Starting phenix.real_space_refine on Sat Mar 2 10:52:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl6_29268/03_2024/8fl6_29268_neut_updated.pdb" } resolution = 2.62 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= 0.048 sd= 0.186 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 6 6.06 5 P 3753 5.49 5 Mg 88 5.21 5 S 307 5.16 5 C 82102 2.51 5 N 28835 2.21 5 O 38614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L9 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 147": "OE1" <-> "OE2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NK TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ARG 109": "NH1" <-> "NH2" Residue "SD PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV TYR 14": "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: 153706 Number of models: 1 Model: "" Number of chains: 71 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: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3278 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 3, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 25, 'rna3p': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "L2" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1535 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 24, 'rna3p_pyr': 32} Link IDs: {'rna2p': 16, 'rna3p': 55} Chain breaks: 4 Chain: "L3" Number of atoms: 73095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3405, 73095 Classifications: {'RNA': 3405} Modifications used: {'rna2p': 5, 'rna2p_pur': 326, 'rna2p_pyr': 209, 'rna3p': 80, 'rna3p_pur': 1510, 'rna3p_pyr': 1257} Link IDs: {'rna2p': 539, 'rna3p': 2865} Chain breaks: 32 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 32 Chain: "L4" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 54} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L5" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1349 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "L6" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} 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: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} 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: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1512 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} 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: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1289 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "LE" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1264 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 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: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1034 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 132} 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: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} 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: "LM" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 751 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "LN" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3239 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 386} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 888 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} 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: "LV" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "LW" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "LX" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} 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: "NC" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 219 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "NF" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 626 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} 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: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2666 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 2 Chain: "NP" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 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: "SB" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2243 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "SC" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 202} Chain breaks: 2 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: 1869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 bond proxies already assigned to first conformer: 1883 Chain: "SF" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 230} 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: 1128 Number of conformers: 2 Conformer: "A" 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 1138 Chain: "SI" Number of atoms: 1937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1950 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: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1917 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} 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: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4932 Classifications: {'peptide': 601} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 2 Chain: "SV" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1184 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Unusual residues: {' MG': 75} Classifications: {'undetermined': 75} Link IDs: {None: 74} Chain: "L4" 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: "LG" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 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: "NP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 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 A07TV SG CYSLR 46 86.834 180.101 120.319 1.00 47.16 S ATOM A07UC SG CYSLR 49 85.504 183.196 122.004 1.00 53.91 S ATOM A081N SG CYSLR 83 83.573 181.955 119.072 1.00 41.89 S ATOM A0827 SG CYSLR 86 87.041 183.212 118.396 1.00 44.94 S ATOM A0AEJ SG CYSLV 12 190.054 112.599 155.400 1.00 30.36 S ATOM A0AF7 SG CYSLV 15 193.214 111.756 153.554 1.00 33.44 S ATOM A0AS8 SG CYSLV 72 192.217 115.482 154.266 1.00 32.80 S ATOM A0AT9 SG CYSLV 77 190.271 113.280 151.775 1.00 40.99 S ATOM A0B3J SG CYSLW 19 95.179 124.939 139.788 1.00 28.16 S ATOM A0B4B SG CYSLW 22 95.894 122.210 142.313 1.00 29.12 S ATOM A0B6U SG CYSLW 34 97.865 125.418 142.364 1.00 23.81 S ATOM A0B7D SG CYSLW 37 98.570 122.973 139.658 1.00 27.48 S ATOM A0BRK SG CYSLX 39 97.693 191.250 128.719 1.00 49.30 S ATOM A0BS7 SG CYSLX 42 94.367 193.047 128.567 1.00 48.20 S ATOM A0BVL SG CYSLX 57 94.604 189.968 130.626 1.00 45.78 S ATOM A0BW1 SG CYSLX 60 94.871 189.521 126.930 1.00 46.57 S ATOM A0GBG SG CYSNP 63 76.363 198.697 199.229 1.00 56.28 S ATOM A0GBZ SG CYSNP 66 74.455 195.308 199.386 1.00 57.73 S ATOM A14GY SG CYSSV 6 65.097 179.561 219.643 1.00 42.39 S ATOM A14HR SG CYSSV 9 61.486 178.366 219.267 1.00 39.13 S ATOM A14MV SG CYSSV 32 64.065 175.899 220.240 1.00 39.35 S ATOM A14NP SG CYSSV 36 64.114 177.224 216.733 1.00 39.00 S Time building chain proxies: 60.94, per 1000 atoms: 0.40 Number of scatterers: 153706 At special positions: 0 Unit cell: (258.352, 240.128, 321.6, 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 6 29.99 K 1 19.00 S 307 16.00 P 3753 15.00 Mg 88 11.99 O 38614 8.00 N 28835 7.00 C 82102 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: 57.55 Conformation dependent library (CDL) restraints added in 11.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 500 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 46 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 83 " pdb=" ZNLV 200 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 12 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 77 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 15 " pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " pdb=" ZNNP 500 " pdb="ZN ZNNP 500 " - pdb=" NE2 HISNP 79 " pdb="ZN ZNNP 500 " - pdb=" ND1 HISNP 85 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 66 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 63 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " Number of angles added : 31 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17040 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: 337 helices and 77 sheets defined 46.6% alpha, 11.8% beta 1174 base pairs and 1826 stacking pairs defined. Time for finding SS restraints: 88.57 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: 3.615A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 4.860A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.513A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'L5' and resid 30 through 45 Processing helix chain 'L5' and resid 76 through 91 removed outlier: 3.761A pdb=" N GLUL5 80 " --> pdb=" O GLYL5 76 " (cutoff:3.500A) Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.186A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLYL5 116 " --> pdb=" O HISL5 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L5' and resid 111 through 116' Processing helix chain 'L5' and resid 139 through 144 removed outlier: 4.680A pdb=" N ASPL5 143 " --> pdb=" O PHEL5 139 " (cutoff:3.500A) Processing helix chain 'L5' and resid 158 through 170 Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.142A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VALL6 22 " --> pdb=" O TRPL6 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 17 through 22' Processing helix chain 'L6' and resid 27 through 47 Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 3.963A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.618A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L6' and resid 140 through 147 removed outlier: 3.747A pdb=" N LEUL6 146 " --> pdb=" O GLUL6 142 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 176 removed outlier: 3.555A pdb=" N PHEL6 176 " --> pdb=" O GLUL6 172 " (cutoff:3.500A) Processing helix chain 'L6' and resid 177 through 192 Processing helix chain 'L6' and resid 193 through 211 Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.550A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.760A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.740A 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 removed outlier: 3.675A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.859A pdb=" N GLNL7 96 " --> pdb=" O THRL7 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALAL7 97 " --> pdb=" O LYSL7 93 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.946A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.596A 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 removed outlier: 3.506A pdb=" N VALL7 145 " --> pdb=" O LEUL7 141 " (cutoff:3.500A) Processing helix chain 'L7' and resid 151 through 190 removed outlier: 3.506A pdb=" N ARGL7 169 " --> pdb=" O LYSL7 165 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.518A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.926A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.217A 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 removed outlier: 3.559A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.631A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.930A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.557A pdb=" N GLUL8 126 " --> pdb=" O ILEL8 122 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.982A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.753A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.269A 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 83 through 88 removed outlier: 4.012A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLYL9 88 " --> pdb=" O PROL9 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 83 through 88' Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.728A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.614A 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: 6.285A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.989A 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: 3.519A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.675A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.286A 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: 3.861A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 72 through 77 removed outlier: 4.882A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 72 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.123A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.672A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.609A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.554A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.518A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHELB 152 " --> pdb=" O VALLB 148 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 146 through 153' Processing helix chain 'LB' and resid 7 through 12 removed outlier: 4.747A pdb=" N ARGLB 11 " --> pdb=" O ASNLB 8 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYSLB 12 " --> pdb=" O LYSLB 9 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.566A pdb=" N TRPLC 45 " --> pdb=" O LYSLC 41 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.722A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.403A 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: 3.541A pdb=" N GLNLC 144 " --> pdb=" O PROLC 140 