusual residues: {' MG': 50} Classifications: {'undetermined': 50} Link IDs: {None: 49} 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: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "LX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 90916 SG CYSLR 46 86.579 181.363 123.518 1.00 54.45 S ATOM 90933 SG CYSLR 49 85.292 184.592 125.305 1.00 59.59 S ATOM 91196 SG CYSLR 83 83.284 183.202 122.603 1.00 52.13 S ATOM 91216 SG CYSLR 86 86.569 184.676 121.685 1.00 55.06 S ATOM 94218 SG CYSLW 19 95.433 126.174 144.669 1.00 42.33 S ATOM 94246 SG CYSLW 22 96.191 123.515 147.280 1.00 39.98 S ATOM 94337 SG CYSLW 34 98.119 126.732 147.288 1.00 40.70 S ATOM 94356 SG CYSLW 37 98.717 124.322 144.474 1.00 39.20 S ATOM 94960 SG CYSLX 39 97.554 193.288 130.970 1.00 68.51 S ATOM 94983 SG CYSLX 42 94.124 194.831 131.020 1.00 65.70 S ATOM 95105 SG CYSLX 57 94.739 191.949 133.267 1.00 69.97 S ATOM 95121 SG CYSLX 60 94.644 191.280 129.567 1.00 66.03 S ATOM A0M7U SG CYSSV 6 65.400 181.252 225.715 1.00 59.75 S ATOM A0M8N SG CYSSV 9 61.824 180.043 225.331 1.00 58.54 S ATOM A0MDR SG CYSSV 32 64.423 177.558 226.283 1.00 59.07 S ATOM A0MEL SG CYSSV 36 64.463 179.080 222.774 1.00 58.44 S Time building chain proxies: 48.76, per 1000 atoms: 0.38 Number of scatterers: 130011 At special positions: 0 Unit cell: (219.76, 242.272, 328.032, 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 4 29.99 K 1 19.00 S 260 16.00 P 3057 15.00 Mg 64 11.99 O 32382 8.00 N 24372 7.00 C 69871 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: 47.47 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 202 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 83 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 46 " pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 24 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15296 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: 296 helices and 73 sheets defined 47.1% alpha, 12.9% beta 1010 base pairs and 1445 stacking pairs defined. Time for finding SS restraints: 70.30 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 33 Proline residue: BA 30 - end of helix Processing helix chain 'BA' and resid 38 through 51 Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.537A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 91 through 96 removed outlier: 4.795A pdb=" N LYSBA 96 " --> pdb=" O ARGBA 92 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.242A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.562A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'L6' and resid 27 through 47 Processing helix chain 'L6' and resid 77 through 85 removed outlier: 3.507A pdb=" N ALAL6 84 " --> pdb=" O GLUL6 80 " (cutoff:3.500A) Processing helix chain 'L6' and resid 87 through 95 removed outlier: 3.984A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.537A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L6' and resid 140 through 147 removed outlier: 4.379A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 192 removed outlier: 3.566A pdb=" N PHEL6 176 " --> pdb=" O GLUL6 172 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYSL6 177 " --> pdb=" O GLUL6 173 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALAL6 178 " --> pdb=" O LYSL6 174 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N PHEL6 179 " --> pdb=" O ASNL6 175 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALAL6 180 " --> pdb=" O PHEL6 176 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SERL6 181 " --> pdb=" O LYSL6 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAL6 187 " --> pdb=" O ARGL6 183 " (cutoff:3.500A) Processing helix chain 'L6' and resid 193 through 211 removed outlier: 3.563A pdb=" N VALL6 207 " --> pdb=" O ALAL6 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLUL6 208 " --> pdb=" O GLUL6 204 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.502A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLNL7 26 " --> pdb=" O ILEL7 22 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.649A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.711A pdb=" N GLYL7 69 " --> pdb=" O ASNL7 65 " (cutoff:3.500A) Proline residue: L7 70 - end of helix No H-bonds generated for 'chain 'L7' and resid 65 through 70' 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: 3.637A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.849A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.768A 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 151 through 190 removed outlier: 5.437A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.590A pdb=" N VALL7 195 " --> pdb=" O LYSL7 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.919A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.280A 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: 5.659A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.839A 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: 4.068A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.562A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 4.973A 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: 3.895A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.874A 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: 6.336A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.900A 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 removed outlier: 3.527A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.739A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.960A 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 10 through 15 removed outlier: 3.594A pdb=" N SERLA 14 " --> pdb=" O ASNLA 10 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYSLA 15 " --> pdb=" O PROLA 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 10 through 15' Processing helix chain 'LA' and resid 25 through 37 Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.303A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) Processing helix chain 'LA' and resid 84 through 106 removed outlier: 3.893A pdb=" N LEULA 104 " --> pdb=" O SERLA 100 " (cutoff:3.500A) Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.389A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.754A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.526A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.625A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.476A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.572A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.166A 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: 4.747A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 4.969A 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 'LD' and resid 4 through 16 Processing helix chain 'LD' and resid 18 through 23 removed outlier: 3.748A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TRPLD 23 " --> pdb=" O LYSLD 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 18 through 23' Processing helix chain 'LD' and resid 28 through 36 removed outlier: 3.694A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASNLD 36 " --> pdb=" O ILELD 32 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 Processing helix chain 'LD' and resid 90 through 113 removed outlier: 3.707A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 Processing helix chain 'LD' and resid 134 through 155 Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.762A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.372A 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: 3.960A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEULE 106 " --> pdb=" O ARGLE 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYSLE 107 " --> pdb=" O ASPLE 103 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 removed outlier: 3.517A pdb=" N VALLF 29 " --> pdb=" O CYSLF 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASPLF 31 " --> pdb=" O HISLF 27 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 47 removed outlier: 3.603A pdb=" N PHELF 39 " --> pdb=" O ASPLF 35 " (cutoff:3.500A) Processing helix chain 'LF' and resid 55 through 60 Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.852A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (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 136 removed outlier: 3.618A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 removed outlier: 3.560A pdb=" N LYSLH 18 " --> pdb=" O LYSLH 14 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALALH 24 " --> pdb=" O LYSLH 20 " (cutoff:3.500A) Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.615A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 93 Processing helix chain 'LH' and resid 105 through 118 Processing helix chain 'LH' and resid 145 through 154 removed outlier: 3.527A pdb=" N VALLH 149 " --> pdb=" O ASPLH 145 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYSLH 152 " --> pdb=" O ASPLH 148 " (cutoff:3.500A) Processing helix chain 'LI' and resid 10 through 21 removed outlier: 3.508A pdb=" N ASNLI 14 " --> pdb=" O ASPLI 10 " (cutoff:3.500A) Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.555A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.239A 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: 4.238A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.696A 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 'LJ' and resid 58 through 67 removed outlier: 4.406A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 4.956A pdb=" N METLJ 81 " --> pdb=" O TYRLJ 77 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 92 through 97 removed outlier: 4.385A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 Proline residue: LJ 104 - end of helix Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.631A pdb=" N LYSLJ 109 " --> pdb=" O ALALJ 105 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.773A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 7 removed outlier: 3.996A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.763A 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 64 through 69 removed outlier: 4.463A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHELK 69 " --> pdb=" O ARGLK 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 64 through 69' Processing helix chain 'LK' and resid 74 through 83 removed outlier: 3.569A pdb=" N LEULK 78 " --> pdb=" O ASNLK 74 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 74 through 83' Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.721A 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: 3.508A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.876A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.135A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.179A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 3.982A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.029A 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 removed outlier: 3.507A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.739A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 5.100A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.419A 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 392 through 403 removed outlier: 3.540A pdb=" N ARGLN 396 " --> pdb=" O LEULN 392 " (cutoff:3.500A) Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.948A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYSLO 23 " --> pdb=" O GLNLO 19 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 Processing helix chain 'LO' and resid 53 through 68 Processing helix chain 'LO' and resid 77 through 86 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.799A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) Processing helix chain 'LP' and