Starting phenix.real_space_refine on Tue Mar 26 04:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl7_29269/03_2024/8fl7_29269_neut_updated.pdb" } resolution = 2.55 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= 0.047 sd= 0.184 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 3685 5.49 5 Mg 88 5.21 5 S 301 5.16 5 C 79711 2.51 5 N 28063 2.21 5 O 37651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L7 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NP PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ARG 109": "NH1" <-> "NH2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 184": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 149506 Number of models: 1 Model: "" Number of chains: 69 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: "L3" Number of atoms: 73178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3409, 73178 Classifications: {'RNA': 3409} Modifications used: {'rna2p': 5, 'rna2p_pur': 326, 'rna2p_pyr': 211, 'rna3p': 80, 'rna3p_pur': 1511, 'rna3p_pyr': 1258} Link IDs: {'rna2p': 541, 'rna3p': 2867} 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: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2175 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 249} Chain breaks: 1 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: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "SI" Number of atoms: 1952 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: 1931 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: "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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Unusual residues: {' MG': 73} Classifications: {'undetermined': 73} Link IDs: {None: 72} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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 A06PJ SG CYSLR 46 86.875 180.127 98.835 1.00 41.73 S ATOM A06Q0 SG CYSLR 49 85.603 183.248 100.577 1.00 48.52 S ATOM A06XB SG CYSLR 83 83.617 181.977 97.702 1.00 36.00 S ATOM A06XV SG CYSLR 86 87.033 183.308 96.925 1.00 37.17 S ATOM A09A7 SG CYSLV 12 189.933 112.644 133.933 1.00 30.42 S ATOM A09AV SG CYSLV 15 193.108 111.810 132.132 1.00 32.75 S ATOM A09NW SG CYSLV 72 192.098 115.551 132.752 1.00 33.42 S ATOM A09OX SG CYSLV 77 190.173 113.296 130.313 1.00 41.59 S ATOM A09Z7 SG CYSLW 19 95.301 124.982 118.303 1.00 24.95 S ATOM A09ZZ SG CYSLW 22 95.900 122.233 120.842 1.00 26.60 S ATOM A0A2I SG CYSLW 34 97.906 125.398 121.006 1.00 22.53 S ATOM A0A31 SG CYSLW 37 98.557 122.944 118.175 1.00 24.83 S ATOM A0AN8 SG CYSLX 39 97.628 191.490 107.200 1.00 41.63 S ATOM A0ANV SG CYSLX 42 94.306 193.083 106.923 1.00 41.46 S ATOM A0AR9 SG CYSLX 57 94.583 189.987 109.007 1.00 40.76 S ATOM A0ARP SG CYSLX 60 94.899 189.558 105.323 1.00 42.93 S ATOM A0ETH SG CYSNP 63 76.545 198.670 177.952 1.00 50.41 S ATOM A0EU0 SG CYSNP 66 74.354 195.440 177.952 1.00 50.16 S ATOM A118A SG CYSSV 6 65.230 179.686 198.180 1.00 36.04 S ATOM A1193 SG CYSSV 9 61.615 178.549 197.836 1.00 34.68 S ATOM A11E7 SG CYSSV 32 64.176 176.010 198.776 1.00 32.86 S ATOM A11F1 SG CYSSV 36 64.255 177.476 195.276 1.00 32.32 S Time building chain proxies: 57.51, per 1000 atoms: 0.38 Number of scatterers: 149506 At special positions: 0 Unit cell: (257.28, 240.128, 300.16, 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 301 16.00 P 3685 15.00 Mg 88 11.99 O 37651 8.00 N 28063 7.00 C 79711 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: 55.26 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 202 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 83 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 46 " 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 15 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb=" ZNLW 101 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 101 " - 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 39 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb=" ZNNP 500 " pdb="ZN ZNNP 500 " - pdb=" ND1 HISNP 85 " pdb="ZN ZNNP 500 " - pdb=" NE2 HISNP 79 " 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 : 32 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16354 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: 321 helices and 80 sheets defined 46.3% alpha, 12.6% beta 1155 base pairs and 1790 stacking pairs defined. Time for finding SS restraints: 80.07 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: 3.580A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 118 removed outlier: 5.182A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.530A 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: 3.725A pdb=" N GLUL5 80 " --> pdb=" O GLYL5 76 " (cutoff:3.500A) Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.236A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 3.898A 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: 4.725A 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: 4.204A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 3.975A 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: 4.103A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 Processing helix chain 'L6' and resid 140 through 147 removed outlier: 3.742A pdb=" N LYSL6 145 " --> pdb=" O ALAL6 141 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEUL6 146 " --> pdb=" O GLUL6 142 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 176 removed outlier: 3.507A 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 removed outlier: 3.612A pdb=" N VALL6 207 " --> pdb=" O ALAL6 203 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUL6 208 " --> pdb=" O GLUL6 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYSL6 209 " --> pdb=" O GLNL6 205 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.816A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.690A 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: 3.692A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.722A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.970A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 150 through 190 removed outlier: 3.501A pdb=" N ILEL7 166 " --> pdb=" O GLUL7 162 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.564A pdb=" N VALL7 195 " --> pdb=" O LYSL7 191 