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.035A 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: 3.566A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.881A 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: 3.878A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.658A 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 60 through 73 Processing helix chain 'LD' and resid 77 through 82 removed outlier: 5.907A pdb=" N LYSLD 82 " --> pdb=" O ILELD 78 " (cutoff:3.500A) Processing helix chain 'LD' and resid 84 through 113 Proline residue: LD 90 - end of helix removed outlier: 6.767A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 3.829A pdb=" N HISLD 121 " --> pdb=" O ARGLD 117 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 removed outlier: 3.595A pdb=" N ALALD 150 " --> pdb=" O LYSLD 146 " (cutoff:3.500A) Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.531A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.773A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLYLE 59 " --> pdb=" O LYSLE 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 54 through 59' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.945A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.180A 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 99 through 121 removed outlier: 4.262A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 removed outlier: 3.528A 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: 4.010A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 5.301A pdb=" N LYSLG 74 " --> pdb=" O PROLG 70 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 removed outlier: 3.549A pdb=" N LEULG 128 " --> pdb=" O GLULG 124 " (cutoff:3.500A) Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 3.964A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALALG 136 " --> pdb=" O ILELG 132 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 131 through 137' Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.549A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 Processing helix chain 'LH' and resid 105 through 117 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.775A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.354A 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: 4.101A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.555A 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 removed outlier: 3.512A pdb=" N SERLI 125 " --> pdb=" O ARGLI 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 3.988A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.597A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N METLJ 81 " --> pdb=" O TYRLJ 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 76 through 81' Processing helix chain 'LJ' and resid 92 through 97 removed outlier: 4.298A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 99 through 104 removed outlier: 4.133A pdb=" N ASPLJ 103 " --> pdb=" O ASPLJ 99 " (cutoff:3.500A) Proline residue: LJ 104 - end of helix No H-bonds generated for 'chain 'LJ' and resid 99 through 104' Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.743A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.732A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 7 removed outlier: 4.075A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.786A 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 41 through 48 Processing helix chain 'LK' and resid 64 through 69 removed outlier: 4.277A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.916A 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: 4.373A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.566A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.521A pdb=" N VALLK 140 " --> pdb=" O LYSLK 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYLK 141 " --> pdb=" O ILELK 137 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.678A pdb=" N METLL 8 " --> pdb=" O HISLL 4 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.880A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYSLL 101 " --> pdb=" O ILELL 97 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.351A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERLL 120 " --> pdb=" O ALALL 116 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 11 through 20 removed outlier: 4.560A pdb=" N LYSLM 15 " --> pdb=" O ASNLM 11 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASNLM 19 " --> pdb=" O LYSLM 15 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLYLM 20 " --> pdb=" O TRPLM 16 " (cutoff:3.500A) Processing helix chain 'LM' and resid 36 through 54 removed outlier: 4.926A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEULM 54 " --> pdb=" O ASNLM 50 " (cutoff:3.500A) Processing helix chain 'LM' and resid 55 through 66 Processing helix chain 'LM' and resid 91 through 101 Processing helix chain 'LM' and resid 105 through 118 removed outlier: 3.705A pdb=" N ARGLM 117 " --> pdb=" O ALALM 113 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.649A pdb=" N LEULN 17 " --> pdb=" O SERLN 13 " (cutoff:3.500A) Proline residue: LN 18 - end of helix No H-bonds generated for 'chain 'LN' and resid 13 through 18' Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.031A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 3.503A pdb=" N CYSLN 134 " --> pdb=" O PHELN 130 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.284A 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: 4.046A 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: 3.652A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 4.378A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHELN 211 " --> pdb=" O VALLN 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 206 through 211' Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.902A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.194A 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 Processing helix chain 'LN' and resid 230 through 236 removed outlier: 4.292A pdb=" N TRPLN 235 " --> pdb=" O GLYLN 230 " (cutoff:3.500A) Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.557A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 removed outlier: 3.638A pdb=" N LYSLO 36 " --> pdb=" O LYSLO 32 " (cutoff:3.500A) Processing helix chain 'LO' and resid 53 through 68 Processing helix chain 'LO' and resid 77 through 86 removed outlier: 3.521A pdb=" N GLYLO 86 " --> pdb=" O GLYLO 82 " (cutoff:3.500A) Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.724A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 58 removed outlier: 3.504A pdb=" N LEULP 46 " --> pdb=" O ALALP 42 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLYLP 58 " --> pdb=" O METLP 54 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.585A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 3.505A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.849A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.554A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.734A 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 113 Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.939A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.724A pdb=" N LEULS 24 " --> pdb=" O GLNLS 20 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.519A pdb=" N LYSLS 46 " --> pdb=" O SERLS 42 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.214A 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: 3.636A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.632A pdb=" N LEULS 102 " --> pdb=" O HISLS 98 " (cutoff:3.500A) Processing helix chain 'LS' and resid 104 through 114 Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.758A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.529A 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: 4.338A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.515A 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 removed outlier: 3.607A pdb=" N VALLU 63 " --> pdb=" O GLULU 59 " (cutoff:3.500A) Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LV' and resid 35 through 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.525A pdb=" N PHELW 8 " --> pdb=" O GLYLW 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'LW' and resid 4 through 11' Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.549A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.178A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 20 through 35 removed outlier: 4.033A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HISLX 34 " --> pdb=" O GLULX 30 " (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: 3.698A pdb=" N GLULY 54 " --> pdb=" O LYSLY 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.626A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.727A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N THRLZ 31 " --> pdb=" O ILELZ 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 24 through 31' Processing helix chain 'NC' and resid 133 through 138 removed outlier: 4.516A pdb=" N THRNC 137 " --> pdb=" O HISNC 133 " (cutoff:3.500A) Processing helix chain 'NC' and resid 139 through 144 Processing helix chain 'NC' and resid 159 through 174 removed outlier: 3.592A pdb=" N ILENC 164 " --> pdb=" O METNC 160 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLUNC 165 " --> pdb=" O GLNNC 161 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASNNC 166 " --> pdb=" O SERNC 162 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 removed outlier: 4.123A pdb=" N LEUNF 9 " --> pdb=" O GLUNF 5 " (cutoff:3.500A) Processing helix chain 'NF' and resid 21 through 34 removed outlier: 4.366A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NK' and resid 9 through 33 removed outlier: 3.547A pdb=" N LYSNK 20 " --> pdb=" O GLUNK 16 " (cutoff:3.500A) Proline residue: NK 23 - end of helix removed outlier: 3.523A pdb=" N ARGNK 28 " --> pdb=" O LYSNK 24 " (cutoff:3.500A) Processing helix chain 'NK' and resid 98 through 112 removed outlier: 3.555A pdb=" N ARGNK 104 " --> pdb=" O ARGNK 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) Processing helix chain 'NL' and resid 116 through 123 Processing helix chain 'NL' and resid 133 through 138 removed outlier: 3.829A pdb=" N HISNL 137 " --> pdb=" O ASPNL 133 " (cutoff:3.500A) Processing helix chain 'NL' and resid 141 through 159 Processing helix chain 'NL' and resid 162 through 173 Processing helix chain 'NL' and resid 185 through 190 removed outlier: 3.517A pdb=" N ARGNL 190 " --> pdb=" O ASPNL 186 " (cutoff:3.500A) 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: 4.007A pdb=" N HISNL 229 " --> pdb=" O PRONL 225 " (cutoff:3.500A) removed outlier: 4.301A 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: 3.724A pdb=" N LEUNL 368 " --> pdb=" O ARGNL 364 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHENL 369 " --> pdb=" O HISNL 365 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARGNL 370 " --> pdb=" O GLNNL 366 " (cutoff:3.500A) removed outlier: 4.103A 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 removed outlier: 3.512A pdb=" N GLNNL 446 " --> pdb=" O PHENL 442 " (cutoff:3.500A) Processing helix chain 'NL' and resid 470 through 477 removed outlier: 3.740A pdb=" N ILENL 476 " --> pdb=" O ALANL 472 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLNNL 477 " --> pdb=" O PHENL 473 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 20 removed outlier: 4.599A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYSNP 20 " --> pdb=" O ALANP 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'NP' and resid 15 through 20' Processing helix chain 'NP' and resid 27 through 36 removed outlier: 3.882A pdb=" N ILENP 31 " --> pdb=" O ASPNP 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HISNP 32 " --> pdb=" O LEUNP 28 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 83 removed outlier: 3.668A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYSNP 83 " --> pdb=" O HISNP 79 " (cutoff:3.500A) Processing helix chain 'NP' and resid 84 through 94 removed outlier: 3.648A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.636A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.498A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.930A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.797A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 4.008A 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: 3.677A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.379A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.079A 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 removed outlier: 3.504A pdb=" N LEUSA 170 " --> pdb=" O GLUSA 166 " (cutoff:3.500A) Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.853A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.669A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.823A 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 265 removed outlier: 3.721A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.725A 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: 4.041A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 321 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.496A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 16 Processing helix chain 'SB' and resid 20 through 26 removed outlier: 