resid 37 through 57 removed outlier: 4.845A pdb=" N ALALP 42 " --> pdb=" O PHELP 38 " (cutoff:3.500A) Proline residue: LP 43 - end of helix Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 4.838A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 4.067A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.593A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SERLR 68 " --> pdb=" O LEULR 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 60 through 68' Processing helix chain 'LR' and resid 83 through 110 Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.660A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 4.055A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.665A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.064A 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 95 removed outlier: 5.798A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) 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: 3.776A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.420A 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: 4.403A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.403A 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 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 removed outlier: 3.584A pdb=" N ARGLU 85 " --> pdb=" O ILELU 81 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.568A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 3.885A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 19 through 35 removed outlier: 3.670A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 Processing helix chain 'LY' and resid 7 through 17 Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.869A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.321A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 30 removed outlier: 4.416A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 24 through 30' Processing helix chain 'NB' and resid 14 through 36 removed outlier: 3.500A pdb=" N LEUNB 32 " --> pdb=" O HISNB 28 " (cutoff:3.500A) Processing helix chain 'NB' and resid 56 through 81 Processing helix chain 'NC' and resid 133 through 138 removed outlier: 4.214A pdb=" N THRNC 137 " --> pdb=" O HISNC 133 " (cutoff:3.500A) Processing helix chain 'NC' and resid 139 through 144 removed outlier: 3.622A pdb=" N PHENC 144 " --> pdb=" O PHENC 140 " (cutoff:3.500A) Processing helix chain 'NC' and resid 159 through 174 Processing helix chain 'NC' and resid 175 through 180 removed outlier: 3.929A pdb=" N ASPNC 179 " --> pdb=" O ASPNC 175 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARGNC 180 " --> pdb=" O GLNNC 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'NC' and resid 175 through 180' Processing helix chain 'NF' and resid 5 through 14 removed outlier: 3.831A pdb=" N LEUNF 9 " --> pdb=" O GLUNF 5 " (cutoff:3.500A) Processing helix chain 'NF' and resid 21 through 34 removed outlier: 4.241A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 removed outlier: 3.547A pdb=" N HISNF 68 " --> pdb=" O THRNF 64 " (cutoff:3.500A) Processing helix chain 'NF' and resid 173 through 178 removed outlier: 3.535A pdb=" N ARGNF 177 " --> pdb=" O PRONF 173 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHENF 178 " --> pdb=" O METNF 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 173 through 178' Processing helix chain 'NF' and resid 205 through 212 removed outlier: 3.569A pdb=" N THRNF 209 " --> pdb=" O SERNF 205 " (cutoff:3.500A) Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NK' and resid 12 through 33 Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 Processing helix chain 'NL' and resid 116 through 123 Processing helix chain 'NL' and resid 133 through 138 removed outlier: 3.869A pdb=" N HISNL 137 " --> pdb=" O ASPNL 133 " (cutoff:3.500A) Processing helix chain 'NL' and resid 141 through 157 Processing helix chain 'NL' and resid 185 through 190 Processing helix chain 'NL' and resid 200 through 207 Proline residue: NL 205 - end of helix Processing helix chain 'NL' and resid 210 through 218 Processing helix chain 'NL' and resid 225 through 230 removed outlier: 3.996A pdb=" N HISNL 229 " --> pdb=" O PRONL 225 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THRNL 230 " --> pdb=" O ALANL 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'NL' and resid 225 through 230' Processing helix chain 'NL' and resid 252 through 280 Processing helix chain 'NL' and resid 289 through 299 Processing helix chain 'NL' and resid 338 through 371 removed outlier: 3.967A pdb=" N LEUNL 368 " --> pdb=" O ARGNL 364 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHENL 369 " --> pdb=" O HISNL 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARGNL 370 " --> pdb=" O GLNNL 366 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEUNL 371 " --> pdb=" O GLUNL 367 " (cutoff:3.500A) Processing helix chain 'NL' and resid 372 through 400 Processing helix chain 'NL' and resid 436 through 449 Processing helix chain 'NL' and resid 470 through 477 removed outlier: 3.609A pdb=" N ILENL 476 " --> pdb=" O ALANL 472 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLNNL 477 " --> pdb=" O PHENL 473 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.380A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.725A 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: 4.134A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.608A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.512A pdb=" N LYSSA 140 " --> pdb=" O LEUSA 136 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.380A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.717A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.531A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.733A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.476A 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: 4.100A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.678A 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: 4.444A 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 190 through 195 removed outlier: 3.911A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.610A 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: 3.634A 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: 5.257A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.427A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.672A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALASD 78 " --> pdb=" O METSD 74 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.565A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.230A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.671A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.193A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.658A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.541A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.782A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 removed outlier: 3.614A pdb=" N ALASE 123 " --> pdb=" O GLUSE 119 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 removed outlier: 4.516A pdb=" N VALSE 143 " --> pdb=" O GLYSE 139 " (cutoff:3.500A) Processing helix chain 'SE' and resid 164 through 178 removed outlier: 4.895A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.669A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.884A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 3.891A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.323A 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 'SF' and resid 33 through 39 Processing helix chain 'SF' and resid 103 through 108 removed outlier: 3.584A pdb=" N METSF 107 " --> pdb=" O PROSF 103 " (cutoff:3.500A) Proline residue: SF 108 - end of helix No H-bonds generated for 'chain 'SF' and resid 103 through 108' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.505A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.531A pdb=" N ILESG 161 " --> pdb=" O SERSG 157 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.530A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.881A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 6.128A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 removed outlier: 3.521A 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 23 through 53 removed outlier: 4.417A pdb=" N LYSSI 27 " --> pdb=" O GLUSI 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYSSI 28 " --> pdb=" O ASNSI 24 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLNSI 50 " --> pdb=" O ALASI 46 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYSSI 52 " --> pdb=" O LYSSI 48 " (cutoff:3.500A) Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.924A 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 163 Processing helix chain 'SI' and resid 178 through 187 removed outlier: 3.536A pdb=" N HISSI 185 " --> pdb=" O VALSI 181 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 removed outlier: 3.646A pdb=" N LEUSI 197 " --> pdb=" O CYSSI 193 " (cutoff:3.500A) Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 5.246A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.020A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.743A 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: 4.518A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.784A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.563A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.066A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 134 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: 3.508A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.463A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 3.605A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 50 removed outlier: 3.509A pdb=" N VALSL 36 " --> pdb=" O ASPSL 32 " (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: 3.658A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 3.600A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEUSL 165 " --> pdb=" O ILESL 161 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 4.020A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 removed outlier: 3.661A pdb=" N GLYSL 199 " --> pdb=" O ASNSL 195 " (cutoff:3.500A) Processing helix chain 'SL' and resid 222 through 241 removed outlier: 4.135A pdb=" N GLUSL 239 " --> pdb=" O LYSSL 235 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYSSL 240 " --> pdb=" O GLYSL 236 " (cutoff:3.500A) Processing helix chain 'SM' and resid 12 through 18 removed outlier: 4.054A pdb=" N ASNSM 16 " --> pdb=" O GLYSM 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYRSM 17 " --> pdb=" O SERSM 13 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'SM' and resid 12 through 18' Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 removed outlier: 4.731A pdb=" N LYSSM 56 " --> pdb=" O LYSSM 52 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.590A pdb=" N LEUSM 74 " --> pdb=" O ILESM 70 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.055A 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 Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 135 removed outlier: 4.250A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 3.671A pdb=" N LEUSM 143 " --> pdb=" O SERSM 139 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.760A 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 218 through 243 Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.958A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.555A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.556A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.563A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.456A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.305A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.575A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.230A 