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.935A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.173A 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: 3.596A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.676A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.994A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.533A pdb=" N GLUL8 126 " --> pdb=" O ILEL8 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.710A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.696A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.249A 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: 3.950A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 5.055A 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: 3.681A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.717A 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: 6.153A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 4.039A 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: 3.547A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.563A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.038A 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 70 through 77 removed outlier: 4.420A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 70 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: 4.102A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.703A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.670A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.582A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.459A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHELB 152 " --> pdb=" O VALLB 148 " (cutoff:3.500A) removed outlier: 5.572A 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 'LC' and resid 36 through 52 removed outlier: 3.857A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEULC 51 " --> pdb=" O PHELC 47 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.945A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.807A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.045A 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: 3.670A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.784A 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: 3.819A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.523A 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 84 through 113 Proline residue: LD 90 - end of helix removed outlier: 6.580A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 4.346A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 Processing helix chain 'LE' and resid 12 through 17 removed outlier: 7.214A pdb=" N SERLE 16 " --> pdb=" O ARGLE 12 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARGLE 17 " --> pdb=" O TYRLE 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 12 through 17' Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.464A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.705A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 6.012A 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: 4.023A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.268A 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: 4.165A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLULE 121 " --> pdb=" O LYSLE 117 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 removed outlier: 3.689A pdb=" N GLNLF 41 " --> pdb=" O ALALF 37 " (cutoff:3.500A) Processing helix chain 'LF' and resid 55 through 60 removed outlier: 3.502A pdb=" N GLYLF 59 " --> pdb=" O ASNLF 55 " (cutoff:3.500A) Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.957A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.572A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYSLG 74 " --> pdb=" O PROLG 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 69 through 74' Processing helix chain 'LG' and resid 122 through 130 removed outlier: 3.665A 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 136 removed outlier: 3.859A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALALG 136 " --> pdb=" O ILELG 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 131 through 136' Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.530A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 removed outlier: 3.514A pdb=" N LYSLH 89 " --> pdb=" O SERLH 85 " (cutoff:3.500A) 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: 3.807A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.198A 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: 4.208A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 4.018A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.732A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.292A 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: 4.645A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 removed outlier: 4.511A pdb=" N ARGLJ 102 " --> pdb=" O LYSLJ 98 " (cutoff:3.500A) removed outlier: 3.950A 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 98 through 104' Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.779A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.641A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLNLJ 132 " --> pdb=" O LYSLJ 128 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 127 through 133' Processing helix chain 'LK' and resid 2 through 7 removed outlier: 4.031A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.828A 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: 4.293A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHELK 69 " --> pdb=" O ARGLK 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 64 through 69' Processing helix chain 'LK' and resid 74 through 83 removed outlier: 3.518A pdb=" N LEULK 78 " --> pdb=" O ASNLK 74 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 74 through 83' Processing helix chain 'LK' and resid 84 through 94 removed outlier: 6.097A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.656A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.531A pdb=" N GLYLK 141 " --> pdb=" O ILELK 137 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.512A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.853A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 106 through 123 Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 11 through 20 removed outlier: 4.432A pdb=" N LYSLM 15 " --> pdb=" O ASNLM 11 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASNLM 19 " --> pdb=" O LYSLM 15 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLYLM 20 " --> pdb=" O TRPLM 16 " (cutoff:3.500A) Processing helix chain 'LM' and resid 36 through 54 removed outlier: 4.935A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.607A 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: 3.511A pdb=" N LEULM 116 " --> pdb=" O ILELM 112 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARGLM 117 " --> pdb=" O ALALM 113 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.738A 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: 4.148A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 139 removed outlier: 4.496A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) Processing helix chain 'LN' and resid 140 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.163A 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: 3.524A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.823A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 230 through 235 Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.833A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.034A 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 removed outlier: 3.514A pdb=" N LYSLN 385 " --> pdb=" O THRLN 381 " (cutoff:3.500A) Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.519A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 removed outlier: 3.660A 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 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.711A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 57 Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.588A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 4.940A 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: 4.117A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.685A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.543A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.619A 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: 5.770A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.634A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.210A 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: 3.513A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.527A 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: 3.867A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.578A 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: 4.167A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 removed outlier: 3.501A pdb=" N ARGLU 85 " --> pdb=" O ILELU 81 " (cutoff:3.500A) Processing helix chain 'LV' and resid 35 through 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.881A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.645A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.334A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 19 through 35 removed outlier: 3.957A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 Processing helix chain 'LY' and resid 7 through 17 Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.819A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLNLY 58 " --> pdb=" O GLULY 54 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.127A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.571A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.875A 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: 4.584A 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: 3.551A pdb=" N ILENC 164 " --> pdb=" O METNC 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUNC 165 " --> pdb=" O GLNNC 161 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASNNC 166 " --> pdb=" O SERNC 162 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 removed outlier: 4.021A pdb=" N LEUNF 9 " --> pdb=" O GLUNF 5 " (cutoff:3.500A) Processing helix chain 'NF' and resid 21 through 34 removed outlier: 4.316A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.775A 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 Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 removed outlier: 3.502A pdb=" N ARGNK 104 " --> pdb=" O ARGNK 100 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARGNK 109 " --> pdb=" O LEUNK 105 " (cutoff:3.500A) Processing helix chain 'NL' and resid 185 through 190 Processing helix chain 'NL' and resid 200 through 207 Proline residue: NL 205 - end of helix Processing helix chain 'NL' and resid 210 through 218 Processing helix chain 'NL' and resid 225 through 230 removed outlier: 4.019A pdb=" N HISNL 229 " --> pdb=" O PRONL 225 " (cutoff:3.500A) removed outlier: 4.144A 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 removed outlier: 3.589A pdb=" N VALNL 264 " --> pdb=" O ALANL 260 " (cutoff:3.500A) Processing helix chain 'NL' and resid 289 through 299 Processing helix chain 'NL' and resid 338 through 371 removed outlier: 3.921A pdb=" N LEUNL 368 " --> pdb=" O ARGNL 364 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHENL 369 " --> pdb=" O HISNL 365 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARGNL 370 " --> pdb=" O GLNNL 366 " (cutoff:3.500A) removed outlier: 3.826A 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: 3.548A pdb=" N GLNNL 446 " --> pdb=" O PHENL 442 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNNL 449 " --> pdb=" O PHENL 445 " (cutoff:3.500A) Processing helix chain 'NL' and resid 470 through 476 removed outlier: 3.924A pdb=" N ILENL 476 " --> pdb=" O ALANL 472 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 20 removed outlier: 4.744A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.581A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLUNP 34 " --> pdb=" O GLUNP 30 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 82 removed outlier: 3.833A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) Processing helix chain 'NP' and resid 83 through 94 removed outlier: 3.528A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.619A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 30 removed outlier: 4.589A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 25 through 30' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.898A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.745A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 