3.609A pdb=" N GLYSB 26 " --> pdb=" O ARGSB 22 " (cutoff:3.500A) Processing helix chain 'SB' and resid 29 through 37 removed outlier: 3.992A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.107A pdb=" N LEUSB 83 " --> pdb=" O TYRSB 79 " (cutoff:3.500A) Proline residue: SB 84 - end of helix Processing helix chain 'SB' and resid 94 through 114 Processing helix chain 'SB' and resid 115 through 120 removed outlier: 3.576A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.724A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLYSB 170 " --> pdb=" O ALASB 166 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 Processing helix chain 'SB' and resid 202 through 215 removed outlier: 3.666A pdb=" N GLUSB 213 " --> pdb=" O ARGSB 209 " (cutoff:3.500A) Processing helix chain 'SB' and resid 216 through 224 Processing helix chain 'SB' and resid 225 through 230 removed outlier: 4.574A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 3.807A pdb=" N METSB 236 " --> pdb=" O THRSB 232 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLUSB 238 " --> pdb=" O ASPSB 234 " (cutoff:3.500A) Proline residue: SB 251 - end of helix Processing helix chain 'SB' and resid 272 through 280 Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 132 through 137 removed outlier: 6.158A pdb=" N VALSC 137 " --> pdb=" O PHESC 133 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.917A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.671A 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: 3.842A 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: 5.303A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.278A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.627A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) removed outlier: 3.659A 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: 3.549A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.229A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.753A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.278A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.580A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.846A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.840A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.784A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 121 Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 169 through 178 Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.751A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 4.853A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.849A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.180A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.443A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLYSF 13 " --> pdb=" O ARGSF 9 " (cutoff:3.500A) Processing helix chain 'SF' and resid 33 through 39 Processing helix chain 'SF' and resid 103 through 108 removed outlier: 3.638A 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 'SF' and resid 181 through 193 removed outlier: 3.548A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.839A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASNSF 205 " --> pdb=" O GLYSF 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 200 through 205' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.907A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 4.043A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 5.018A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.695A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.696A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 Processing helix chain 'SH' and resid 154 through 180 removed outlier: 3.508A pdb=" N LYSSH 166 " --> pdb=" O GLUSH 162 " (cutoff:3.500A) Processing helix chain 'SI' and resid 23 through 53 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.639A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 4.236A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.618A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.220A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.904A 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: 4.642A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.943A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.628A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.911A 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 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.769A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N METSK 197 " --> pdb=" O ILESK 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'SK' and resid 192 through 197' Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.476A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 4.044A 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 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: 3.853A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 3.536A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) removed outlier: 3.515A 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: 4.282A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 241 removed outlier: 3.574A pdb=" N SERSL 238 " --> pdb=" O THRSL 234 " (cutoff:3.500A) Processing helix chain 'SM' and resid 12 through 17 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: 3.707A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 76 removed outlier: 4.064A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Processing helix chain 'SM' and resid 77 through 99 removed outlier: 3.859A pdb=" N LYSSM 81 " --> pdb=" O PROSM 77 " (cutoff:3.500A) 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 148 removed outlier: 3.568A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUSM 143 " --> pdb=" O SERSM 139 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHESM 147 " --> pdb=" O LEUSM 143 " (cutoff:3.500A) Proline residue: SM 148 - end of helix Processing helix chain 'SM' and resid 154 through 176 Processing helix chain 'SM' and resid 216 through 243 removed outlier: 3.716A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 267 through 279 removed outlier: 4.435A pdb=" N CYSSM 272 " --> pdb=" O ASPSM 268 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N METSM 273 " --> pdb=" O SERSM 269 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.833A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.784A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.347A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.532A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.397A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 3.583A pdb=" N ILESQ 56 " --> pdb=" O LYSSQ 52 " (cutoff:3.500A) removed outlier: 4.055A 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 96 removed outlier: 4.034A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.330A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 removed outlier: 3.619A pdb=" N PHESR 46 " --> pdb=" O ARGSR 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.827A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.642A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 161 removed outlier: 3.557A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.583A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.552A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.051A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 3.948A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.598A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARGSR 295 " --> pdb=" O CYSSR 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 290 through 295' Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.559A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLYSR 314 " --> pdb=" O LEUSR 310 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.512A pdb=" N GLUSR 345 " --> pdb=" O ALASR 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THRSR 346 " --> pdb=" O HISSR 342 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLYSR 350 " --> pdb=" O THRSR 346 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.210A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUSR 357 " --> pdb=" O VALSR 353 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 352 through 362' Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.402A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 5.146A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.396A 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 421 through 426 removed outlier: 4.032A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 443 removed outlier: 3.853A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASPSR 443 " --> pdb=" O ALASR 439 " (cutoff:3.500A) Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.770A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.684A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 4.063A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 5.248A 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: 3.670A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLYSR 528 " --> pdb=" O METSR 524 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.587A pdb=" N ARGSR 544 " --> pdb=" O ALASR 540 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.296A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.691A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N METSR 600 " --> pdb=" O ALASR 596 " (cutoff:3.500A) Processing helix chain 'SR' and resid 618 through 623 Processing helix chain 'SV' and resid 33 through 43 removed outlier: 3.633A pdb=" N LYSSV 43 " --> pdb=" O ASNSV 39 " (cutoff:3.500A) Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.594A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.558A pdb=" N ALASV 58 " --> pdb=" O ALASV 54 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.464A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.826A 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 130 removed outlier: 3.545A pdb=" N ARGSV 95 " --> pdb=" O ASPSV 91 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.099A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L5' and resid 48 through 51 removed outlier: 3.640A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'L5' and resid 92 through 95 Processing sheet with id= 4, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 5, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 6, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.642A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.582A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLYL8 40 " --> pdb=" O ARGL8 46 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARGL8 46 " --> pdb=" O GLYL8 40 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.186A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.353A 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= 9, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.578A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.280A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILELA 149 " --> pdb=" O GLULA 115 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.581A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 13, first strand: chain 'LA' and resid 124 through 131 removed outlier: 3.780A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 15, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.403A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.153A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.632A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LE' and resid 39 through 42 removed outlier: 4.046A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 20, first strand: chain 'LF' and resid 61 through 65 removed outlier: 5.938A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 24 through 27 removed outlier: 4.961A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LG' and resid 59 through 63 removed outlier: 4.485A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.790A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.834A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.573A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.627A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.572A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.187A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.114A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 31, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.276A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LN' and resid 44 through 50 removed outlier: 8.175A pdb=" N THRLN 44 " --> pdb=" O LYSLN 349 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LN' and resid 53 through 59 removed outlier: 3.557A pdb=" N GLULN 74 " --> pdb=" O ILELN 56 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.697A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LN' and resid 179 through 184 removed outlier: 5.044A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 88 through 93 Processing sheet with id= 37, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.147A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.760A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 40, first strand: chain 'LR' and resid 19 through 24 removed outlier: 5.301A pdb=" N LYSLR 19 " --> pdb=" O THRLR 