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: 4.098A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 119 removed outlier: 3.529A pdb=" N VALSQ 112 " --> pdb=" O THRSQ 108 " (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 70 Proline residue: SR 70 - end of helix Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 121 removed outlier: 3.520A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASPSR 121 " --> pdb=" O METSR 117 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 146 removed outlier: 3.632A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) Processing helix chain 'SR' and resid 147 through 161 removed outlier: 3.536A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.638A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 234 through 247 removed outlier: 4.307A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILESR 241 " --> pdb=" O GLUSR 237 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 4.680A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 295 through 300 removed outlier: 5.420A pdb=" N SERSR 300 " --> pdb=" O ILESR 296 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 314 removed outlier: 3.523A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 4.704A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 357 removed outlier: 3.967A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 3.513A pdb=" N LEUSR 401 " --> pdb=" O ARGSR 397 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 4.624A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 418' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 3.943A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.764A 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: 4.413A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 475 through 503 removed outlier: 5.545A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 3.548A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYSSR 514 " --> pdb=" O ARGSR 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 509 through 514' Processing helix chain 'SR' and resid 516 through 528 removed outlier: 3.690A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.653A pdb=" N ARGSR 547 " --> pdb=" O ALASR 543 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.377A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 601 removed outlier: 3.501A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N METSR 600 " --> pdb=" O ALASR 596 " (cutoff:3.500A) Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 3.696A pdb=" N VALSV 49 " --> pdb=" O ASNSV 45 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 45 through 50' Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.542A pdb=" N GLYSV 60 " --> pdb=" O ARGSV 56 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.858A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 5.146A 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 135 removed outlier: 3.533A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSSV 102 " --> pdb=" O GLUSV 98 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VALSV 121 " --> pdb=" O GLUSV 117 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.241A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 3, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.441A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.281A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.745A 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: 3.732A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LA' and resid 16 through 20 removed outlier: 5.328A pdb=" N SERLA 111 " --> pdb=" O LYSLA 153 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'LA' and resid 116 through 122 removed outlier: 3.726A pdb=" N HISLA 116 " --> pdb=" O ILELA 149 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LB' and resid 118 through 121 removed outlier: 5.120A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.690A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.204A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.791A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LE' and resid 39 through 43 removed outlier: 4.189A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 15, first strand: chain 'LF' and resid 61 through 65 removed outlier: 5.972A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LG' and resid 24 through 27 removed outlier: 5.058A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N METLG 62 " --> pdb=" O ILELG 40 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.256A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.634A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.889A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.569A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.366A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LJ' and resid 9 through 13 removed outlier: 4.613A pdb=" N LYSLJ 9 " --> pdb=" O ILELJ 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEULJ 42 " --> pdb=" O VALLJ 26 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 24, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.249A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LN' and resid 53 through 59 removed outlier: 6.777A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.803A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LN' and resid 179 through 184 removed outlier: 4.853A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 286 through 289 removed outlier: 3.607A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 30, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.638A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.033A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.215A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.937A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 35, first strand: chain 'LR' and resid 20 through 24 Processing sheet with id= 36, first strand: chain 'LT' and resid 46 through 49 removed outlier: 4.985A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGLT 76 " --> pdb=" O ARGLT 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LT' and resid 56 through 59 removed outlier: 4.482A pdb=" N THRLT 59 " --> pdb=" O LYSLT 63 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYSLT 63 " --> pdb=" O THRLT 59 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.653A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LY' and resid 2 through 5 removed outlier: 4.765A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYSLY 67 " --> pdb=" O VALLY 23 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.651A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.811A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.255A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'SC' and resid 90 through 95 removed outlier: 8.547A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARGSC 105 " --> pdb=" O LYSSC 94 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.137A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.424A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 47, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.516A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SF' and resid 110 through 113 removed outlier: 4.244A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSSF 145 " --> pdb=" O ASNSF 140 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SERSF 138 " --> pdb=" O ARGSF 147 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SF' and resid 58 through 64 Processing sheet with id= 50, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.296A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.936A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 53, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.451A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.548A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLUSG 183 " --> pdb=" O LYSSG 91 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SH' and resid 72 through 76 removed outlier: 3.692A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.628A pdb=" N GLYSI 150 " --> pdb=" O PHESI 98 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SK' and resid 1 through 5 removed outlier: 3.570A pdb=" N ALASK 204 " --> pdb=" O METSK 1 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 59, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 60, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 61, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 62, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.275A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUSL 82 " --> pdb=" O THRSL 201 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SL' and resid 127 through 130 removed outlier: 3.633A pdb=" N CYSSL 96 " --> pdb=" O PHESL 154 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SL' and resid 210 through 217 removed outlier: 5.916A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 66, first strand: chain 'SM' and resid 352 through 356 removed outlier: 3.606A pdb=" N GLUSM 353 " --> pdb=" O LEUSM 330 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 4.766A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THRSQ 203 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.843A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 70, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.655A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.238A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.400A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEUSR 172 " --> pdb=" O ALASR 250 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SV' and resid 18 through 22 2819 hydrogen bonds defined for protein. 8382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2676 hydrogen bonds 4626 hydrogen bond angles 0 basepair planarities 1010 basepair parallelities 1445 stacking parallelities Total time for adding SS restraints: 150.84 Time building geometry restraints manager: 51.47 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: 26717 1.33 - 1.45: 47310 1.45 - 1.58: 58255 1.58 - 1.70: 6071 1.70 - 1.82: 420 Bond restraints: 138773 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.520 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.398 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.449 -0.094 2.00e-02 2.50e+03 2.23e+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 1.16e+01 bond pdb=" C1' GDPSR1001 " pdb=" N9 GDPSR1001 " ideal model delta sigma weight residual 1.485 1.424 0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 138768 not shown) Histogram of bond angle deviations from ideal: 97.95 - 106.20: 18371 106.20 - 114.46: 87308 114.46 - 122.72: 75144 122.72 - 130.98: 20330 130.98 - 139.24: 901 Bond angle restraints: 202054 Sorted by residual: angle pdb=" N VALSE 140 " pdb=" CA VALSE 140 " pdb=" C VALSE 140 " ideal model delta sigma weight residual 112.12 107.91 4.21 8.40e-01 1.42e+00 2.51e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 121.13 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CA TYRLN 228 " pdb=" CB TYRLN 228 " pdb=" CG TYRLN 228 " ideal model delta sigma weight residual 113.90 120.66 -6.76 1.80e+00 3.09e-01 1.41e+01 angle pdb=" CB METL8 118 " pdb=" CG METL8 118 " pdb=" SD METL8 118 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.11e+01 angle pdb=" O4' GL31854 " pdb=" C1' GL31854 " pdb=" N9 GL31854 " ideal model delta sigma weight residual 108.20 113.16 -4.96 1.50e+00 4.44e-01 1.09e+01 ... (remaining 