4.127A 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: 3.729A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.378A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.763A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.602A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.847A 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: 3.551A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.653A 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: 4.143A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.677A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.508A 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: 3.538A pdb=" N GLYSB 26 " --> pdb=" O ARGSB 22 " (cutoff:3.500A) Processing helix chain 'SB' and resid 29 through 37 removed outlier: 4.107A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.141A 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: 3.591A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.688A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.734A 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: 4.590A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 3.549A pdb=" N METSB 236 " --> pdb=" O THRSB 232 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 4.886A 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 removed outlier: 3.537A pdb=" N LYSSB 277 " --> pdb=" O LEUSB 273 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 132 through 137 removed outlier: 6.211A pdb=" N VALSC 137 " --> pdb=" O PHESC 133 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.759A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.665A 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 265 removed outlier: 3.740A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix removed outlier: 3.917A pdb=" N ILESC 264 " --> pdb=" O LYSSC 260 " (cutoff:3.500A) Proline residue: SC 265 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.298A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.400A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.632A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.587A 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: 4.240A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.804A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.322A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.796A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.812A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.904A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.586A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (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 164 through 178 removed outlier: 4.876A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.519A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 5.054A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THRSE 224 " --> pdb=" O GLUSE 220 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.778A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.207A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.450A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.452A 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: 3.612A 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: 3.539A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.816A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.107A 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: 4.271A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.531A pdb=" N THRSG 165 " --> pdb=" O ILESG 161 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 5.184A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.746A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 removed outlier: 3.571A pdb=" N ALASH 99 " --> pdb=" O SERSH 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYSSH 100 " --> pdb=" O GLUSH 96 " (cutoff:3.500A) Processing helix chain 'SI' and resid 23 through 53 removed outlier: 3.505A pdb=" N LYSSI 51 " --> pdb=" O LYSSI 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLYSI 53 " --> pdb=" O GLUSI 49 " (cutoff:3.500A) Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.651A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.267A 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 removed outlier: 3.528A pdb=" N VALSI 143 " --> pdb=" O METSI 139 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 4.098A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HISSI 185 " --> pdb=" O VALSI 181 " (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: 3.642A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.165A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.976A 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: 4.705A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.940A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.626A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.895A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 89 Proline residue: SK 89 - end of helix Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.794A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.400A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 4.138A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SM' and resid 12 through 18 removed outlier: 6.094A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) 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: 3.690A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 76 removed outlier: 3.530A pdb=" N LEUSM 74 " --> pdb=" O ILESM 70 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Processing helix chain 'SM' and resid 77 through 99 removed outlier: 3.824A 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: 3.782A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUSM 134 " --> pdb=" O ALASM 130 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 4.209A 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: 3.603A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEUSM 242 " --> pdb=" O LEUSM 238 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.892A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.768A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.604A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.461A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.525A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.337A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 