35 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LT' and resid 46 through 49 removed outlier: 5.076A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARGLT 76 " --> pdb=" O ARGLT 85 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.633A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.717A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LY' and resid 2 through 5 removed outlier: 4.998A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.456A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.576A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SC' and resid 90 through 95 removed outlier: 9.286A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEUSC 109 " --> pdb=" O ALASC 90 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.422A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.483A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 51, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.651A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SF' and resid 110 through 114 removed outlier: 4.036A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSSF 145 " --> pdb=" O ASNSF 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SERSF 138 " --> pdb=" O ARGSF 147 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.431A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.437A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 57, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.752A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.696A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SH' and resid 72 through 76 removed outlier: 4.122A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.531A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 62, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 63, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 64, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 65, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.092A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SL' and resid 127 through 130 removed outlier: 3.668A pdb=" N GLNSL 128 " --> pdb=" O ILESL 95 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SL' and resid 210 through 217 removed outlier: 6.027A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.583A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 70, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 4.984A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.787A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 73, first strand: chain 'SQ' and resid 213 through 217 Processing sheet with id= 74, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.452A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.584A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.390A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SV' and resid 18 through 22 2992 hydrogen bonds defined for protein. 8894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3103 hydrogen bonds 5290 hydrogen bond angles 0 basepair planarities 1174 basepair parallelities 1826 stacking parallelities Total time for adding SS restraints: 310.94 Time building geometry restraints manager: 62.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 16464 1.31 - 1.43: 66438 1.43 - 1.56: 73558 1.56 - 1.69: 7485 1.69 - 1.81: 493 Bond restraints: 164438 Sorted by residual: bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML32401 " pdb=" C1' A2ML32401 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML3 398 " pdb=" C1' A2ML3 398 " ideal model delta sigma weight residual 1.305 1.550 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C2' A2ML33825 " pdb=" C1' A2ML33825 " ideal model delta sigma weight residual 1.305 1.550 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C2' A2ML33867 " pdb=" C1' A2ML33867 " ideal model delta sigma weight residual 1.305 1.549 -0.244 2.00e-02 2.50e+03 1.48e+02 ... (remaining 164433 not shown) Histogram of bond angle deviations from ideal: 87.79 - 98.09: 14 98.09 - 108.38: 40411 108.38 - 118.68: 112686 118.68 - 128.98: 83068 128.98 - 139.27: 3769 Bond angle restraints: 239948 Sorted by residual: angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 127.97 -39.47 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 126.93 -38.43 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C1' A2ML31524 " pdb=" N9 A2ML31524 " pdb=" C8 A2ML31524 " ideal model delta sigma weight residual 88.50 126.84 -38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2ML33724 " pdb=" N9 A2ML33724 " pdb=" C8 A2ML33724 " ideal model delta sigma weight residual 88.50 126.78 -38.28 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2ML31871 " pdb=" N9 A2ML31871 " pdb=" C8 A2ML31871 " ideal model delta sigma weight residual 88.50 126.60 -38.10 3.00e+00 1.11e-01 1.61e+02 ... (remaining 239943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 95763 35.94 - 71.88: 8775 71.88 - 107.82: 1309 107.82 - 143.76: 21 143.76 - 179.70: 13 Dihedral angle restraints: 105881 sinusoidal: 79536 harmonic: 26345 Sorted by residual: dihedral pdb=" C4' CL3 502 " pdb=" C3' CL3 502 " pdb=" C2' CL3 502 " pdb=" C1' CL3 502 " ideal model delta sinusoidal sigma weight residual -35.00 34.47 -69.47 1 8.00e+00 1.56e-02 9.74e+01 dihedral pdb=" C5' CL3 502 " pdb=" C4' CL3 502 " pdb=" C3' CL3 502 " pdb=" O3' CL3 502 " ideal model delta sinusoidal sigma weight residual 147.00 80.36 66.64 1 8.00e+00 1.56e-02 9.05e+01 dihedral pdb=" O4' CL34303 " pdb=" C1' CL34303 " pdb=" N1 CL34303 " pdb=" C2 CL34303 " ideal model delta sinusoidal sigma weight residual 200.00 30.59 169.41 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 105878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 28229 0.088 - 0.175: 1036 0.175 - 0.263: 42 0.263 - 0.351: 6 0.351 - 0.439: 15 Chirality restraints: 29328 Sorted by residual: chirality pdb=" C2' A2ML31871 " pdb=" C3' A2ML31871 " pdb=" O2' A2ML31871 " pdb=" C1' A2ML31871 " both_signs ideal model delta sigma weight residual False -2.39 -2.83 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C2' A2ML34571 " pdb=" C3' A2ML34571 " pdb=" O2' A2ML34571 " pdb=" C1' A2ML34571 " both_signs ideal model delta sigma weight residual False -2.39 -2.80 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C2' A2ML33718 " pdb=" C3' A2ML33718 " pdb=" O2' A2ML33718 " pdb=" C1' A2ML33718 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 29325 not shown) Planarity restraints: 16466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.929 2.00e-02 2.50e+03 6.21e-01 8.68e+03 pdb=" C4' OMGL34228 " -0.206 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.723 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.185 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.980 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.622 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.674 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.453 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.053 2.00e-02 2.50e+03 6.08e-01 8.30e+03 pdb=" C4' OMGL34494 " -0.454 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.700 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.592 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.628 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.195 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.948 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.208 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL33701 " 0.912 2.00e-02 2.50e+03 6.05e-01 8.23e+03 pdb=" C4' OMCL33701 " -0.204 2.00e-02 2.50e+03 pdb=" O4' OMCL33701 " -0.741 2.00e-02 2.50e+03 pdb=" C3' OMCL33701 " 0.213 2.00e-02 2.50e+03 pdb=" O3' OMCL33701 " -0.926 2.00e-02 2.50e+03 pdb=" C2' OMCL33701 " 0.614 2.00e-02 2.50e+03 pdb=" O2' OMCL33701 " 0.617 2.00e-02 2.50e+03 pdb=" C1' OMCL33701 " -0.453 2.00e-02 2.50e+03 pdb=" N1 OMCL33701 " -0.030 2.00e-02 2.50e+03 ... (remaining 16463 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 824 2.54 - 3.19: 126170 3.19 - 3.84: 336691 3.84 - 4.49: 484764 4.49 - 5.14: 662561 Nonbonded interactions: 1611010 Sorted by model distance: nonbonded pdb=" OP2 AL31337 " pdb="MG MGL35110 " model vdw 1.894 2.170 nonbonded pdb=" OP1 CL31384 " pdb="MG MGL35123 " model vdw 1.917 2.170 nonbonded pdb=" O6 GL3 356 " pdb="MG MGL35130 " model vdw 1.956 2.170 nonbonded pdb=" OE1 GLNLW 30 " pdb="MG MGL35152 " model vdw 1.957 2.170 nonbonded pdb=" O2' GL3 695 " pdb=" OP2 GL3 697 " model vdw 1.960 2.440 ... (remaining 1611005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 26.830 Check model and map are aligned: 1.670 Set scattering table: 1.070 Process input model: 659.340 Find NCS groups from input model: 3.670 Set up NCS constraints: 0.380 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:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 709.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.008 0.246 164438 Z= 0.446 Angle : 0.774 39.467 239948 Z= 0.341 Chirality : 0.039 0.439 29328 Planarity : 0.025 0.621 16466 Dihedral : 21.829 179.701 88841 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 8934 helix: 1.01 (0.09), residues: 3428 sheet: 0.62 (0.15), residues: 1126 loop : 0.09 (0.09), residues: 4380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPSV 86 HIS 0.013 0.001 HISLA 25 PHE 0.019 0.002 PHESL 173 TYR 0.033 0.002 TYRLC 84 ARG 0.017 0.001 ARGSL 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1618 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1618 time to evaluate : 8.269 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: L5 163 MET cc_start: 0.8167 (mtt) cc_final: 0.7779 (mtt) REVERT: L7 180 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8095 (tp40) REVERT: L8 104 MET cc_start: 0.7959 (ttp) cc_final: 0.7746 (ttp) REVERT: LC 9 GLU cc_start: 0.7531 (tt0) cc_final: 0.7318 (tt0) REVERT: LC 99 ASP cc_start: 0.8082 (t0) cc_final: 0.7744 (t70) REVERT: LF 95 ASN cc_start: 0.8348 (t0) cc_final: 0.7685 (t0) REVERT: LI 10 ASP cc_start: 0.8137 (t0) cc_final: 0.7829 (t0) REVERT: LM 12 GLN cc_start: 0.6703 (mm-40) cc_final: 0.6491 (mm-40) REVERT: LN 332 MET cc_start: 0.7458 (ttm) cc_final: 0.7070 (ttm) REVERT: LV 43 ARG cc_start: 0.7406 (tpt170) cc_final: 0.6587 (ttt180) REVERT: LX 88 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7215 (pp20) REVERT: LZ 37 TYR cc_start: 0.8087 (p90) cc_final: 0.7865 (p90) REVERT: LZ 39 SER cc_start: 0.9134 (p) cc_final: 0.8919 (t) REVERT: NF 54 ARG cc_start: 0.8903 (mmm160) cc_final: 0.8575 (mmm160) REVERT: NK 25 GLU cc_start: 0.7903 (tt0) cc_final: 0.7680 (tt0) REVERT: NL 124 ASN cc_start: 0.8532 (t0) cc_final: 0.8276 (t0) REVERT: SA 264 TYR cc_start: 0.8342 (m-80) cc_final: 0.8110 (m-80) REVERT: SG 171 ASP cc_start: 0.8568 (t0) cc_final: 0.8153 (t0) REVERT: SI 237 MET cc_start: 0.8006 (mmp) cc_final: 0.7630 (mmm) REVERT: SL 153 ASP cc_start: 0.7569 (m-30) cc_final: 0.7214 (m-30) REVERT: SR 48 MET cc_start: 0.8190 (mtm) cc_final: 0.7745 (mtp) REVERT: SR 303 ASP cc_start: 0.5390 (m-30) cc_final: 0.4999 (m-30) REVERT: SR 550 THR cc_start: 0.7873 (p) cc_final: 0.7657 (m) outliers start: 0 outliers final: 4 residues processed: 1618 average time/residue: 2.3859 time to fit residues: 5478.2601 Evaluate side-chains 1094 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1090 time to evaluate : 8.