202049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 81236 35.66 - 71.31: 7194 71.31 - 106.97: 1032 106.97 - 142.62: 13 142.62 - 178.28: 18 Dihedral angle restraints: 89493 sinusoidal: 65917 harmonic: 23576 Sorted by residual: dihedral pdb=" O4' CL3 115 " pdb=" C1' CL3 115 " pdb=" N1 CL3 115 " pdb=" C2 CL3 115 " ideal model delta sinusoidal sigma weight residual -160.00 13.28 -173.28 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' CL3 100 " pdb=" C1' CL3 100 " pdb=" N1 CL3 100 " pdb=" C2 CL3 100 " ideal model delta sinusoidal sigma weight residual -160.00 10.39 -170.39 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' UL34406 " pdb=" C1' UL34406 " pdb=" N1 UL34406 " pdb=" C2 UL34406 " ideal model delta sinusoidal sigma weight residual 200.00 39.06 160.94 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 89490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 21489 0.043 - 0.086: 2592 0.086 - 0.130: 752 0.130 - 0.173: 86 0.173 - 0.216: 9 Chirality restraints: 24928 Sorted by residual: chirality pdb=" C1' AL32042 " pdb=" O4' AL32042 " pdb=" C2' AL32042 " pdb=" N9 AL32042 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' CL34926 " pdb=" O4' CL34926 " pdb=" C2' CL34926 " pdb=" N1 CL34926 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1' AL31891 " pdb=" O4' AL31891 " pdb=" C2' AL31891 " pdb=" N9 AL31891 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 24925 not shown) Planarity restraints: 14248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.047 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 GL1 39 " 0.044 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " 0.008 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.005 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.003 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CL2 2 " -0.001 2.00e-02 2.50e+03 2.09e-02 9.80e+00 pdb=" N1 CL2 2 " 0.004 2.00e-02 2.50e+03 pdb=" C2 CL2 2 " -0.003 2.00e-02 2.50e+03 pdb=" O2 CL2 2 " 0.006 2.00e-02 2.50e+03 pdb=" N3 CL2 2 " 0.009 2.00e-02 2.50e+03 pdb=" C4 CL2 2 " -0.030 2.00e-02 2.50e+03 pdb=" N4 CL2 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 CL2 2 " 0.045 2.00e-02 2.50e+03 pdb=" C6 CL2 2 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL32486 " -0.035 2.00e-02 2.50e+03 1.80e-02 9.76e+00 pdb=" N9 GL32486 " 0.041 2.00e-02 2.50e+03 pdb=" C8 GL32486 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GL32486 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GL32486 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GL32486 " -0.024 2.00e-02 2.50e+03 pdb=" O6 GL32486 " -0.001 2.00e-02 2.50e+03 pdb=" N1 GL32486 " 0.012 2.00e-02 2.50e+03 pdb=" C2 GL32486 " -0.012 2.00e-02 2.50e+03 pdb=" N2 GL32486 " 0.005 2.00e-02 2.50e+03 pdb=" N3 GL32486 " 0.005 2.00e-02 2.50e+03 pdb=" C4 GL32486 " 0.010 2.00e-02 2.50e+03 ... (remaining 14245 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 835 2.58 - 3.22: 115911 3.22 - 3.86: 282621 3.86 - 4.50: 391790 4.50 - 5.14: 540483 Nonbonded interactions: 1331640 Sorted by model distance: nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36022 " model vdw 1.941 2.170 nonbonded pdb=" OG1 THRSR 202 " pdb="MG MGSR1003 " model vdw 1.943 2.170 nonbonded pdb=" O2B GDPSR1001 " pdb="MG MGSR1003 " model vdw 1.948 2.170 nonbonded pdb=" O2' GL3 695 " pdb=" OP2 GL3 697 " model vdw 1.955 2.440 nonbonded pdb=" O LEULB 35 " pdb=" OG1 THRLB 39 " model vdw 1.963 2.440 ... (remaining 1331635 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 25.320 Check model and map are aligned: 1.410 Set scattering table: 0.890 Process input model: 427.780 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 466.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.170 138773 Z= 0.187 Angle : 0.541 13.129 202054 Z= 0.284 Chirality : 0.034 0.216 24928 Planarity : 0.004 0.079 14248 Dihedral : 21.448 178.277 74197 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 7963 helix: 1.76 (0.09), residues: 3108 sheet: 0.81 (0.15), residues: 1155 loop : 0.48 (0.10), residues: 3700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPL9 120 HIS 0.014 0.001 HISSM 245 PHE 0.019 0.001 PHENL 473 TYR 0.042 0.001 TYRLN 228 ARG 0.023 0.001 ARGSI 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 941 time to evaluate : 7.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 104 ILE cc_start: 0.7595 (mt) cc_final: 0.7338 (mt) REVERT: BA 129 ILE cc_start: 0.8631 (mt) cc_final: 0.7889 (mt) REVERT: BA 144 ASP cc_start: 0.6224 (m-30) cc_final: 0.5876 (m-30) REVERT: BA 152 ILE cc_start: 0.8642 (mt) cc_final: 0.8260 (mt) REVERT: L6 194 ILE cc_start: 0.7688 (tp) cc_final: 0.7457 (tt) REVERT: L6 198 ARG cc_start: 0.5794 (mtt180) cc_final: 0.5584 (mtt90) REVERT: L9 29 GLN cc_start: 0.8463 (tt0) cc_final: 0.8246 (tt0) REVERT: LE 114 GLN cc_start: 0.7358 (mp10) cc_final: 0.7133 (tm-30) REVERT: LE 116 LYS cc_start: 0.4677 (ttmm) cc_final: 0.4361 (mtpp) REVERT: LF 82 TYR cc_start: 0.8379 (t80) cc_final: 0.8063 (t80) REVERT: LG 39 ILE cc_start: 0.8379 (mm) cc_final: 0.8150 (mm) REVERT: LH 34 SER cc_start: 0.7390 (p) cc_final: 0.7167 (p) REVERT: LL 125 MET cc_start: 0.5292 (tpt) cc_final: 0.4666 (tpt) REVERT: LX 47 MET cc_start: 0.8887 (tpp) cc_final: 0.8376 (tpt) REVERT: LZ 29 MET cc_start: 0.8129 (mmm) cc_final: 0.7702 (mmm) REVERT: NC 134 ILE cc_start: 0.7901 (tp) cc_final: 0.7580 (mm) REVERT: SC 57 TYR cc_start: 0.7975 (m-80) cc_final: 0.7765 (m-80) REVERT: SH 66 SER cc_start: 0.8879 (t) cc_final: 0.8461 (p) REVERT: SH 72 THR cc_start: 0.9151 (m) cc_final: 0.8869 (p) REVERT: SH 92 GLU cc_start: 0.8246 (tt0) cc_final: 0.7719 (tt0) REVERT: SH 102 VAL cc_start: 0.8300 (t) cc_final: 0.8076 (p) REVERT: SH 106 MET cc_start: 0.7346 (mmm) cc_final: 0.6148 (mmm) REVERT: SH 147 LYS cc_start: 0.8065 (tptt) cc_final: 0.7614 (tptp) REVERT: SH 149 TYR cc_start: 0.6619 (t80) cc_final: 0.6324 (t80) REVERT: SI 69 TRP cc_start: 0.7800 (m100) cc_final: 0.7368 (m100) REVERT: SK 1 MET cc_start: 0.4785 (mmm) cc_final: 0.2567 (tpp) REVERT: SL 110 THR cc_start: 0.8900 (m) cc_final: 0.8655 (p) REVERT: SL 130 ILE cc_start: 0.7588 (mt) cc_final: 0.7123 (pt) REVERT: SL 157 THR cc_start: 0.8564 (t) cc_final: 0.8327 (t) REVERT: SL 184 ASN cc_start: 0.7577 (t0) cc_final: 0.7024 (p0) REVERT: SL 193 GLU cc_start: 0.7978 (tp30) cc_final: 0.7651 (tp30) REVERT: SM 140 MET cc_start: 0.8319 (mmt) cc_final: 0.8084 (mmt) REVERT: SQ 88 ASN cc_start: 0.6840 (m-40) cc_final: 0.6619 (m110) REVERT: SQ 123 ASP cc_start: 0.6643 (t0) cc_final: 0.6046 (p0) REVERT: SQ 206 TYR cc_start: 0.7357 (m-80) cc_final: 0.6923 (m-80) REVERT: SR 150 TYR cc_start: 0.8542 (t80) cc_final: 0.8149 (t80) REVERT: SR 210 MET cc_start: 0.8651 (ptm) cc_final: 0.8421 (ptm) REVERT: SV 72 GLU cc_start: 0.7809 (pp20) cc_final: 0.7370 (pp20) outliers start: 0 outliers final: 0 residues processed: 941 average time/residue: 1.0918 time to fit residues: 1805.5016 Evaluate side-chains 675 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 675 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 921 optimal weight: 8.9990 chunk 826 optimal weight: 6.9990 chunk 458 optimal weight: 0.0000 chunk 282 optimal weight: 10.0000 chunk 557 optimal weight: 0.9980 chunk 441 optimal weight: 4.9990 chunk 855 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 519 optimal weight: 1.9990 chunk 636 optimal weight: 5.9990 chunk 990 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 131 GLN L9 57 GLN L9 182 HIS LA 34 GLN LA 80 GLN LC 37 HIS LC 50 GLN LC 91 HIS LH 107 HIS LN 42 HIS LP 79 ASN LP 100 ASN LQ 52 GLN LQ 126 ASN LU 15 HIS LW 76 HIS NF 68 HIS ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NL 366 GLN NL 436 ASN SA 212 ASN SC 136 HIS SC 190 HIS SC 211 HIS SD 63 GLN SD 151 ASN SE 225 ASN SF 22 HIS SF 95 GLN SG 8 GLN SG 42 ASN SH 67 GLN SI 225 HIS SK 82 GLN SK 83 HIS SL 112 GLN SM 170 HIS SM 211 HIS SQ 24 GLN SQ 217 GLN SR 157 HIS SR 209 HIS SR 239 GLN SV 45 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 138773 Z= 0.179 Angle : 0.504 9.241 202054 Z= 0.266 Chirality : 0.034 0.237 24928 Planarity : 0.004 0.055 14248 Dihedral : 22.683 179.424 57708 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.97 % Allowed : 4.94 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.72 (0.09), residues: 7963 helix: 2.22 (0.09), residues: 3203 sheet: 0.66 (0.15), residues: 1142 loop : 0.42 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPL9 120 HIS 0.011 0.001 HISSH 119 PHE 0.020 0.001 PHESH 120 TYR 0.026 0.001 TYRLN 228 ARG 0.007 0.000 ARGSH 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 729 time to evaluate : 7.401 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 131 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7049 (mt-10) REVERT: L6 198 ARG cc_start: 0.6004 (mtt180) cc_final: 0.5798 (mmt90) REVERT: LC 93 MET cc_start: 0.8300 (mtp) cc_final: 0.8041 (mtp) REVERT: LE 116 LYS cc_start: 0.4334 (ttmm) cc_final: 0.3478 (mmtt) REVERT: LF 82 TYR cc_start: 0.8355 (t80) cc_final: 0.8040 (t80) REVERT: LH 34 SER cc_start: 0.7588 (p) cc_final: 0.7327 (p) REVERT: LL 125 MET cc_start: 0.5243 (tpt) cc_final: 0.4599 (tpt) REVERT: LO 19 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7441 (tp-100) REVERT: LX 25 MET cc_start: 0.5506 (mmt) cc_final: 0.4647 (mtt) REVERT: LZ 29 MET cc_start: 0.8156 (mmm) cc_final: 0.7512 (mtt) REVERT: NB 32 LEU cc_start: 0.7626 (mm) cc_final: 0.7252 (mt) REVERT: NB 47 ASP cc_start: 0.6927 (p0) cc_final: 0.6665 (p0) REVERT: SA 60 HIS cc_start: 0.6393 (m170) cc_final: 0.6077 (m-70) REVERT: SE 127 ASP cc_start: 0.1313 (OUTLIER) cc_final: 0.0361 (m-30) REVERT: SF 97 ASN cc_start: 0.8061 (m-40) cc_final: 0.7831 (m-40) REVERT: SG 1 MET cc_start: 0.8261 (ptt) cc_final: 0.7890 (ptt) REVERT: SH 66 SER cc_start: 0.8875 (t) cc_final: 0.8359 (p) REVERT: SH 92 GLU cc_start: 0.8115 (tt0) cc_final: 0.7709 (tt0) REVERT: SH 106 MET cc_start: 0.7311 (mmm) cc_final: 0.6862 (mmm) REVERT: SH 119 HIS cc_start: 0.7872 (m-70) cc_final: 0.7357 (m-70) REVERT: SK 1 MET cc_start: 0.4631 (mmm) cc_final: 0.2480 (tpp) REVERT: SL 130 ILE cc_start: 0.7411 (mt) cc_final: 0.7073 (pt) REVERT: SL 184 ASN cc_start: 0.7450 (t0) cc_final: 0.7038 (p0) REVERT: SL 193 GLU cc_start: 0.7942 (tp30) cc_final: 0.7544 (tp30) REVERT: SQ 25 ASN cc_start: 0.7616 (t0) cc_final: 0.7204 (m110) REVERT: SQ 33 CYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8002 (t) REVERT: SQ 39 TYR cc_start: 0.7658 (m-80) cc_final: 0.7361 (m-80) REVERT: SQ 88 ASN cc_start: 0.7007 (m-40) cc_final: 0.6776 (m110) REVERT: SR 150 TYR cc_start: 0.8394 (t80) cc_final: 0.8008 (t80) REVERT: SR 405 MET cc_start: 0.6686 (mtm) cc_final: 0.6276 (mtm) REVERT: SR 477 MET cc_start: 0.5748 (ttt) cc_final: 0.5349 (tpp) REVERT: SV 72 GLU cc_start: 0.7934 (pp20) cc_final: 0.7475 (pp20) outliers start: 65 outliers final: 43 residues processed: 754 average time/residue: 1.0682 time to fit residues: 1424.0336 Evaluate side-chains 695 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 650 time to evaluate : 7.