3.917A 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: 4.016A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.321A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 removed outlier: 3.630A pdb=" N LEUSQ 156 " --> pdb=" O GLNSQ 152 " (cutoff:3.500A) 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: 3.632A 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 121 removed outlier: 3.772A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASPSR 121 " --> pdb=" O METSR 117 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.657A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 161 Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.513A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALSR 188 " --> pdb=" O PHESR 184 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.586A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 3.597A pdb=" N GLNSR 239 " --> pdb=" O THRSR 235 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILESR 241 " --> pdb=" O GLUSR 237 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 removed outlier: 3.631A pdb=" N PHESR 272 " --> pdb=" O GLNSR 268 " (cutoff:3.500A) Proline residue: SR 277 - end of helix removed outlier: 3.867A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.595A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) removed outlier: 3.574A 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 Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.776A pdb=" N GLUSR 345 " --> pdb=" O ALASR 341 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THRSR 346 " --> pdb=" O HISSR 342 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.020A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.304A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 5.200A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.207A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.083A 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: 3.983A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASPSR 443 " --> pdb=" O ALASR 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 443' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.735A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.976A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLNSR 486 " --> pdb=" O GLNSR 482 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 3.654A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 5.215A 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: 3.553A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.689A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.654A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 5.015A 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 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.642A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.532A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.270A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 135 removed outlier: 3.571A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYSSV 125 " --> pdb=" O VALSV 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.213A 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: 3.634A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASNL5 23 " --> pdb=" O ASPL5 129 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASPL5 129 " --> pdb=" O ASNL5 23 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.227A 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 15 removed outlier: 4.657A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.155A 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: 6.614A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLYL8 40 " --> pdb=" O ARGL8 46 " (cutoff:3.500A) removed outlier: 5.212A 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: 6.084A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.357A 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: 3.629A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.738A 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: 7.570A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) removed outlier: 6.688A 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: 5.461A 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: 3.933A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.109A 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: 6.547A 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: 4.137A 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: 4.668A 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: 4.008A 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: 5.945A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TRPLF 99 " --> pdb=" O PHELF 115 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 36 through 39 removed outlier: 5.027A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.733A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LG' and resid 82 through 85 removed outlier: 4.184A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LH' and resid 94 through 100 removed outlier: 6.871A pdb=" N ASNLH 94 " --> pdb=" O LEULH 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.615A 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: 4.494A 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: 3.611A 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: 4.367A 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: 4.117A 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: 6.136A 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: 5.258A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYSLL 65 " --> pdb=" O THRLL 48 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LN' and resid 53 through 59 removed outlier: 6.731A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.626A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 179 through 185 removed outlier: 4.989A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LN' and resid 286 through 290 removed outlier: 3.615A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLYLN 290 " --> pdb=" O ASNLN 328 