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 47 ILE Chi-restraints excluded: chain SC residue 50 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SR residue 446 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 1062 optimal weight: 0.9980 chunk 953 optimal weight: 6.9990 chunk 529 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 643 optimal weight: 8.9990 chunk 509 optimal weight: 3.9990 chunk 986 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 599 optimal weight: 7.9990 chunk 733 optimal weight: 5.9990 chunk 1142 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 137 GLN BA 147 HIS ** L5 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L5 167 GLN L6 67 HIS L6 175 ASN L8 33 GLN L9 86 HIS LA 56 GLN LD 143 HIS LE 58 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 44 GLN LG 135 ASN LH 73 HIS LH 107 HIS LH 151 ASN LJ 132 GLN LK 19 HIS LK 85 GLN LL 70 GLN LN 42 HIS LN 109 HIS LN 328 ASN LO 33 GLN LP 18 ASN LP 121 ASN LU 20 ASN LU 92 ASN LY 28 ASN NL 141 ASN NL 354 GLN NP 13 HIS SA 276 ASN SB 275 GLN SC 135 GLN SC 136 HIS SC 190 HIS SD 24 ASN SD 63 GLN SE 141 ASN SE 149 ASN SE 206 GLN SE 208 ASN SH 108 ASN SI 153 ASN SK 83 HIS SL 46 HIS SL 121 HIS SL 128 GLN SL 184 ASN ** SL 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 225 HIS SM 170 HIS SM 245 HIS SM 375 HIS SQ 58 ASN SQ 152 GLN SR 41 HIS SR 157 HIS SR 209 HIS SR 504 GLN SV 17 HIS SV 39 ASN SV 104 GLN SV 119 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 164438 Z= 0.269 Angle : 0.733 19.067 239948 Z= 0.390 Chirality : 0.037 0.348 29328 Planarity : 0.007 0.132 16466 Dihedral : 23.056 179.572 69721 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.43 % Allowed : 9.90 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.13 (0.09), residues: 8934 helix: 1.69 (0.09), residues: 3517 sheet: 0.60 (0.15), residues: 1146 loop : 0.09 (0.09), residues: 4271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPLW 49 HIS 0.010 0.001 HISLA 25 PHE 0.024 0.002 PHESD 37 TYR 0.021 0.002 TYRNP 111 ARG 0.009 0.001 ARGSE 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1135 time to evaluate : 8.321 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 116 MET cc_start: 0.6947 (mmm) cc_final: 0.6690 (mmm) REVERT: L5 163 MET cc_start: 0.8178 (mtt) cc_final: 0.7649 (mtp) REVERT: L7 191 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7922 (pttt) REVERT: L9 15 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: LI 65 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: LK 116 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8307 (ptmt) REVERT: LL 89 THR cc_start: 0.8753 (m) cc_final: 0.8502 (p) REVERT: LL 122 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8128 (mtmm) REVERT: LN 332 MET cc_start: 0.7415 (ttm) cc_final: 0.7094 (ttm) REVERT: LR 108 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7169 (pttp) REVERT: LT 40 GLU cc_start: 0.8178 (tp30) cc_final: 0.7277 (tp30) REVERT: LT 43 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8699 (mp) REVERT: LT 83 MET cc_start: 0.8370 (mmm) cc_final: 0.8119 (mtp) REVERT: LV 43 ARG cc_start: 0.7580 (tpt-90) cc_final: 0.6713 (ttt180) REVERT: LW 79 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8222 (ptp-170) REVERT: LX 87 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7170 (tttt) REVERT: LY 8 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7915 (mm) REVERT: LZ 37 TYR cc_start: 0.8116 (p90) cc_final: 0.7874 (p90) REVERT: NL 124 ASN cc_start: 0.8428 (t0) cc_final: 0.8205 (t0) REVERT: SA 264 TYR cc_start: 0.8331 (m-80) cc_final: 0.8130 (m-80) REVERT: SH 113 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: SI 237 MET cc_start: 0.8075 (mmp) cc_final: 0.7694 (mmm) REVERT: SI 255 ASN cc_start: 0.7338 (t0) cc_final: 0.7124 (t0) REVERT: SL 78 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7896 (mt) REVERT: SM 105 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6701 (tp30) REVERT: SR 48 MET cc_start: 0.8126 (mtm) cc_final: 0.7529 (mtp) REVERT: SR 295 ARG cc_start: 0.7115 (mmm160) cc_final: 0.6914 (mmm160) REVERT: SV 70 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: SV 98 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7117 (mp0) outliers start: 188 outliers final: 82 residues processed: 1219 average time/residue: 2.2529 time to fit residues: 3998.2879 Evaluate side-chains 1155 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1058 time to evaluate : 8.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 63 ARG Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L7 residue 62 MET Chi-restraints excluded: chain L7 residue 92 THR Chi-restraints excluded: chain L7 residue 191 LYS Chi-restraints excluded: chain L9 residue 15 GLN Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 130 SER Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LD residue 137 ILE Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 109 SER Chi-restraints excluded: chain LG residue 40 ILE Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 116 LYS Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 108 LYS Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 43 LEU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LX residue 87 LYS Chi-restraints excluded: chain LY residue 8 ILE Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 8 ARG Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SC residue 50 LEU Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 252 LYS Chi-restraints excluded: chain SF residue 88 VAL Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 95 SER Chi-restraints excluded: chain SK residue 197 MET Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 190 LEU Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SQ residue 209 ASP Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 536 ASP Chi-restraints excluded: chain SR residue 582 ASP Chi-restraints excluded: chain SV residue 70 GLU Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 127 VAL Chi-restraints excluded: chain SV residue 130 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 634 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 chunk 950 optimal weight: 0.0010 chunk 777 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 1144 optimal weight: 0.2980 chunk 1236 optimal weight: 7.9990 chunk 1019 optimal weight: 0.3980 chunk 1134 optimal weight: 0.7980 chunk 390 optimal weight: 6.9990 chunk 918 optimal weight: 5.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L5 112 HIS L6 13 HIS L6 67 HIS LC 125 GLN LF 44 GLN LF 95 ASN LG 36 ASN LH 93 ASN LK 85 GLN LL 70 GLN LM 49 HIS LN 175 GLN LN 322 HIS LP 18 ASN LP 69 ASN LQ 107 ASN LS 65 GLN LU 20 ASN LU 92 ASN LY 58 GLN NK 98 ASN NL 354 GLN NP 13 HIS SA 43 ASN SB 275 GLN SC 191 GLN SD 63 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 139 HIS SG 8 GLN SG 106 GLN SG 138 GLN SH 108 ASN SI 153 ASN SL 46 HIS SL 121 HIS SL 128 GLN SM 245 HIS SQ 58 ASN SQ 152 GLN SR 91 HIS SV 39 ASN SV 87 ASN SV 104 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 164438 Z= 0.143 Angle : 0.654 19.593 239948 Z= 0.358 Chirality : 0.033 0.327 29328 Planarity : 0.006 0.126 16466 Dihedral : 22.959 179.661 69717 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.19 % Allowed : 12.10 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.37 (0.09), residues: 8934 helix: 2.02 (0.09), residues: 3523 sheet: 0.57 (0.15), residues: 1154 loop : 0.14 (0.09), residues: 4257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPLN 196 HIS 0.011 0.001 HISSH 127 PHE 0.023 0.001 PHESD 37 TYR 0.024 0.001 TYRNP 111 ARG 0.012 0.000 ARGLG 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1140 time to evaluate : 8.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 123 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.7155 (ttm-80) REVERT: BA 133 LEU cc_start: 0.8154 (mt) cc_final: 0.7953 (mm) REVERT: L5 163 MET cc_start: 0.8169 (mtt) cc_final: 0.7587 (mtp) REVERT: L7 62 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8251 (ttt) REVERT: L7 191 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7833 (pttt) REVERT: L8 55 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: L8 81 ASP cc_start: 0.6606 (t0) cc_final: 0.6299 (t0) REVERT: LF 95 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7159 (t0) REVERT: LG 112 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (ttm) REVERT: LI 65 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: LL 89 THR cc_start: 0.8690 (m) cc_final: 0.8487 (p) REVERT: LL 122 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8057 (mtmm) REVERT: LN 332 MET cc_start: 0.7388 (ttm) cc_final: 0.7081 (ttm) REVERT: LT 40 GLU cc_start: 0.8087 (tp30) cc_final: 0.7354 (tp30) REVERT: LT 83 MET cc_start: 0.8345 (mmm) cc_final: 0.8121 (mtp) REVERT: LV 43 ARG cc_start: 0.7506 (tpt-90) cc_final: 0.6674 (ttt180) REVERT: LW 79 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7912 (ptp-170) REVERT: LX 26 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8159 (t) REVERT: LX 36 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7900 (mtmt) REVERT: LZ 37 TYR cc_start: 0.8115 (p90) cc_final: 0.7878 (p90) REVERT: NF 13 ARG cc_start: 0.8430 (mtt180) cc_final: 0.8175 (mtt180) REVERT: NF 41 LYS cc_start: 0.7626 (mmtm) cc_final: 0.7391 (mmtp) REVERT: SH 113 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: SI 237 MET cc_start: 0.7956 (mmp) cc_final: 0.7657 (mmm) REVERT: SI 255 ASN cc_start: 0.7281 (t0) cc_final: 0.7069 (t0) REVERT: SL 78 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7870 (mt) REVERT: SM 105 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6602 (tp30) REVERT: SM 140 MET cc_start: 0.8809 (mmm) cc_final: 0.8583 (mmm) REVERT: SR 48 MET cc_start: 0.8077 (mtm) cc_final: 0.7457 (mtp) outliers start: 169 outliers final: 53 residues processed: 1219 average time/residue: 2.2906 time to fit residues: 4120.0808 Evaluate side-chains 1109 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1044 time to evaluate : 7.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 63 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 62 MET Chi-restraints excluded: chain L7 residue 118 MET Chi-restraints excluded: chain L7 residue 191 LYS Chi-restraints excluded: chain L8 residue 55 MET Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 129 ASP Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 95 ASN Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 56 GLN Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LP residue 69 ASN Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 182 ASN Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SI residue 95 SER Chi-restraints excluded: chain SK residue 197 MET Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 117 LEU Chi-restraints excluded: chain SL residue 190 LEU Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 582 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 1130 optimal weight: 0.0970 chunk 860 optimal weight: 10.0000 chunk 593 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 546 optimal weight: 4.9990 chunk 768 optimal weight: 9.9990 chunk 1148 optimal weight: 1.9990 chunk 1215 optimal weight: 4.9990 chunk 600 optimal weight: 0.0970 chunk 1088 optimal weight: 0.1980 chunk 327 optimal weight: 7.9990 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L5 46 GLN L6 67 HIS L7 96 GLN LD 27 ASN LD 66 ASN LF 44 GLN LL 70 GLN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LP 69 ASN LS 65 GLN LU 12 ASN LU 20 ASN LU 92 ASN NL 124 ASN NL 354 GLN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS NP 32 HIS SA 203 GLN SB 275 GLN SC 135 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 139 HIS SG 106 GLN SH 108 ASN SI 136 ASN SI 153 ASN SL 46 HIS SL 128 GLN SL 184 ASN SL 218 HIS SM 110 ASN SM 170 HIS SM 245 HIS SQ 58 ASN SQ 152 GLN SV 39 ASN SV 76 ASN SV 104 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 164438 Z= 0.157 Angle : 0.646 19.229 239948 Z= 0.353 Chirality : 0.033 0.320 29328 Planarity : 0.006 0.128 16466 Dihedral : 22.884 179.602 69713 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.51 % Allowed : 13.29 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.45 (0.09), residues: 8934 helix: 2.12 (0.09), residues: 3541 sheet: 0.57 (0.15), residues: 1149 loop : 0.16 (0.09), residues: 4244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPLW 49 HIS 0.006 0.001 HISSH 127 PHE 0.026 0.001 PHESD 37 TYR 0.021 0.001 TYRNP 111 ARG 0.011 0.000 ARGSQ 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1074 time to evaluate : 7.515 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 116 MET cc_start: 0.6989 (mmm) cc_final: 0.6649 (mpp) REVERT: BA 147 HIS cc_start: 0.5745 (t-90) cc_final: 0.5499 (t70) REVERT: L5 163 MET cc_start: 0.8152 (mtt) cc_final: 0.7564 (mtp) REVERT: L8 126 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: LF 31 ASP cc_start: 0.7595 (m-30) cc_final: 0.7379 (m-30) REVERT: LG 112 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8267 (ttm) REVERT: LI 65 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: LJ 113 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6565 (tp30) REVERT: LL 28 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6314 (pp20) REVERT: LL 117 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8171 (mp) REVERT: LL 122 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8020 (mtmm) REVERT: LN 250 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8231 (mtpt) REVERT: LN 289 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: LN 332 MET cc_start: 0.7332 (ttm) cc_final: 0.7034 (ttm) REVERT: LP 64 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7339 (mp) REVERT: LT 40 GLU cc_start: 0.8084 (tp30) cc_final: 0.7434 (tp30) REVERT: LW 79 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7951 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8110 (p90) cc_final: 0.7885 (p90) REVERT: SA 264 TYR cc_start: 0.8055 (m-80) cc_final: 0.7824 (m-80) REVERT: SG 152 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7385 (mt-10) REVERT: SI 237 MET cc_start: 0.7934 (mmp) cc_final: 0.7672 (mmm) REVERT: SI 255 ASN cc_start: 0.7330 (t0) cc_final: 0.7129 (t0) REVERT: SL 78 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7914 (mt) REVERT: SM 105 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: SR 48 MET cc_start: 0.8039 (mtm) cc_final: 0.7455 (mtp) REVERT: SV 70 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7519 (mp0) outliers start: 194 outliers final: 87 residues processed: 1176 average time/residue: 2.2063 time to fit residues: 3807.1714 Evaluate side-chains 1136 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1035 time to evaluate : 8.