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain LA residue 34 GLN Chi-restraints excluded: chain LC residue 1 MET Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 51 ILE Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LE residue 113 ASP Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LO residue 60 ILE Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LO residue 102 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LW residue 64 MET Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LZ residue 27 ILE Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NC residue 142 THR Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SH residue 58 GLU Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 224 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SV residue 25 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 550 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 824 optimal weight: 1.9990 chunk 674 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 992 optimal weight: 5.9990 chunk 1072 optimal weight: 9.9990 chunk 883 optimal weight: 8.9990 chunk 984 optimal weight: 0.6980 chunk 338 optimal weight: 7.9990 chunk 796 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L6 111 GLN L7 90 HIS L8 131 GLN LB 21 GLN LB 44 ASN LC 50 GLN LF 118 ASN LH 33 HIS LI 14 ASN LL 6 GLN LN 186 ASN LO 19 GLN LX 56 HIS LX 72 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 132 ASN SG 8 GLN ** SH 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 204 ASN SM 335 ASN SM 376 GLN SR 64 GLN SR 516 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 138773 Z= 0.331 Angle : 0.575 10.528 202054 Z= 0.299 Chirality : 0.038 0.246 24928 Planarity : 0.005 0.125 14248 Dihedral : 22.647 179.928 57708 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.68 % Allowed : 7.14 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.36 (0.09), residues: 7963 helix: 1.97 (0.09), residues: 3215 sheet: 0.43 (0.15), residues: 1134 loop : 0.18 (0.10), residues: 3614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRPSE 237 HIS 0.010 0.001 HISSA 60 PHE 0.022 0.002 PHELZ 12 TYR 0.030 0.002 TYRSL 142 ARG 0.009 0.001 ARGL9 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 673 time to evaluate : 7.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 131 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6882 (mm-30) REVERT: L7 96 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6955 (mm-40) REVERT: LA 115 GLU cc_start: 0.7427 (pt0) cc_final: 0.7101 (pt0) REVERT: LE 116 LYS cc_start: 0.4549 (ttmm) cc_final: 0.3462 (mmtt) REVERT: LE 118 GLU cc_start: 0.6092 (tp30) cc_final: 0.5855 (tp30) REVERT: LF 82 TYR cc_start: 0.8347 (t80) cc_final: 0.7881 (t80) REVERT: LH 34 SER cc_start: 0.8011 (p) cc_final: 0.7663 (p) REVERT: LJ 38 TYR cc_start: 0.8268 (p90) cc_final: 0.8001 (p90) REVERT: LL 108 MET cc_start: 0.8409 (mmm) cc_final: 0.8063 (mmm) REVERT: LL 125 MET cc_start: 0.5301 (tpt) cc_final: 0.4865 (tpt) REVERT: LO 59 GLU cc_start: 0.7983 (tt0) cc_final: 0.7525 (tt0) REVERT: LX 25 MET cc_start: 0.5670 (mmt) cc_final: 0.4831 (mtt) REVERT: LZ 29 MET cc_start: 0.8186 (mmm) cc_final: 0.7706 (mtt) REVERT: NB 13 MET cc_start: 0.8583 (ttm) cc_final: 0.8323 (ttp) REVERT: SE 127 ASP cc_start: 0.1021 (OUTLIER) cc_final: 0.0209 (m-30) REVERT: SF 97 ASN cc_start: 0.8140 (m-40) cc_final: 0.7917 (m-40) REVERT: SF 139 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.4621 (m-70) REVERT: SH 66 SER cc_start: 0.9056 (t) cc_final: 0.8592 (p) REVERT: SH 106 MET cc_start: 0.7620 (mmm) cc_final: 0.7131 (mmm) REVERT: SH 117 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6861 (tm-30) REVERT: SH 119 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7408 (m-70) REVERT: SK 1 MET cc_start: 0.4731 (mmm) cc_final: 0.2486 (tpp) REVERT: SL 125 THR cc_start: 0.8953 (m) cc_final: 0.8692 (p) REVERT: SL 130 ILE cc_start: 0.7536 (mt) cc_final: 0.7128 (pt) REVERT: SL 156 LEU cc_start: 0.8592 (mp) cc_final: 0.8275 (tt) REVERT: SQ 33 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8048 (t) REVERT: SQ 39 TYR cc_start: 0.7552 (m-80) cc_final: 0.7234 (m-80) REVERT: SQ 206 TYR cc_start: 0.7123 (m-80) cc_final: 0.6915 (m-80) REVERT: SR 150 TYR cc_start: 0.8336 (t80) cc_final: 0.7980 (t80) REVERT: SR 508 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (tpt) REVERT: SV 72 GLU cc_start: 0.7978 (pp20) cc_final: 0.7516 (pp20) outliers start: 112 outliers final: 77 residues processed: 726 average time/residue: 1.1503 time to fit residues: 1486.4647 Evaluate side-chains 710 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 628 time to evaluate : 7.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 67 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 111 GLN Chi-restraints excluded: chain L6 residue 175 ASN Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 152 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LF residue 55 ASN Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LO residue 60 ILE Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LW residue 64 MET Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LZ residue 27 ILE Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NC residue 141 GLU Chi-restraints excluded: chain NC residue 142 THR Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain NF residue 64 THR Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain SC residue 154 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 225 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SH residue 46 VAL Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 118 CYS Chi-restraints excluded: chain SH residue 119 HIS Chi-restraints excluded: chain SI residue 63 SER Chi-restraints excluded: chain SI residue 67 ASP Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SL residue 119 ASN Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 224 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SQ residue 123 ASP Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 508 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 980 optimal weight: 7.9990 chunk 746 optimal weight: 1.9990 chunk 515 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 chunk 473 optimal weight: 6.9990 chunk 666 optimal weight: 8.9990 chunk 996 optimal weight: 4.9990 chunk 1054 optimal weight: 5.9990 chunk 520 optimal weight: 3.9990 chunk 944 optimal weight: 30.0000 chunk 284 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 34 GLN LA 80 GLN LF 116 GLN LH 33 HIS LI 14 ASN ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LW 66 HIS LX 72 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 208 ASN ** SF 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN ** SH 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 66 HIS SM 154 HIS SM 253 GLN SQ 217 GLN SR 3 HIS SV 122 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 138773 Z= 0.307 Angle : 0.552 10.577 202054 Z= 0.287 Chirality : 0.037 0.249 24928 Planarity : 0.004 0.059 14248 Dihedral : 22.636 178.985 57708 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.90 % Allowed : 8.75 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.24 (0.09), residues: 7963 helix: 1.95 (0.09), residues: 3217 sheet: 0.28 (0.15), residues: 1123 loop : 0.05 (0.10), residues: 3623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRPSE 237 HIS 0.041 0.001 HISL6 67 PHE 0.017 0.002 PHELZ 12 TYR 0.026 0.002 TYRSL 142 ARG 0.008 0.001 ARGSH 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 652 time to evaluate : 7.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 131 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7088 (mm-30) REVERT: L7 96 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6987 (mm-40) REVERT: LA 115 GLU cc_start: 0.7394 (pt0) cc_final: 0.7059 (pt0) REVERT: LE 116 LYS cc_start: 0.4674 (ttmm) cc_final: 0.3493 (mmtt) REVERT: LF 82 TYR cc_start: 0.8360 (t80) cc_final: 0.7908 (t80) REVERT: LH 34 SER cc_start: 0.7629 (p) cc_final: 0.7317 (p) REVERT: LJ 38 TYR cc_start: 0.8437 (p90) cc_final: 0.8080 (p90) REVERT: LL 108 MET cc_start: 0.8297 (mmm) cc_final: 0.8007 (mmm) REVERT: LO 19 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7406 (tp-100) REVERT: LO 59 GLU cc_start: 0.7994 (tt0) cc_final: 0.7534 (tt0) REVERT: LX 25 MET cc_start: 0.5694 (mmt) cc_final: 0.4867 (mtt) REVERT: LX 84 ARG cc_start: 0.7676 (tpm170) cc_final: 0.7135 (tpm170) REVERT: LY 56 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8930 (tt) REVERT: LZ 29 MET cc_start: 0.8188 (mmm) cc_final: 0.7680 (mtt) REVERT: NB 13 MET cc_start: 0.8587 (ttm) cc_final: 0.8314 (ttp) REVERT: SE 127 ASP cc_start: 0.1204 (OUTLIER) cc_final: 0.0275 (m-30) REVERT: SH 66 SER cc_start: 0.9054 (t) cc_final: 0.8599 (p) REVERT: SH 92 GLU cc_start: 0.7856 (tt0) cc_final: 0.7615 (tt0) REVERT: SH 106 MET cc_start: 0.7665 (mmm) cc_final: 0.7266 (mmm) REVERT: SH 117 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7256 (tp30) REVERT: SK 1 MET cc_start: 0.4446 (mmm) cc_final: 0.2372 (tpp) REVERT: SK 197 MET cc_start: 0.8345 (ptm) cc_final: 0.7879 (ptm) REVERT: SL 130 ILE cc_start: 0.7629 (mt) cc_final: 0.7180 (pt) REVERT: SL 156 LEU cc_start: 0.8608 (mp) cc_final: 0.8307 (tt) REVERT: SQ 33 CYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8075 (t) REVERT: SQ 39 TYR cc_start: 0.7544 (m-80) cc_final: 0.7280 (m-80) REVERT: SR 150 TYR cc_start: 0.8292 (t80) cc_final: 0.7992 (t80) REVERT: SV 72 GLU cc_start: 0.8064 (pp20) cc_final: 0.7611 (pp20) REVERT: SV 93 MET cc_start: 0.8496 (ttp) cc_final: 0.8230 (ptt) outliers start: 127 outliers final: 84 residues processed: 724 average time/residue: 1.0659 time to fit residues: 1368.8954 Evaluate side-chains 699 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 612 time to evaluate : 7.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 121 LEU Chi-restraints excluded: chain BA residue 126 SER Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 34 GLN Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LD residue 148 ASP Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LF residue 55 ASN Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 33 HIS Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LO residue 60 ILE Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 41 ILE Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LW residue 64 MET Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NC residue 142 THR Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 154 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 225 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 224 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 292 ASP Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 878 optimal weight: 10.0000 chunk 598 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 785 optimal weight: 8.9990 chunk 435 optimal weight: 4.9990 chunk 899 optimal weight: 5.9990 chunk 728 optimal weight: 3.9990 chunk 1 optimal weight: 50.0000 chunk 538 optimal weight: 6.9990 chunk 946 optimal weight: 0.2980 chunk 266 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS ** L6 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 116 GLN ** LH 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LI 14 ASN ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LW 57 ASN NK 90 HIS NK 99 GLN SF 95 GLN SF 97 ASN SG 8 GLN ** SH 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 119 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 138773 Z= 0.240 Angle : 0.516 10.995 202054 Z= 0.269 Chirality : 0.035 0.243 24928 Planarity : 0.004 0.052 14248 Dihedral : 22.615 179.524 57708 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.80 % Allowed : 9.95 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 7963 helix: 2.06 (0.09), residues: 3210 sheet: 0.19 (0.15), residues: 1129 loop : 0.04 (0.10), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRPSE 237 HIS 0.024 0.001 HISLH 33 PHE 0.021 0.001 PHESH 120 TYR 0.022 0.001 TYRSL 142 ARG 0.005 0.000 ARGL8 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 658 time to evaluate : 7.