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASNLN 328 " --> pdb=" O GLYLN 290 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 76 through 80 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.717A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.224A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LO' and resid 70 through 74 removed outlier: 4.114A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.787A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 42, first strand: chain 'LR' and resid 19 through 24 removed outlier: 5.299A pdb=" N LYSLR 19 " --> pdb=" O THRLR 35 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LT' and resid 56 through 60 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'LT' and resid 8 through 12 removed outlier: 6.106A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LT' and resid 6 through 12 removed outlier: 4.668A pdb=" N HISLT 99 " --> pdb=" O PHELT 11 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LV' and resid 6 through 10 removed outlier: 5.821A pdb=" N LYSLV 6 " --> pdb=" O VALLV 23 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.551A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LY' and resid 2 through 5 removed outlier: 4.636A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.741A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.492A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.548A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.407A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLYSC 177 " --> pdb=" O PROSC 185 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.523A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 55, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.814A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SF' and resid 110 through 114 removed outlier: 3.946A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.268A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.626A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 61, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.599A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.858A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SH' and resid 72 through 76 removed outlier: 3.815A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.540A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SI' and resid 166 through 169 Processing sheet with id= 66, first strand: chain 'SK' and resid 1 through 5 removed outlier: 3.544A pdb=" N ALASK 204 " --> pdb=" O METSK 1 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 68, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 69, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 70, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 71, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.620A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 73, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 4.917A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.812A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 76, first strand: chain 'SQ' and resid 213 through 217 Processing sheet with id= 77, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.359A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.585A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.385A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'SV' and resid 18 through 22 2884 hydrogen bonds defined for protein. 8575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3049 hydrogen bonds 5182 hydrogen bond angles 0 basepair planarities 1155 basepair parallelities 1790 stacking parallelities Total time for adding SS restraints: 297.35 Time building geometry restraints manager: 60.27 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: 16296 1.31 - 1.43: 64634 1.43 - 1.56: 71263 1.56 - 1.69: 7353 1.69 - 1.81: 485 Bond restraints: 160031 Sorted by residual: bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML32815 " pdb=" C1' A2ML32815 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML31524 " pdb=" C1' A2ML31524 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.51e+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 1.51e+02 bond pdb=" C2' A2ML33867 " pdb=" C1' A2ML33867 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.51e+02 ... (remaining 160026 not shown) Histogram of bond angle deviations from ideal: 88.39 - 98.59: 14 98.59 - 108.78: 45294 108.78 - 118.97: 106480 118.97 - 129.16: 78711 129.16 - 139.35: 3178 Bond angle restraints: 233677 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 88.50 126.92 -38.42 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C1' A2ML3 400 " pdb=" N9 A2ML3 400 " pdb=" C8 A2ML3 400 " ideal model delta sigma weight residual 88.50 126.79 -38.29 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2ML31524 " pdb=" N9 A2ML31524 " pdb=" C8 A2ML31524 " ideal model delta sigma weight residual 88.50 126.79 -38.29 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2ML32401 " pdb=" N9 A2ML32401 " pdb=" C8 A2ML32401 " ideal model delta sigma weight residual 88.50 126.69 -38.19 3.00e+00 1.11e-01 1.62e+02 ... (remaining 233672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 93193 35.74 - 71.48: 8496 71.48 - 107.22: 1329 107.22 - 142.96: 17 142.96 - 178.71: 12 Dihedral angle restraints: 103047 sinusoidal: 77746 harmonic: 25301 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 33.42 -68.42 1 8.00e+00 1.56e-02 9.48e+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 82.13 64.87 1 8.00e+00 1.56e-02 8.63e+01 dihedral pdb=" O4' CL34303 " pdb=" C1' CL34303 " pdb=" N1 CL34303 " pdb=" C2 CL34303 " ideal model delta sinusoidal sigma weight residual 200.00 33.97 166.03 1 1.50e+01 4.44e-03 8.41e+01 ... (remaining 103044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 27473 0.084 - 0.169: 1011 0.169 - 0.253: 43 0.253 - 0.337: 6 0.337 - 0.422: 16 Chirality restraints: 28549 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 -2.81 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C2' A2ML32363 " pdb=" C3' A2ML32363 " pdb=" O2' A2ML32363 " pdb=" C1' A2ML32363 " both_signs ideal model delta sigma weight residual False -2.39 -2.81 0.42 2.00e-01 2.50e+01 4.33e+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 -2.81 