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L8 residue 123 ILE Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 130 SER Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 61 VAL Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LJ residue 113 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 117 ILE Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 250 LYS Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 60 ILE Chi-restraints excluded: chain LP residue 64 ILE Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain SA residue 138 MET Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 117 LYS Chi-restraints excluded: chain SC residue 56 ARG Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 182 ASN Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SI residue 95 SER Chi-restraints excluded: chain SK residue 197 MET Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 117 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 190 LEU Chi-restraints excluded: chain SL residue 234 THR Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 496 LEU Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 582 ASP Chi-restraints excluded: chain SR residue 608 GLU Chi-restraints excluded: chain SV residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 1012 optimal weight: 0.5980 chunk 690 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 905 optimal weight: 6.9990 chunk 501 optimal weight: 7.9990 chunk 1037 optimal weight: 10.0000 chunk 840 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 620 optimal weight: 1.9990 chunk 1091 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L7 96 GLN LA 25 HIS LJ 132 GLN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 3 HIS LP 18 ASN LP 93 ASN LS 65 GLN LU 20 ASN LU 92 ASN LY 58 GLN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN ** SE 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SI 153 ASN SI 225 HIS SL 46 HIS SL 128 GLN SL 189 ASN SM 170 HIS SM 209 HIS SM 245 HIS SQ 152 GLN SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 164438 Z= 0.374 Angle : 0.743 18.897 239948 Z= 0.392 Chirality : 0.040 0.367 29328 Planarity : 0.007 0.139 16466 Dihedral : 22.927 179.570 69713 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.09 % Allowed : 13.70 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.13 (0.09), residues: 8934 helix: 1.83 (0.09), residues: 3552 sheet: 0.46 (0.15), residues: 1140 loop : -0.03 (0.09), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPLW 49 HIS 0.013 0.002 HISLA 25 PHE 0.032 0.002 PHESR 18 TYR 0.024 0.002 TYRLB 32 ARG 0.009 0.001 ARGLV 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1068 time to evaluate : 8.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 116 MET cc_start: 0.6971 (mmm) cc_final: 0.6689 (mpp) REVERT: L5 63 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6874 (ptm160) REVERT: L5 163 MET cc_start: 0.8237 (mtt) cc_final: 0.7654 (mtp) REVERT: L6 129 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7959 (mmt180) REVERT: L6 158 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6998 (mmm160) REVERT: L7 191 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7894 (pttt) REVERT: L8 55 MET cc_start: 0.8484 (mtm) cc_final: 0.8003 (mtp) REVERT: L8 126 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: LA 99 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: LE 118 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6576 (mm-30) REVERT: LF 31 ASP cc_start: 0.7678 (m-30) cc_final: 0.7436 (m-30) REVERT: LG 112 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (ttm) REVERT: LI 65 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: LK 116 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8410 (ptmt) REVERT: LL 28 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6474 (pp20) REVERT: LL 56 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: LL 122 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8053 (mtmm) REVERT: LN 289 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: LP 64 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7506 (mp) REVERT: LT 43 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8669 (mp) REVERT: LW 79 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8121 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8169 (p90) cc_final: 0.7909 (p90) REVERT: NP 77 LYS cc_start: 0.7995 (mppt) cc_final: 0.7744 (mppt) REVERT: SA 157 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7732 (tttp) REVERT: SC 71 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7052 (mtp180) REVERT: SE 108 GLN cc_start: 0.8442 (mp10) cc_final: 0.8204 (mp10) REVERT: SF 155 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7397 (mmmt) REVERT: SG 152 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7530 (mt-10) REVERT: SH 113 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: SI 237 MET cc_start: 0.7976 (mmp) cc_final: 0.7692 (mmm) REVERT: SL 78 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8013 (mt) REVERT: SL 94 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7425 (p0) REVERT: SM 105 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: SR 42 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7711 (ttp-170) REVERT: SR 48 MET cc_start: 0.8095 (mtm) cc_final: 0.7447 (mtp) REVERT: SR 405 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6260 (mtp) REVERT: SV 70 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: SV 98 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7034 (mp0) outliers start: 239 outliers final: 132 residues processed: 1193 average time/residue: 2.2258 time to fit residues: 3892.1951 Evaluate side-chains 1185 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1027 time to evaluate : 8.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain BA residue 160 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 63 ARG Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 92 THR Chi-restraints excluded: chain L7 residue 191 LYS Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 123 ILE Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LC residue 125 GLN Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 27 LEU Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 63 ILE Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 56 GLN Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 107 THR Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 116 LYS Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 56 ASP Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 69 THR Chi-restraints excluded: chain LP residue 64 ILE Chi-restraints excluded: chain LP residue 107 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 43 LEU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 50 LYS Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 34 LYS Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 64 THR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 138 MET Chi-restraints excluded: chain SA residue 157 LYS Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SB residue 234 ASP Chi-restraints excluded: chain SB residue 267 ASN Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 56 ARG Chi-restraints excluded: chain SC residue 71 ARG Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 155 LYS Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 228 ASP Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 132 LYS Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 117 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 190 LEU Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SL residue 233 VAL Chi-restraints excluded: chain SM residue 6 LYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SM residue 275 LYS Chi-restraints excluded: chain SQ residue 181 VAL Chi-restraints excluded: chain SR residue 42 ARG Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 344 VAL Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SV residue 24 ASN Chi-restraints excluded: chain SV residue 70 GLU Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 409 optimal weight: 3.9990 chunk 1095 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 713 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 1217 optimal weight: 0.9980 chunk 1010 optimal weight: 3.9990 chunk 563 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 402 optimal weight: 3.9990 chunk 638 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L5 46 GLN L6 67 HIS L6 175 ASN L7 96 GLN LF 50 ASN LG 135 ASN LI 43 ASN LI 127 GLN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LS 107 GLN LU 20 ASN LU 92 ASN LY 58 GLN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NL 354 GLN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SG 106 GLN SL 46 HIS SL 128 GLN SL 189 ASN SM 170 HIS SM 245 HIS SQ 58 ASN SQ 152 GLN SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 164438 Z= 0.292 Angle : 0.705 19.222 239948 Z= 0.378 Chirality : 0.037 0.368 29328 Planarity : 0.007 0.135 16466 Dihedral : 22.931 179.145 69713 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.86 % Allowed : 14.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.10 (0.09), residues: 8934 helix: 1.84 (0.09), residues: 3549 sheet: 0.41 (0.15), residues: 1138 loop : -0.06 (0.09), residues: 4247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPLW 49 HIS 0.009 0.001 HISLA 25 PHE 0.031 0.002 PHESD 37 TYR 0.022 0.002 TYRL8 72 ARG 0.008 0.001 ARGLG 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1064 time to evaluate : 8.276 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 116 MET cc_start: 0.6929 (mmm) cc_final: 0.6674 (mpp) REVERT: L5 163 MET cc_start: 0.8273 (mtt) cc_final: 0.7786 (mtp) REVERT: L6 129 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7938 (mmt180) REVERT: L6 158 ARG cc_start: 0.7342 (mmm160) cc_final: 0.7085 (mmm160) REVERT: L7 191 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7878 (pttt) REVERT: L8 55 MET cc_start: 0.8398 (mtm) cc_final: 0.7983 (mtp) REVERT: L8 126 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: LA 99 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: LF 31 ASP cc_start: 0.7401 (m-30) cc_final: 0.7176 (m-30) REVERT: LG 112 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8256 (ttm) REVERT: LI 65 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: LK 116 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8394 (ptmt) REVERT: LL 28 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6425 (pp20) REVERT: LL 56 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: LL 122 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8007 (mtmm) REVERT: LN 289 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: LP 64 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7467 (mp) REVERT: LT 43 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8640 (mp) REVERT: LT 83 MET cc_start: 0.8397 (mmm) cc_final: 0.8167 (mtp) REVERT: LW 79 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8075 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8161 (p90) cc_final: 0.7906 (p90) REVERT: SA 61 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: SA 157 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7738 (tttp) REVERT: SD 32 ARG cc_start: 0.7641 (ptp-170) cc_final: 0.7238 (ptp-170) REVERT: SE 108 GLN cc_start: 0.8463 (mp10) cc_final: 0.8237 (mp10) REVERT: SF 155 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7407 (mmmt) REVERT: SG 152 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7439 (mt-10) REVERT: SH 58 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: SH 113 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: SI 237 MET cc_start: 0.7902 (mmp) cc_final: 0.7673 (mmm) REVERT: SL 94 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7376 (p0) REVERT: SM 105 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: SQ 52 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7499 (mmtt) REVERT: SR 42 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7753 (ttp-170) REVERT: SR 48 MET cc_start: 0.8080 (mtm) cc_final: 0.7385 (mtp) REVERT: SR 303 ASP cc_start: 0.5278 (OUTLIER) cc_final: 0.4615 (m-30) REVERT: SV 98 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6987 (mp0) outliers start: 221 outliers final: 131 residues processed: 1185 average time/residue: 2.2174 time to fit residues: 3852.7658 Evaluate side-chains 1190 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1035 time to evaluate : 8.