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 131 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7104 (mm-30) REVERT: L7 96 GLN cc_start: 0.7225 (mm-40) cc_final: 0.7001 (mm-40) REVERT: LA 115 GLU cc_start: 0.7370 (pt0) cc_final: 0.7115 (pt0) REVERT: LB 53 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8177 (mtp) REVERT: LE 116 LYS cc_start: 0.4623 (ttmm) cc_final: 0.3469 (mmtt) REVERT: LF 82 TYR cc_start: 0.8352 (t80) cc_final: 0.7916 (t80) REVERT: LJ 38 TYR cc_start: 0.8470 (p90) cc_final: 0.8104 (p90) REVERT: LO 19 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7668 (tp40) REVERT: LO 59 GLU cc_start: 0.7981 (tt0) cc_final: 0.7507 (tt0) REVERT: LX 25 MET cc_start: 0.5515 (mmt) cc_final: 0.4708 (mtt) REVERT: LX 84 ARG cc_start: 0.7738 (tpm170) cc_final: 0.7096 (tpm170) REVERT: LX 88 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7350 (tp30) REVERT: LY 54 GLU cc_start: 0.8282 (tp30) cc_final: 0.7999 (tp30) REVERT: LY 56 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8913 (tt) REVERT: LZ 29 MET cc_start: 0.8161 (mmm) cc_final: 0.7684 (mtt) REVERT: NB 13 MET cc_start: 0.8555 (ttm) cc_final: 0.8289 (ttp) REVERT: SE 127 ASP cc_start: 0.1710 (OUTLIER) cc_final: 0.0923 (m-30) REVERT: SF 139 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.4298 (m-70) REVERT: SH 66 SER cc_start: 0.9021 (t) cc_final: 0.8581 (p) REVERT: SI 63 SER cc_start: 0.8817 (t) cc_final: 0.8379 (p) REVERT: SK 1 MET cc_start: 0.4233 (mmm) cc_final: 0.2427 (tpp) REVERT: SK 197 MET cc_start: 0.8281 (ptm) cc_final: 0.7904 (ptm) REVERT: SL 130 ILE cc_start: 0.7691 (mt) cc_final: 0.7210 (pt) REVERT: SL 156 LEU cc_start: 0.8669 (mp) cc_final: 0.8316 (tt) REVERT: SQ 33 CYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8050 (t) REVERT: SQ 39 TYR cc_start: 0.7531 (m-80) cc_final: 0.7312 (m-80) REVERT: SQ 206 TYR cc_start: 0.6852 (m-80) cc_final: 0.6532 (m-10) REVERT: SR 150 TYR cc_start: 0.8285 (t80) cc_final: 0.7968 (t80) REVERT: SR 508 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8051 (mmp) REVERT: SV 72 GLU cc_start: 0.8031 (pp20) cc_final: 0.7574 (pp20) REVERT: SV 93 MET cc_start: 0.8478 (ttp) cc_final: 0.8274 (ptt) outliers start: 120 outliers final: 88 residues processed: 726 average time/residue: 1.0519 time to fit residues: 1366.4448 Evaluate side-chains 711 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 617 time to evaluate : 6.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 121 LEU Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 152 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 53 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LF residue 55 ASN Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 33 HIS Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LJ residue 12 LEU Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LW residue 57 ASN Chi-restraints excluded: chain LW residue 64 MET Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NC residue 142 THR Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 225 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SL residue 119 ASN Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 224 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SQ residue 123 ASP Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 508 MET Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 354 optimal weight: 0.9980 chunk 949 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 619 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 1055 optimal weight: 10.0000 chunk 876 optimal weight: 3.9990 chunk 488 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 349 optimal weight: 0.9990 chunk 554 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 34 GLN LB 44 ASN LF 116 GLN ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 33 GLN SF 95 GLN SG 8 GLN ** SH 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 375 HIS SV 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 138773 Z= 0.234 Angle : 0.510 8.754 202054 Z= 0.266 Chirality : 0.035 0.234 24928 Planarity : 0.004 0.051 14248 Dihedral : 22.585 179.330 57708 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.15 % Allowed : 10.44 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.26 (0.09), residues: 7963 helix: 2.07 (0.09), residues: 3221 sheet: 0.14 (0.15), residues: 1147 loop : -0.00 (0.10), residues: 3595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRPSE 237 HIS 0.013 0.001 HISLH 33 PHE 0.028 0.001 PHENL 473 TYR 0.024 0.001 TYRSL 142 ARG 0.010 0.000 ARGLW 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 644 time to evaluate : 7.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 131 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7208 (mt-10) REVERT: L7 96 GLN cc_start: 0.7232 (mm-40) cc_final: 0.7026 (mm-40) REVERT: LA 115 GLU cc_start: 0.7412 (pt0) cc_final: 0.7146 (pt0) REVERT: LB 53 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8053 (mtp) REVERT: LE 116 LYS cc_start: 0.4829 (ttmm) cc_final: 0.3552 (mmtt) REVERT: LF 82 TYR cc_start: 0.8352 (t80) cc_final: 0.7863 (t80) REVERT: LJ 38 TYR cc_start: 0.8551 (p90) cc_final: 0.8239 (p90) REVERT: LO 19 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7310 (tp40) REVERT: LO 59 GLU cc_start: 0.7986 (tt0) cc_final: 0.7508 (tt0) REVERT: LX 47 MET cc_start: 0.8919 (tpp) cc_final: 0.8420 (tpt) REVERT: LX 84 ARG cc_start: 0.7776 (tpm170) cc_final: 0.7122 (tpm170) REVERT: LX 88 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7618 (tp30) REVERT: LY 56 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8918 (tt) REVERT: LZ 29 MET cc_start: 0.8186 (mmm) cc_final: 0.7689 (mtt) REVERT: NB 13 MET cc_start: 0.8557 (ttm) cc_final: 0.8303 (ttp) REVERT: SE 127 ASP cc_start: 0.1837 (OUTLIER) cc_final: 0.1099 (m-30) REVERT: SF 139 HIS cc_start: 0.6107 (OUTLIER) cc_final: 0.4264 (m-70) REVERT: SH 66 SER cc_start: 0.9044 (t) cc_final: 0.8588 (p) REVERT: SH 106 MET cc_start: 0.7832 (mmm) cc_final: 0.7619 (mmm) REVERT: SH 117 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7120 (tm-30) REVERT: SI 63 SER cc_start: 0.8770 (t) cc_final: 0.8310 (p) REVERT: SK 1 MET cc_start: 0.4257 (mmm) cc_final: 0.2453 (tpt) REVERT: SK 197 MET cc_start: 0.8270 (ptm) cc_final: 0.7932 (ptm) REVERT: SL 130 ILE cc_start: 0.7724 (mt) cc_final: 0.7243 (pt) REVERT: SL 156 LEU cc_start: 0.8706 (mp) cc_final: 0.8343 (tt) REVERT: SQ 33 CYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8057 (t) REVERT: SR 150 TYR cc_start: 0.8255 (t80) cc_final: 0.7917 (t80) REVERT: SR 477 MET cc_start: 0.6858 (mmm) cc_final: 0.5477 (ttt) REVERT: SV 72 GLU cc_start: 0.8037 (pp20) cc_final: 0.7567 (pp20) REVERT: SV 119 GLN cc_start: 0.7526 (tp40) cc_final: 0.7214 (tp-100) outliers start: 144 outliers final: 106 residues processed: 735 average time/residue: 1.1441 time to fit residues: 1505.3246 Evaluate side-chains 730 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 619 time to evaluate : 7.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 34 GLN Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 53 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LD residue 148 ASP Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LF residue 55 ASN Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 32 VAL Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LJ residue 12 LEU Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 99 LEU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 28 VAL Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LW residue 58 THR Chi-restraints excluded: chain LW residue 64 MET Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NC residue 142 THR Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain NF residue 64 THR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NL residue 351 LEU Chi-restraints excluded: chain SA residue 23 THR Chi-restraints excluded: chain SA residue 42 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 288 ASP Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 67 THR Chi-restraints excluded: chain SD residue 225 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 15 ASN Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 46 VAL Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 126 VAL Chi-restraints excluded: chain SI residue 67 ASP Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SK residue 48 VAL Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SL residue 119 ASN Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 224 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 35 ASP Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 292 ASP Chi-restraints excluded: chain SR residue 577 VAL Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 1017 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 601 optimal weight: 0.9980 chunk 770 optimal weight: 8.9990 chunk 597 optimal weight: 8.9990 chunk 888 optimal weight: 50.0000 chunk 589 optimal weight: 8.9990 chunk 1051 optimal weight: 10.0000 chunk 658 optimal weight: 40.0000 chunk 641 optimal weight: 0.3980 chunk 485 optimal weight: 0.0870 overall best weight: 3.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 34 GLN LB 44 ASN LF 116 GLN ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN ** SH 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 171 ASN SI 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 138773 Z= 0.253 Angle : 0.522 13.231 202054 Z= 0.270 Chirality : 0.035 0.232 24928 Planarity : 0.004 0.049 14248 Dihedral : 22.576 178.948 57708 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 11.25 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.17 (0.09), residues: 7963 helix: 2.04 (0.09), residues: 3212 sheet: 0.07 (0.15), residues: 1129 loop : -0.07 (0.10), residues: 3622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRPSE 237 HIS 0.008 0.001 HISSK 118 PHE 0.013 0.001 PHELE 140 TYR 0.021 0.001 TYRSL 142 ARG 0.009 0.000 ARGSH 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 638 time to evaluate : 7.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 131 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7214 (mt-10) REVERT: L6 163 LYS cc_start: 0.6331 (tttp) cc_final: 0.5816 (tptm) REVERT: L8 50 MET cc_start: 0.8984 (ttm) cc_final: 0.8538 (mtp) REVERT: LB 53 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8042 (mtp) REVERT: LE 116 LYS cc_start: 0.4849 (ttmm) cc_final: 0.3548 (mmtt) REVERT: LF 82 TYR cc_start: 0.8371 (t80) cc_final: 0.7885 (t80) REVERT: LH 22 LEU cc_start: 0.9012 (tp) cc_final: 0.8774 (tp) REVERT: LJ 38 TYR cc_start: 0.8568 (p90) cc_final: 0.8248 (p90) REVERT: LL 125 MET cc_start: 0.5458 (tpt) cc_final: 0.4862 (tpt) REVERT: LO 19 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7348 (tp40) REVERT: LO 59 GLU cc_start: 0.7984 (tt0) cc_final: 0.7531 (tt0) REVERT: LX 25 MET cc_start: 0.5633 (mmt) cc_final: 0.4867 (mtt) REVERT: LX 84 ARG cc_start: 0.7899 (tpm170) cc_final: 0.7252 (tpm170) REVERT: LX 88 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7791 (tp30) REVERT: LY 56 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8920 (tt) REVERT: LZ 29 MET cc_start: 0.8137 (mmm) cc_final: 0.7676 (mtt) REVERT: NB 13 MET cc_start: 0.8555 (ttm) cc_final: 0.8305 (ttp) REVERT: SE 127 ASP cc_start: 0.1872 (OUTLIER) cc_final: 0.1209 (m-30) REVERT: SF 139 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.4249 (m-70) REVERT: SH 66 SER cc_start: 0.9095 (t) cc_final: 0.8646 (p) REVERT: SI 63 SER cc_start: 0.8752 (t) cc_final: 0.8168 (p) REVERT: SK 1 MET cc_start: 0.3667 (mmm) cc_final: 0.2268 (tpp) REVERT: SK 197 MET cc_start: 0.8226 (ptm) cc_final: 0.7919 (ptm) REVERT: SL 155 PHE cc_start: 0.8104 (m-80) cc_final: 0.7817 (m-10) REVERT: SL 156 LEU cc_start: 0.8701 (mp) cc_final: 0.8352 (tt) REVERT: SQ 33 CYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8089 (t) REVERT: SQ 217 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: SR 150 TYR cc_start: 0.8272 (t80) cc_final: 0.7959 (t80) REVERT: SV 72 GLU cc_start: 0.8008 (pp20) cc_final: 0.7535 (pp20) outliers start: 138 outliers final: 115 residues processed: 721 average time/residue: 1.1127 time to fit residues: 1435.4665 Evaluate side-chains 740 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 619 time to evaluate : 7.