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 28546 not shown) Planarity restraints: 15921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.051 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' OMGL34494 " -0.454 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.716 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.593 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.623 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.203 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.945 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.202 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.949 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL31625 " -0.937 2.00e-02 2.50e+03 6.06e-01 8.27e+03 pdb=" C4' OMGL31625 " 0.172 2.00e-02 2.50e+03 pdb=" O4' OMGL31625 " 0.906 2.00e-02 2.50e+03 pdb=" C3' OMGL31625 " -0.289 2.00e-02 2.50e+03 pdb=" O3' OMGL31625 " 0.792 2.00e-02 2.50e+03 pdb=" C2' OMGL31625 " -0.592 2.00e-02 2.50e+03 pdb=" O2' OMGL31625 " -0.532 2.00e-02 2.50e+03 pdb=" C1' OMGL31625 " 0.483 2.00e-02 2.50e+03 pdb=" N9 OMGL31625 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.901 2.00e-02 2.50e+03 6.04e-01 8.21e+03 pdb=" C4' OMGL34228 " -0.213 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.700 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.195 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.953 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.617 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.639 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.447 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.040 2.00e-02 2.50e+03 ... (remaining 15918 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 1745 2.59 - 3.23: 132725 3.23 - 3.87: 334349 3.87 - 4.50: 467311 4.50 - 5.14: 632920 Nonbonded interactions: 1569050 Sorted by model distance: nonbonded pdb=" OP2 AL31337 " pdb="MG MGL36009 " model vdw 1.958 2.170 nonbonded pdb=" OP2 GL34156 " pdb=" O2' AL34157 " model vdw 1.977 2.440 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36021 " model vdw 1.982 2.170 nonbonded pdb=" OP2 GL31335 " pdb="MG MGL36008 " model vdw 1.984 2.170 nonbonded pdb=" OP2 OMGL1 75 " pdb=" OH TYRLI 74 " model vdw 1.990 2.440 ... (remaining 1569045 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: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 26.480 Check model and map are aligned: 1.610 Set scattering table: 1.000 Process input model: 624.480 Find NCS groups from input model: 3.650 Set up NCS constraints: 0.430 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: 0.030 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 676.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.007 0.247 160031 Z= 0.403 Angle : 0.745 39.467 233677 Z= 0.323 Chirality : 0.036 0.422 28549 Planarity : 0.025 0.609 15921 Dihedral : 21.700 178.706 86693 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.32 % Favored : 98.67 % Rotamer: Outliers : 0.01 % Allowed : 0.07 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.88 (0.09), residues: 8584 helix: 1.16 (0.09), residues: 3269 sheet: 0.65 (0.15), residues: 1124 loop : 0.23 (0.09), residues: 4191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 11 HIS 0.006 0.001 HISLA 25 PHE 0.017 0.001 PHESR 18 TYR 0.030 0.001 TYRLC 84 ARG 0.009 0.001 ARGL8 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1631 time to evaluate : 7.969 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 126 TYR cc_start: 0.7454 (m-80) cc_final: 0.6925 (m-80) REVERT: LC 30 MET cc_start: 0.8604 (mtp) cc_final: 0.8398 (mtp) REVERT: LC 136 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7973 (mmtp) REVERT: LD 139 MET cc_start: 0.7930 (ttm) cc_final: 0.7689 (mtp) REVERT: LH 37 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7797 (mptt) REVERT: LI 53 ASP cc_start: 0.7523 (m-30) cc_final: 0.7302 (m-30) REVERT: LN 5 LYS cc_start: 0.8068 (mptt) cc_final: 0.7835 (ttmt) REVERT: LN 332 MET cc_start: 0.8185 (ttm) cc_final: 0.7478 (ttm) REVERT: LO 51 ASN cc_start: 0.8727 (p0) cc_final: 0.8416 (p0) REVERT: LP 24 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7577 (mt-10) REVERT: LS 111 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7011 (mt-10) REVERT: LV 43 ARG cc_start: 0.7918 (tpt-90) cc_final: 0.7217 (tmt170) REVERT: LW 24 SER cc_start: 0.8307 (p) cc_final: 0.8069 (m) REVERT: NP 101 GLU cc_start: 0.8225 (tt0) cc_final: 0.8019 (tt0) REVERT: SA 35 ASP cc_start: 0.8353 (p0) cc_final: 0.8129 (p0) REVERT: SA 281 MET cc_start: 0.8600 (mmm) cc_final: 0.8193 (mmt) REVERT: SF 122 ASP cc_start: 0.7744 (p0) cc_final: 0.7543 (p0) REVERT: SG 152 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7757 (mt-10) REVERT: SH 95 SER cc_start: 0.8665 (t) cc_final: 0.8366 (t) REVERT: SQ 12 LEU cc_start: 0.8631 (mt) cc_final: 0.8291 (mp) REVERT: SQ 204 ILE cc_start: 0.8213 (mm) cc_final: 0.7996 (mp) REVERT: SR 48 MET cc_start: 0.8013 (mtm) cc_final: 0.7651 (mtp) REVERT: SR 117 MET cc_start: 0.8193 (mtm) cc_final: 0.7952 (ttp) outliers start: 1 outliers final: 2 residues processed: 1631 average time/residue: 2.4936 time to fit residues: 5654.0179 Evaluate side-chains 1103 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1101 time to evaluate : 6.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LN residue 301 ASN Chi-restraints excluded: chain SR residue 192 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1026 optimal weight: 0.3980 chunk 921 optimal weight: 7.9990 chunk 511 optimal weight: 4.9990 chunk 314 optimal weight: 0.8980 chunk 621 optimal weight: 6.9990 chunk 492 optimal weight: 1.9990 chunk 953 optimal weight: 8.9990 chunk 368 optimal weight: 10.0000 chunk 579 optimal weight: 3.9990 chunk 709 optimal weight: 4.9990 chunk 1104 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 137 GLN L5 112 HIS L6 67 HIS L6 159 ASN L8 75 GLN LA 75 GLN LA 133 HIS LC 36 ASN LD 34 ASN LE 58 HIS LE 127 GLN LF 119 GLN LH 93 ASN ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 85 GLN LK 93 ASN LK 120 GLN LM 49 HIS LM 58 GLN LN 42 HIS LN 123 HIS LN 208 ASN LN 322 HIS LQ 43 ASN LQ 107 ASN LS 20 GLN LU 20 ASN LV 45 GLN LZ 20 ASN NF 60 GLN NL 341 GLN NL 412 GLN NP 75 ASN SA 215 ASN SB 244 HIS SC 190 HIS SC 211 HIS SD 63 GLN SE 43 GLN SE 