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain BA residue 160 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 92 THR Chi-restraints excluded: chain L7 residue 191 LYS Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 123 ILE Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 125 GLN Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 63 ILE Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 138 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 78 LEU Chi-restraints excluded: chain LK residue 116 LYS Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 56 ASP Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 91 SER Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LP residue 64 ILE Chi-restraints excluded: chain LP residue 107 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 65 GLN Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 43 LEU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LX residue 81 SER Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 34 LYS Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 64 THR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 157 LYS Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 309 ILE Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 234 ASP Chi-restraints excluded: chain SB residue 267 ASN Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 56 ARG Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 106 THR Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 155 LYS Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 58 GLU Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SK residue 58 ILE Chi-restraints excluded: chain SK residue 72 VAL Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 117 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SL residue 233 VAL Chi-restraints excluded: chain SL residue 234 THR Chi-restraints excluded: chain SM residue 6 LYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SQ residue 149 MET Chi-restraints excluded: chain SQ residue 181 VAL Chi-restraints excluded: chain SR residue 42 ARG Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 496 LEU Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 582 ASP Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 1173 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 693 optimal weight: 5.9990 chunk 888 optimal weight: 6.9990 chunk 688 optimal weight: 0.2980 chunk 1024 optimal weight: 0.5980 chunk 679 optimal weight: 7.9990 chunk 1212 optimal weight: 1.9990 chunk 758 optimal weight: 5.9990 chunk 739 optimal weight: 1.9990 chunk 559 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L6 67 HIS L6 175 ASN L7 96 GLN LI 43 ASN LI 127 GLN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LU 20 ASN LU 92 ASN LY 58 GLN NF 33 HIS NL 354 GLN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN ** SB 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 135 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SL 128 GLN SM 170 HIS SM 245 HIS SQ 58 ASN SQ 152 GLN SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 164438 Z= 0.154 Angle : 0.655 19.300 239948 Z= 0.357 Chirality : 0.033 0.339 29328 Planarity : 0.006 0.128 16466 Dihedral : 22.881 178.899 69713 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.41 % Allowed : 15.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.09), residues: 8934 helix: 2.07 (0.09), residues: 3538 sheet: 0.42 (0.15), residues: 1156 loop : 0.05 (0.09), residues: 4240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPL9 120 HIS 0.006 0.001 HISSM 245 PHE 0.031 0.001 PHESD 37 TYR 0.018 0.001 TYRNP 111 ARG 0.011 0.000 ARGNL 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1075 time to evaluate : 8.522 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 116 MET cc_start: 0.6910 (mmm) cc_final: 0.6668 (mpp) REVERT: L5 163 MET cc_start: 0.8256 (mtt) cc_final: 0.7757 (mtp) REVERT: L6 129 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7935 (mmt180) REVERT: L8 55 MET cc_start: 0.8259 (mtm) cc_final: 0.7857 (mtp) REVERT: L8 126 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: LF 31 ASP cc_start: 0.7360 (m-30) cc_final: 0.7064 (m-30) REVERT: LG 112 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: LI 65 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: LJ 86 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8445 (m) REVERT: LL 28 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6361 (pp20) REVERT: LL 122 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7963 (mtmm) REVERT: LN 289 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: LP 64 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7338 (mp) REVERT: LT 83 MET cc_start: 0.8394 (mmm) cc_final: 0.8123 (mtp) REVERT: LW 79 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7933 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8151 (p90) cc_final: 0.7902 (p90) REVERT: NL 346 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8229 (mtmm) REVERT: NP 77 LYS cc_start: 0.7927 (mppt) cc_final: 0.7437 (mppt) REVERT: SA 61 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: SD 32 ARG cc_start: 0.7611 (ptp-170) cc_final: 0.7349 (ptp-170) REVERT: SE 108 GLN cc_start: 0.8372 (mp10) cc_final: 0.8171 (mp10) REVERT: SG 152 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7414 (mt-10) REVERT: SH 113 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: SH 135 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8213 (p0) REVERT: SL 94 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7332 (p0) REVERT: SM 105 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: SR 303 ASP cc_start: 0.5182 (OUTLIER) cc_final: 0.4652 (m-30) REVERT: SR 405 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6176 (mtp) REVERT: SV 70 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: SV 98 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6922 (mp0) outliers start: 186 outliers final: 105 residues processed: 1178 average time/residue: 2.2040 time to fit residues: 3809.1238 Evaluate side-chains 1171 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1047 time to evaluate : 8.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain BA residue 160 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 46 ASN Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 63 ILE Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 56 GLN Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 97 VAL Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 91 SER Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 64 ILE Chi-restraints excluded: chain LP residue 107 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 267 ASN Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 182 ASN Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SK residue 72 VAL Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 117 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SM residue 6 LYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SQ residue 181 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 496 LEU Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 582 ASP Chi-restraints excluded: chain SV residue 70 GLU Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 750 optimal weight: 4.9990 chunk 484 optimal weight: 0.9980 chunk 724 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 770 optimal weight: 0.8980 chunk 826 optimal weight: 10.0000 chunk 599 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 953 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L6 67 HIS L7 96 GLN LC 125 GLN LF 50 ASN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LP 121 ASN LU 92 ASN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NL 124 ASN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN SC 135 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SL 128 GLN SL 189 ASN SM 170 HIS SM 245 HIS SQ 58 ASN SQ 152 GLN SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 164438 Z= 0.254 Angle : 0.688 19.111 239948 Z= 0.370 Chirality : 0.036 0.353 29328 Planarity : 0.007 0.133 16466 Dihedral : 22.864 178.948 69713 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.56 % Allowed : 16.08 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.22 (0.09), residues: 8934 helix: 1.98 (0.09), residues: 3545 sheet: 0.40 (0.15), residues: 1144 loop : -0.02 (0.09), residues: 4245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPLW 49 HIS 0.007 0.001 HISLA 25 PHE 0.033 0.002 PHESD 37 TYR 0.020 0.002 TYRL8 72 ARG 0.012 0.000 ARGNL 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1051 time to evaluate : 8.423 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 116 MET cc_start: 0.6919 (mmm) cc_final: 0.6676 (mpp) REVERT: L5 35 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7415 (ttp-110) REVERT: L5 163 MET cc_start: 0.8317 (mtt) cc_final: 0.7833 (mtp) REVERT: L6 121 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: L6 129 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (mmt180) REVERT: L7 173 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7460 (tm-30) REVERT: L8 55 MET cc_start: 0.8288 (mtm) cc_final: 0.7945 (mtp) REVERT: L8 126 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: LA 99 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: LF 31 ASP cc_start: 0.7415 (m-30) cc_final: 0.7128 (m-30) REVERT: LG 112 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8267 (ttm) REVERT: LI 65 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: LL 28 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6396 (pp20) REVERT: LL 122 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7978 (mtmm) REVERT: LN 84 MET cc_start: 0.7637 (ttm) cc_final: 0.7288 (mtp) REVERT: LN 289 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: LS 7 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7324 (ttp-110) REVERT: LT 83 MET cc_start: 0.8397 (mmm) cc_final: 0.8195 (mtp) REVERT: LW 79 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8006 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8167 (p90) cc_final: 0.7913 (p90) REVERT: NP 77 LYS cc_start: 0.8006 (mppt) cc_final: 0.7688 (mppt) REVERT: SA 61 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: SA 157 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7713 (tttp) REVERT: SD 32 ARG cc_start: 0.7589 (ptp-170) cc_final: 0.7368 (ptp-170) REVERT: SE 108 GLN cc_start: 0.8426 (mp10) cc_final: 0.8207 (mp10) REVERT: SF 118 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: SG 152 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7445 (mt-10) REVERT: SH 113 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: SL 94 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7363 (p0) REVERT: SM 105 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6640 (tp30) REVERT: SR 48 MET cc_start: 0.8053 (mtm) cc_final: 0.7394 (mtp) REVERT: SR 303 ASP cc_start: 0.5351 (OUTLIER) cc_final: 0.4942 (m-30) REVERT: SR 405 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6189 (mtp) REVERT: SV 98 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: SV 104 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7744 (mt0) outliers start: 198 outliers final: 116 residues processed: 1156 average time/residue: 2.2363 time to fit residues: 3799.0107 Evaluate side-chains 1174 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1038 time to evaluate : 8.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain BA residue 160 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 79 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 56 GLN Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 78 LEU Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 91 SER Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 105 LEU Chi-restraints excluded: chain LP residue 107 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 65 GLN Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 9 LEU Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 64 THR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 157 LYS Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 309 ILE Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 234 ASP Chi-restraints excluded: chain SB residue 267 ASN Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 88 VAL Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SK residue 72 VAL Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 106 THR Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SM residue 6 LYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SQ residue 181 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 496 LEU Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 104 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 1102 optimal weight: 8.9990 chunk 1161 optimal weight: 3.9990 chunk 1059 optimal weight: 1.9990 chunk 1129 optimal weight: 0.9980 chunk 680 optimal weight: 4.9990 chunk 492 optimal weight: 5.9990 chunk 887 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 1021 optimal weight: 6.9990 chunk 1068 optimal weight: 3.9990 chunk 1125 optimal weight: 0.0870 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L5 46 GLN L6 67 HIS L7 96 GLN LF 50 ASN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 60 ASN LP 18 ASN LP 121 ASN LU 92 ASN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NK 82 ASN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN SB 275 GLN SC 135 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 139 HIS SG 106 GLN SL 121 HIS SL 128 GLN SM 170 HIS SM 245 HIS ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 152 GLN SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 164438 Z= 0.228 Angle : 0.681 19.216 239948 Z= 0.367 Chirality : 0.035 0.350 29328 Planarity : 0.007 0.132 16466 Dihedral : 22.867 178.976 69713 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.37 % Allowed : 16.43 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.22 (0.09), residues: 8934 helix: 1.97 (0.09), residues: 3551 sheet: 0.39 (0.15), residues: 1144 loop : -0.02 (0.09), residues: 4239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLW 49 HIS 0.008 0.001 HISSM 245 PHE 0.037 0.001 PHESD 37 TYR 0.024 0.002 TYRSK 113 ARG 0.012 0.000 ARGNL 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1053 time to evaluate : 8.317 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 116 MET cc_start: 0.6919 (mmm) cc_final: 0.6670 (mpp) REVERT: L5 163 MET cc_start: 0.8311 (mtt) cc_final: 0.7822 (mtp) REVERT: L6 121 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: L6 129 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.8001 (mmt180) REVERT: L7 173 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7451 (tm-30) REVERT: L7 191 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7880 (pttt) REVERT: L8 55 MET cc_start: 0.8276 (mtm) cc_final: 0.7923 (mtp) REVERT: L8 126 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: LA 99 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: LC 9 GLU cc_start: 0.7496 (tt0) cc_final: 0.7263 (tt0) REVERT: LE 114 GLN cc_start: 0.6484 (tm-30) cc_final: 0.6181 (tm130) REVERT: LF 31 ASP cc_start: 0.7460 (m-30) cc_final: 0.7165 (m-30) REVERT: LG 112 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8253 (ttm) REVERT: LI 65 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: LK 58 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: LL 28 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6328 (pp20) REVERT: LL 56 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: LL 122 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7965 (mtmm) REVERT: LN 84 MET cc_start: 0.7636 (ttm) cc_final: 0.7297 (mtp) REVERT: LN 289 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: LN 396 ARG cc_start: 0.7151 (tmm-80) cc_final: 0.6743 (tmm-80) REVERT: LT 83 MET cc_start: 0.8409 (mmm) cc_final: 0.8208 (mtp) REVERT: LW 79 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7969 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8163 (p90) cc_final: 0.7914 (p90) REVERT: NP 77 LYS cc_start: 0.8008 (mppt) cc_final: 0.7705 (mppt) REVERT: NP 108 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7226 (tpt) REVERT: SA 61 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: SA 157 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7719 (tttp) REVERT: SD 32 ARG cc_start: 0.7546 (ptp-170) cc_final: 0.7333 (ptp-170) REVERT: SE 108 GLN cc_start: 0.8426 (mp10) cc_final: 0.8206 (mp10) REVERT: SF 118 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: SG 152 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7443 (mt-10) REVERT: SH 113 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: SL 94 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7354 (p0) REVERT: SM 105 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: SR 48 MET cc_start: 0.8051 (mtm) cc_final: 0.7395 (mtp) REVERT: SR 303 ASP cc_start: 0.5305 (OUTLIER) cc_final: 0.4914 (m-30) REVERT: SR 405 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.6207 (mtp) REVERT: SV 98 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6951 (mp0) outliers start: 183 outliers final: 123 residues processed: 1145 average time/residue: 2.2582 time to fit residues: 3836.7785 Evaluate side-chains 1183 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1037 time to evaluate : 7.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain BA residue 160 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 191 LYS Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 79 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LK residue 78 LEU Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 56 ASP Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 105 LEU Chi-restraints excluded: chain LP residue 107 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 65 GLN Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 9 LEU Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NF residue 64 THR Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 157 LYS Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 309 ILE Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 234 ASP Chi-restraints excluded: chain SB residue 267 ASN Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 88 VAL Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SK residue 72 VAL Chi-restraints excluded: chain SL residue 36 VAL Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 128 GLN Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 233 VAL Chi-restraints excluded: chain SM residue 6 LYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SQ residue 181 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 496 LEU Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 582 ASP Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 741 optimal weight: 4.9990 chunk 1194 optimal weight: 9.9990 chunk 729 optimal weight: 0.5980 chunk 566 optimal weight: 0.8980 chunk 830 optimal weight: 3.9990 chunk 1253 optimal weight: 5.9990 chunk 1153 optimal weight: 5.9990 chunk 998 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 770 optimal weight: 1.9990 chunk 611 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L5 46 GLN L6 67 HIS L7 96 GLN LF 50 ASN LG 135 ASN LI 127 GLN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LP 121 ASN ** LS 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 92 ASN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN SB 275 GLN SC 135 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SL 121 HIS SL 128 GLN ** SL 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 164438 Z= 0.205 Angle : 0.675 19.227 239948 Z= 0.365 Chirality : 0.034 0.363 29328 Planarity : 0.007 0.131 16466 Dihedral : 22.863 178.873 69713 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.19 % Allowed : 16.74 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.25 (0.09), residues: 8934 helix: 2.02 (0.09), residues: 3545 sheet: 0.39 (0.15), residues: 1141 loop : -0.00 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLW 49 HIS 0.008 0.001 HISSM 245 PHE 0.039 0.001 PHESD 37 TYR 0.027 0.001 TYRSK 113 ARG 0.019 0.000 ARGNL 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17868 Ramachandran restraints generated. 8934 Oldfield, 0 Emsley, 8934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1042 time to evaluate : 8.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 116 MET cc_start: 0.6936 (mmm) cc_final: 0.6672 (mpp) REVERT: L5 163 MET cc_start: 0.8308 (mtt) cc_final: 0.7816 (mtp) REVERT: L6 121 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7278 (mtp180) REVERT: L6 129 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.8000 (mmt180) REVERT: L6 146 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8377 (pp) REVERT: L7 173 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7411 (tm-30) REVERT: L8 55 MET cc_start: 0.8263 (mtm) cc_final: 0.7910 (mtp) REVERT: L8 126 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: LA 99 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: LF 31 ASP cc_start: 0.7438 (m-30) cc_final: 0.7125 (m-30) REVERT: LG 112 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: LI 65 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: LK 58 MET cc_start: 0.8907 (mtm) cc_final: 0.8493 (mtm) REVERT: LL 28 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6316 (pp20) REVERT: LL 122 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: LN 84 MET cc_start: 0.7627 (ttm) cc_final: 0.7295 (mtp) REVERT: LN 289 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: LN 396 ARG cc_start: 0.7145 (tmm-80) cc_final: 0.6738 (tmm-80) REVERT: LT 83 MET cc_start: 0.8397 (mmm) cc_final: 0.8197 (mtp) REVERT: LW 79 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7980 (ptp-170) REVERT: LZ 37 TYR cc_start: 0.8166 (p90) cc_final: 0.7915 (p90) REVERT: NL 346 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8235 (mtmm) REVERT: NP 77 LYS cc_start: 0.7986 (mppt) cc_final: 0.7654 (mppt) REVERT: NP 108 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7171 (tpt) REVERT: SA 61 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: SA 157 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7694 (tttp) REVERT: SE 108 GLN cc_start: 0.8446 (mp10) cc_final: 0.8223 (mp10) REVERT: SF 118 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: SG 152 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7441 (mt-10) REVERT: SH 58 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: SH 113 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: SH 132 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7536 (tttp) REVERT: SL 94 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7341 (p0) REVERT: SM 105 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: SR 48 MET cc_start: 0.8050 (mtm) cc_final: 0.7388 (mtp) REVERT: SR 303 ASP cc_start: 0.5297 (OUTLIER) cc_final: 0.4916 (m-30) REVERT: SR 405 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6190 (mtp) REVERT: SV 98 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: SV 119 GLN cc_start: 0.7404 (tp-100) cc_final: 0.6970 (tm-30) outliers start: 169 outliers final: 122 residues processed: 1132 average time/residue: 2.2397 time to fit residues: 3727.7061 Evaluate side-chains 1177 residues out of total 7882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1032 time to evaluate : 7.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 143 VAL Chi-restraints excluded: chain BA residue 160 VAL Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 135 LEU Chi-restraints excluded: chain L9 residue 118 SER Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 79 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 154 ILE Chi-restraints excluded: chain LF residue 22 THR Chi-restraints excluded: chain LF residue 63 ILE Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 65 GLN Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 78 LEU Chi-restraints excluded: chain LL residue 26 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 91 SER Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 122 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 289 GLN Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 105 LEU Chi-restraints excluded: chain LP residue 107 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 65 GLN Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 10 THR Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 79 ARG Chi-restraints excluded: chain LW residue 82 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 74 THR Chi-restraints excluded: chain LY residue 22 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 9 LEU Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 29 ASP Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain NP residue 117 LEU Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 157 LYS Chi-restraints excluded: chain SA residue 186 SER Chi-restraints excluded: chain SA residue 309 ILE Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 267 ASN Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 287 VAL Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SD residue 238 ASP Chi-restraints excluded: chain SE residue 103 ARG Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 88 VAL Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 58 GLU Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 113 GLU Chi-restraints excluded: chain SH residue 132 LYS Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SK residue 72 VAL Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 233 VAL Chi-restraints excluded: chain SM residue 6 LYS Chi-restraints excluded: chain SM residue 105 GLU Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SQ residue 181 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 496 LEU Chi-restraints excluded: chain SR residue 519 VAL Chi-restraints excluded: chain SR residue 582 ASP Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1258 random chunks: chunk 792 optimal weight: 2.9990 chunk 1063 optimal weight: 0.0970 chunk 305 optimal weight: 4.9990 chunk 920 optimal weight: 0.0070 chunk 147 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 chunk 999 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 1026 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 147 HIS L6 19 GLN L6 67 HIS L6 175 ASN L7 96 GLN LF 50 ASN LG 135 ASN LI 127 GLN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LP 121 ASN ** LS 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 92 ASN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SA 203 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SL 121 HIS SL 128 GLN ** SL 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 152 GLN SQ 186 GLN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.092856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067026 restraints weight = 361393.316| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.40 r_work: 0.2896 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 164438 Z= 0.153 Angle : 0.663 19.359 239948 Z= 0.361 Chirality : 0.033 0.369 29328 Planarity : 0.006 0.128 16466 Dihedral : 22.871 178.858 69713 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.11 % Allowed : 16.77 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.31 (0.09), residues: 8934 helix: 2.08 (0.09), residues: 3539 sheet: 0.41 (0.15), residues: 1142 loop : 0.03 (0.09), residues: 4253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLW 49 HIS 0.008 0.001 HISSM 245 PHE 0.043 0.001 PHESD 37 TYR 0.031 0.001 TYRLO 27 ARG 0.016 0.000 ARGNL 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 59998.39 seconds wall clock time: 1038 minutes 37.38 seconds (62317.38 seconds total)