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 121 LEU Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 152 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 53 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LD residue 148 ASP Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LF residue 55 ASN Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 32 VAL Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 83 GLU Chi-restraints excluded: chain LJ residue 12 LEU Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LJ residue 96 VAL Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LK residue 85 GLN Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 99 LEU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 181 MET Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 28 VAL Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LW residue 64 MET Chi-restraints excluded: chain LX residue 38 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain NL residue 351 LEU Chi-restraints excluded: chain SA residue 42 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 288 ASP Chi-restraints excluded: chain SA residue 319 LEU Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 225 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 198 THR Chi-restraints excluded: chain SE residue 200 THR Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 236 HIS Chi-restraints excluded: chain SF residue 44 ILE Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 15 ASN Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 126 VAL Chi-restraints excluded: chain SI residue 67 ASP Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 211 THR Chi-restraints excluded: chain SL residue 106 THR Chi-restraints excluded: chain SL residue 119 ASN Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 224 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 35 ASP Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SQ residue 217 GLN Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 222 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 292 ASP Chi-restraints excluded: chain SR residue 577 VAL Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 650 optimal weight: 0.6980 chunk 419 optimal weight: 6.9990 chunk 628 optimal weight: 0.3980 chunk 316 optimal weight: 40.0000 chunk 206 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 668 optimal weight: 4.9990 chunk 716 optimal weight: 10.0000 chunk 519 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 826 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 44 ASN ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 33 ASN SF 95 GLN SG 8 GLN SH 51 HIS SI 255 ASN SK 178 GLN SM 335 ASN SM 376 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 138773 Z= 0.180 Angle : 0.484 11.251 202054 Z= 0.252 Chirality : 0.033 0.233 24928 Planarity : 0.004 0.050 14248 Dihedral : 22.553 179.982 57708 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.96 % Allowed : 11.84 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.34 (0.09), residues: 7963 helix: 2.19 (0.09), residues: 3202 sheet: 0.15 (0.15), residues: 1103 loop : 0.01 (0.10), residues: 3658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRPSE 237 HIS 0.006 0.001 HISSK 118 PHE 0.013 0.001 PHESQ 215 TYR 0.019 0.001 TYRSQ 206 ARG 0.006 0.000 ARGSE 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 642 time to evaluate : 7.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 121 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7767 (mt) REVERT: BA 131 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7213 (mt-10) REVERT: LB 53 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: LE 116 LYS cc_start: 0.4791 (ttmm) cc_final: 0.3479 (mmtt) REVERT: LF 82 TYR cc_start: 0.8355 (t80) cc_final: 0.7867 (t80) REVERT: LH 22 LEU cc_start: 0.9035 (tp) cc_final: 0.8822 (tp) REVERT: LI 43 ASN cc_start: 0.7884 (m-40) cc_final: 0.7554 (t0) REVERT: LJ 38 TYR cc_start: 0.8531 (p90) cc_final: 0.8216 (p90) REVERT: LL 125 MET cc_start: 0.5389 (tpt) cc_final: 0.4798 (tpt) REVERT: LN 158 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: LO 19 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7224 (tp-100) REVERT: LO 59 GLU cc_start: 0.7937 (tt0) cc_final: 0.7447 (tt0) REVERT: LX 25 MET cc_start: 0.5618 (mmt) cc_final: 0.4864 (mtt) REVERT: LX 47 MET cc_start: 0.8935 (tpp) cc_final: 0.8441 (tpt) REVERT: LX 84 ARG cc_start: 0.7878 (tpm170) cc_final: 0.7485 (tpm170) REVERT: LY 56 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8897 (tt) REVERT: LZ 29 MET cc_start: 0.8143 (mmm) cc_final: 0.7645 (mtt) REVERT: NB 13 MET cc_start: 0.8603 (ttm) cc_final: 0.8348 (ttp) REVERT: SE 127 ASP cc_start: 0.1884 (OUTLIER) cc_final: 0.1242 (m-30) REVERT: SE 177 MET cc_start: 0.6619 (mtm) cc_final: 0.6078 (mtm) REVERT: SF 139 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.4243 (m-70) REVERT: SG 86 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7786 (pt) REVERT: SH 66 SER cc_start: 0.9003 (t) cc_final: 0.8570 (p) REVERT: SH 91 VAL cc_start: 0.8701 (t) cc_final: 0.8486 (t) REVERT: SH 92 GLU cc_start: 0.7759 (pt0) cc_final: 0.7287 (pt0) REVERT: SI 63 SER cc_start: 0.8715 (t) cc_final: 0.8151 (p) REVERT: SK 1 MET cc_start: 0.3815 (mmm) cc_final: 0.2169 (tpt) REVERT: SK 197 MET cc_start: 0.8218 (ptm) cc_final: 0.7925 (ptm) REVERT: SL 155 PHE cc_start: 0.8077 (m-80) cc_final: 0.7839 (m-10) REVERT: SL 156 LEU cc_start: 0.8678 (mp) cc_final: 0.8328 (tt) REVERT: SQ 33 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (t) REVERT: SR 150 TYR cc_start: 0.8283 (t80) cc_final: 0.7960 (t80) REVERT: SR 477 MET cc_start: 0.6747 (mmm) cc_final: 0.5511 (ttt) REVERT: SV 72 GLU cc_start: 0.8043 (pp20) cc_final: 0.7544 (pp20) outliers start: 131 outliers final: 103 residues processed: 721 average time/residue: 1.1139 time to fit residues: 1436.3538 Evaluate side-chains 731 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 620 time to evaluate : 7.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 110 VAL Chi-restraints excluded: chain BA residue 121 LEU Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 152 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 53 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LD residue 148 ASP Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 32 VAL Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LJ residue 12 LEU Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LK residue 85 GLN Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 135 GLU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 158 GLN Chi-restraints excluded: chain LN residue 181 MET Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 28 VAL Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LX residue 38 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NF residue 16 TYR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain NL residue 351 LEU Chi-restraints excluded: chain SA residue 23 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 288 ASP Chi-restraints excluded: chain SA residue 319 LEU Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 67 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 198 THR Chi-restraints excluded: chain SE residue 200 THR Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SE residue 236 HIS Chi-restraints excluded: chain SF residue 44 ILE Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 15 ASN Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 126 VAL Chi-restraints excluded: chain SI residue 67 ASP Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 48 VAL Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 211 THR Chi-restraints excluded: chain SL residue 106 THR Chi-restraints excluded: chain SL residue 119 ASN Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 35 ASP Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 292 ASP Chi-restraints excluded: chain SR residue 577 VAL Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 956 optimal weight: 50.0000 chunk 1007 optimal weight: 8.9990 chunk 919 optimal weight: 20.0000 chunk 979 optimal weight: 0.0570 chunk 589 optimal weight: 0.3980 chunk 426 optimal weight: 0.9990 chunk 769 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 885 optimal weight: 6.9990 chunk 926 optimal weight: 2.9990 chunk 976 optimal weight: 5.9990 overall best weight: 2.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SE 85 GLN SG 8 GLN ** SH 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 171 ASN SI 255 ASN SK 178 GLN SM 335 ASN SM 376 GLN SV 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 138773 Z= 0.170 Angle : 0.476 12.331 202054 Z= 0.247 Chirality : 0.032 0.237 24928 Planarity : 0.004 0.051 14248 Dihedral : 22.521 179.968 57708 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.75 % Allowed : 12.31 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.35 (0.09), residues: 7963 helix: 2.19 (0.09), residues: 3207 sheet: 0.17 (0.15), residues: 1111 loop : 0.02 (0.10), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPSE 237 HIS 0.006 0.001 HISSK 118 PHE 0.019 0.001 PHESH 131 TYR 0.018 0.001 TYRSL 142 ARG 0.005 0.000 ARGLK 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 647 time to evaluate : 7.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 121 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7210 (mt) REVERT: BA 131 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7236 (mt-10) REVERT: LB 53 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: LE 116 LYS cc_start: 0.4805 (ttmm) cc_final: 0.3486 (mmtt) REVERT: LF 82 TYR cc_start: 0.8337 (t80) cc_final: 0.7852 (t80) REVERT: LI 43 ASN cc_start: 0.7830 (m-40) cc_final: 0.7523 (t0) REVERT: LL 125 MET cc_start: 0.5284 (tpt) cc_final: 0.4672 (tpt) REVERT: LN 158 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: LO 19 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7254 (tp-100) REVERT: LO 59 GLU cc_start: 0.7940 (tt0) cc_final: 0.7443 (tt0) REVERT: LX 25 MET cc_start: 0.5613 (mmt) cc_final: 0.4909 (mtt) REVERT: LY 56 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8885 (tt) REVERT: LZ 29 MET cc_start: 0.8162 (mmm) cc_final: 0.7688 (mtt) REVERT: NB 13 MET cc_start: 0.8577 (ttm) cc_final: 0.8322 (ttp) REVERT: SE 127 ASP cc_start: 0.1987 (OUTLIER) cc_final: 0.1365 (m-30) REVERT: SE 177 MET cc_start: 0.6607 (mtm) cc_final: 0.6084 (mtm) REVERT: SF 139 HIS cc_start: 0.6017 (OUTLIER) cc_final: 0.4134 (m-70) REVERT: SG 86 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7818 (pt) REVERT: SG 140 GLN cc_start: 0.7516 (tp40) cc_final: 0.7280 (tt0) REVERT: SG 143 GLU cc_start: 0.5739 (mm-30) cc_final: 0.5481 (mm-30) REVERT: SH 66 SER cc_start: 0.8980 (t) cc_final: 0.8511 (p) REVERT: SH 92 GLU cc_start: 0.7751 (pt0) cc_final: 0.7328 (pt0) REVERT: SI 63 SER cc_start: 0.8705 (t) cc_final: 0.8153 (p) REVERT: SK 1 MET cc_start: 0.3960 (mmm) cc_final: 0.2332 (tpt) REVERT: SK 197 MET cc_start: 0.8215 (ptm) cc_final: 0.8003 (ptm) REVERT: SL 155 PHE cc_start: 0.8041 (m-80) cc_final: 0.7793 (m-10) REVERT: SL 156 LEU cc_start: 0.8663 (mp) cc_final: 0.8382 (tt) REVERT: SL 205 ILE cc_start: 0.7916 (tp) cc_final: 0.7521 (pt) REVERT: SQ 33 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8093 (t) REVERT: SQ 58 ASN cc_start: 0.8596 (t0) cc_final: 0.7850 (t0) REVERT: SQ 217 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: SR 150 TYR cc_start: 0.8277 (t80) cc_final: 0.7951 (t80) REVERT: SR 477 MET cc_start: 0.6704 (mmm) cc_final: 0.5502 (ttt) REVERT: SV 72 GLU cc_start: 0.8048 (pp20) cc_final: 0.7542 (pp20) outliers start: 117 outliers final: 97 residues processed: 717 average time/residue: 1.0634 time to fit residues: 1368.7459 Evaluate side-chains 731 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 625 time to evaluate : 7.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 121 LEU Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 152 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 53 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LD residue 148 ASP Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 32 VAL Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LJ residue 12 LEU Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LK residue 85 GLN Chi-restraints excluded: chain LK residue 135 GLU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LN residue 158 GLN Chi-restraints excluded: chain LN residue 181 MET Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 28 VAL Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LO residue 93 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LX residue 38 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain NL residue 351 LEU Chi-restraints excluded: chain SA residue 23 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 288 ASP Chi-restraints excluded: chain SA residue 319 LEU Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 67 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 198 THR Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 44 ILE Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 46 VAL Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 126 VAL Chi-restraints excluded: chain SI residue 67 ASP Chi-restraints excluded: chain SK residue 48 VAL Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 211 THR Chi-restraints excluded: chain SL residue 106 THR Chi-restraints excluded: chain SL residue 119 ASN Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 220 MET Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 35 ASP Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SQ residue 217 GLN Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 292 ASP Chi-restraints excluded: chain SR residue 577 VAL Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 643 optimal weight: 4.9990 chunk 1036 optimal weight: 9.9990 chunk 632 optimal weight: 4.9990 chunk 491 optimal weight: 1.9990 chunk 720 optimal weight: 0.9990 chunk 1086 optimal weight: 7.9990 chunk 1000 optimal weight: 0.0040 chunk 865 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 668 optimal weight: 7.9990 chunk 530 optimal weight: 4.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 44 ASN ** LJ 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SG 8 GLN ** SH 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 178 GLN SM 335 ASN SM 376 GLN SQ 217 GLN SV 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 138773 Z= 0.199 Angle : 0.490 12.593 202054 Z= 0.254 Chirality : 0.033 0.232 24928 Planarity : 0.004 0.051 14248 Dihedral : 22.502 179.364 57708 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.62 % Allowed : 12.55 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.30 (0.09), residues: 7963 helix: 2.16 (0.09), residues: 3208 sheet: 0.07 (0.15), residues: 1109 loop : 0.00 (0.10), residues: 3646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPSE 237 HIS 0.007 0.001 HISSK 118 PHE 0.021 0.001 PHESH 74 TYR 0.018 0.001 TYRSL 142 ARG 0.006 0.000 ARGLK 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15926 Ramachandran restraints generated. 7963 Oldfield, 0 Emsley, 7963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 639 time to evaluate : 7.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 121 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7237 (mt) REVERT: BA 131 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7279 (mt-10) REVERT: LA 115 GLU cc_start: 0.6374 (pt0) cc_final: 0.6105 (pt0) REVERT: LA 151 THR cc_start: 0.8494 (p) cc_final: 0.8011 (p) REVERT: LB 53 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7988 (mtp) REVERT: LE 116 LYS cc_start: 0.4803 (ttmm) cc_final: 0.3454 (mmtt) REVERT: LF 82 TYR cc_start: 0.8361 (t80) cc_final: 0.7898 (t80) REVERT: LI 43 ASN cc_start: 0.7843 (m-40) cc_final: 0.7533 (t0) REVERT: LL 125 MET cc_start: 0.5262 (tpt) cc_final: 0.5061 (tpt) REVERT: LN 158 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: LO 19 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7253 (tp-100) REVERT: LO 59 GLU cc_start: 0.7945 (tt0) cc_final: 0.7450 (tt0) REVERT: LX 25 MET cc_start: 0.5578 (mmt) cc_final: 0.4898 (mtt) REVERT: LX 47 MET cc_start: 0.8927 (tpp) cc_final: 0.8389 (tpt) REVERT: LY 56 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8889 (tt) REVERT: LZ 29 MET cc_start: 0.8133 (mmm) cc_final: 0.7655 (mtt) REVERT: NB 13 MET cc_start: 0.8603 (ttm) cc_final: 0.8339 (ttp) REVERT: NB 33 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7248 (ttp80) REVERT: NK 13 MET cc_start: 0.7675 (mmm) cc_final: 0.7438 (mmm) REVERT: SE 127 ASP cc_start: 0.2059 (OUTLIER) cc_final: 0.1502 (m-30) REVERT: SE 177 MET cc_start: 0.6716 (mtm) cc_final: 0.6148 (mtm) REVERT: SF 139 HIS cc_start: 0.6030 (OUTLIER) cc_final: 0.4135 (m-70) REVERT: SG 86 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7818 (pt) REVERT: SG 140 GLN cc_start: 0.7586 (tp40) cc_final: 0.7262 (tt0) REVERT: SH 55 LEU cc_start: 0.8861 (mp) cc_final: 0.8625 (mt) REVERT: SH 66 SER cc_start: 0.8989 (t) cc_final: 0.8509 (p) REVERT: SH 92 GLU cc_start: 0.7691 (pt0) cc_final: 0.7269 (pt0) REVERT: SI 63 SER cc_start: 0.8701 (t) cc_final: 0.8141 (p) REVERT: SK 1 MET cc_start: 0.3916 (mmm) cc_final: 0.2280 (tpt) REVERT: SK 197 MET cc_start: 0.8253 (ptm) cc_final: 0.8033 (ptm) REVERT: SL 155 PHE cc_start: 0.8083 (m-80) cc_final: 0.7812 (m-10) REVERT: SL 156 LEU cc_start: 0.8714 (mp) cc_final: 0.8503 (tt) REVERT: SL 205 ILE cc_start: 0.7972 (tp) cc_final: 0.7514 (pt) REVERT: SQ 33 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8123 (t) REVERT: SQ 58 ASN cc_start: 0.8643 (t0) cc_final: 0.7962 (t0) REVERT: SQ 217 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6512 (mm110) REVERT: SR 150 TYR cc_start: 0.8292 (t80) cc_final: 0.7951 (t80) REVERT: SV 72 GLU cc_start: 0.8041 (pp20) cc_final: 0.7536 (pp20) outliers start: 108 outliers final: 97 residues processed: 709 average time/residue: 1.0527 time to fit residues: 1341.4017 Evaluate side-chains 736 residues out of total 7099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 630 time to evaluate : 7.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 121 LEU Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 145 VAL Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 108 ASP Chi-restraints excluded: chain LA residue 110 ASP Chi-restraints excluded: chain LA residue 152 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 53 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 93 VAL Chi-restraints excluded: chain LD residue 148 ASP Chi-restraints excluded: chain LF residue 26 THR Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 32 VAL Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LJ residue 12 LEU Chi-restraints excluded: chain LJ residue 88 ASP Chi-restraints excluded: chain LK residue 85 GLN Chi-restraints excluded: chain LK residue 135 GLU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LN residue 158 GLN Chi-restraints excluded: chain LN residue 181 MET Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 278 THR Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 28 VAL Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LP residue 62 VAL Chi-restraints excluded: chain LP residue 100 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 40 GLU Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 43 MET Chi-restraints excluded: chain LX residue 38 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 47 THR Chi-restraints excluded: chain NC residue 133 HIS Chi-restraints excluded: chain NC residue 137 THR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NL residue 298 CYS Chi-restraints excluded: chain NL residue 351 LEU Chi-restraints excluded: chain SA residue 23 THR Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 288 ASP Chi-restraints excluded: chain SA residue 319 LEU Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 67 THR Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 127 ASP Chi-restraints excluded: chain SE residue 200 THR Chi-restraints excluded: chain SE residue 202 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 211 ASP Chi-restraints excluded: chain SF residue 44 ILE Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 139 HIS Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 126 VAL Chi-restraints excluded: chain SI residue 67 ASP Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 48 VAL Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 211 THR Chi-restraints excluded: chain SL residue 106 THR Chi-restraints excluded: chain SL residue 185 LEU Chi-restraints excluded: chain SL residue 202 VAL Chi-restraints excluded: chain SM residue 209 HIS Chi-restraints excluded: chain SM residue 220 MET Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 33 CYS Chi-restraints excluded: chain SQ residue 35 ASP Chi-restraints excluded: chain SQ residue 62 HIS Chi-restraints excluded: chain SQ residue 83 ASP Chi-restraints excluded: chain SQ residue 217 GLN Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 292 ASP Chi-restraints excluded: chain SR residue 577 VAL Chi-restraints excluded: chain SV residue 4 GLU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1091 random chunks: chunk 687 optimal weight: 50.0000 chunk 921 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 798 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 240 optimal weight: 40.0000 chunk 866 optimal weight: 6.9990 chunk 362 optimal weight: 0.8980 chunk 890 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 111 GLN ** L8 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 97 ASN LH 35 HIS LI 14 ASN ** LJ 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 85 GLN ** LK 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 271 GLN LP 30 HIS LT 56 ASN NF 4 ASN SG 8 GLN SI 171 ASN SK 178 GLN ** SM 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 27 GLN SV 119 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054627 restraints weight = 453252.291| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.68 r_work: 0.2997 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 138773 Z= 0.449 Angle : 0.657 11.430 202054 Z= 0.334 Chirality : 0.041 0.241 24928 Planarity : 0.005 0.060 14248 Dihedral : 22.584 179.114 57708 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.86 % Favored : 97.12 % Rotamer: Outliers : 1.81 % Allowed : 12.57 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 7963 helix: 1.71 (0.09), residues: 3210 sheet: -0.15 (0.15), residues: 1135 loop : -0.32 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPSE 237 HIS 0.011 0.002 HISSK 118 PHE 0.050 0.002 PHESQ 215 TYR 0.023 0.002 TYRSL 142 ARG 0.007 0.001 ARGNL 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27363.87 seconds wall clock time: 482 minutes 15.75 seconds (28935.75 seconds total)