94 GLN SF 97 ASN SF 140 ASN SG 8 GLN SG 188 GLN SH 60 GLN SH 127 HIS SI 94 HIS SI 185 HIS SK 83 HIS SM 211 HIS SQ 216 GLN SR 37 HIS SR 157 HIS SR 209 HIS SR 542 GLN SR 612 HIS SV 24 ASN SV 39 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 160031 Z= 0.197 Angle : 0.712 20.506 233677 Z= 0.379 Chirality : 0.035 0.340 28549 Planarity : 0.007 0.133 15921 Dihedral : 23.074 179.694 68254 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.39 % Favored : 98.59 % Rotamer: Outliers : 2.11 % Allowed : 10.44 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8584 helix: 1.91 (0.09), residues: 3317 sheet: 0.62 (0.15), residues: 1127 loop : 0.24 (0.09), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPL9 120 HIS 0.006 0.001 HISLA 25 PHE 0.016 0.001 PHELC 145 TYR 0.016 0.001 TYRLN 228 ARG 0.009 0.000 ARGSD 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1128 time to evaluate : 8.151 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 116 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6183 (mmm) REVERT: BA 123 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7334 (ttm-80) REVERT: BA 160 VAL cc_start: 0.5158 (p) cc_final: 0.4757 (t) REVERT: L5 28 GLU cc_start: 0.7409 (pm20) cc_final: 0.7173 (pm20) REVERT: L5 126 TYR cc_start: 0.7550 (m-80) cc_final: 0.7286 (m-80) REVERT: LB 45 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: LC 30 MET cc_start: 0.8641 (mtp) cc_final: 0.8276 (mtp) REVERT: LC 136 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7959 (mmtp) REVERT: LE 88 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6982 (mtm180) REVERT: LH 37 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7748 (mptt) REVERT: LI 53 ASP cc_start: 0.7475 (m-30) cc_final: 0.7254 (m-30) REVERT: LN 5 LYS cc_start: 0.8053 (mptt) cc_final: 0.7852 (ttmt) REVERT: LN 246 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7153 (mpp-170) REVERT: LN 332 MET cc_start: 0.8161 (ttm) cc_final: 0.7657 (ttm) REVERT: LO 20 LEU cc_start: 0.8618 (mt) cc_final: 0.8297 (tt) REVERT: LO 51 ASN cc_start: 0.8673 (p0) cc_final: 0.8454 (p0) REVERT: LQ 129 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6372 (mp) REVERT: LV 43 ARG cc_start: 0.7991 (tpt-90) cc_final: 0.7341 (tmt170) REVERT: LV 59 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7597 (mmtm) REVERT: LY 3 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8470 (mmt90) REVERT: NF 13 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7295 (mtp180) REVERT: NF 35 ARG cc_start: 0.8201 (tmm-80) cc_final: 0.7556 (ttp-170) REVERT: NL 381 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6774 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8445 (mt) cc_final: 0.8231 (mt) REVERT: NP 101 GLU cc_start: 0.8194 (tt0) cc_final: 0.7985 (tt0) REVERT: SB 206 ASP cc_start: 0.7361 (m-30) cc_final: 0.7135 (m-30) REVERT: SF 3 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7229 (ptp-170) REVERT: SG 11 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6916 (m-30) REVERT: SG 37 ASP cc_start: 0.7263 (t70) cc_final: 0.6696 (t70) REVERT: SG 152 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7783 (mt-10) REVERT: SQ 12 LEU cc_start: 0.8634 (mt) cc_final: 0.8256 (mp) REVERT: SQ 207 MET cc_start: 0.5133 (ppp) cc_final: 0.4492 (ppp) REVERT: SR 48 MET cc_start: 0.7983 (mtm) cc_final: 0.7616 (mtp) REVERT: SR 310 LEU cc_start: 0.7653 (mt) cc_final: 0.7441 (mt) outliers start: 157 outliers final: 65 residues processed: 1193 average time/residue: 2.2624 time to fit residues: 3884.0747 Evaluate side-chains 1123 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1047 time to evaluate : 7.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 143 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 45 GLN Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LG residue 9 SER Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LN residue 246 ARG Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LX residue 40 SER Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 3 ARG Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain LY residue 50 LYS Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 29 MET Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 15 LEU Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 84 THR Chi-restraints excluded: chain SA residue 150 LEU Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 112 MET Chi-restraints excluded: chain SE residue 115 LEU Chi-restraints excluded: chain SF residue 3 ARG Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SG residue 11 ASP Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 182 SER Chi-restraints excluded: chain SH residue 56 LEU Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 345 GLU Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 24 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 613 optimal weight: 0.9980 chunk 342 optimal weight: 6.9990 chunk 919 optimal weight: 6.9990 chunk 751 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 1106 optimal weight: 0.9990 chunk 1195 optimal weight: 7.9990 chunk 985 optimal weight: 10.0000 chunk 1097 optimal weight: 1.9990 chunk 377 optimal weight: 6.9990 chunk 887 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 75 GLN L8 120 ASN L8 125 ASN LA 25 HIS LA 75 GLN LA 116 HIS LB 44 ASN LC 36 ASN LD 34 ASN LE 127 GLN LF 50 ASN LF 116 GLN LH 93 ASN LH 107 HIS LK 66 ASN LM 58 GLN LN 3 HIS LP 30 HIS LQ 52 GLN LQ 107 ASN LU 20 ASN SB 81 HIS SB 244 HIS SC 250 GLN SD 63 GLN SD 206 ASN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SH 107 ASN SI 50 GLN SK 74 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 209 HIS SR 27 GLN SR 91 HIS SV 24 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 160031 Z= 0.299 Angle : 0.718 20.026 233677 Z= 0.383 Chirality : 0.038 0.381 28549 Planarity : 0.007 0.137 15921 Dihedral : 23.025 179.823 68250 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.81 % Favored : 98.18 % Rotamer: Outliers : 2.82 % Allowed : 11.69 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 8584 helix: 1.88 (0.09), residues: 3347 sheet: 0.53 (0.15), residues: 1117 loop : 0.08 (0.09), residues: 4120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPL9 120 HIS 0.011 0.001 HISSR 538 PHE 0.019 0.002 PHELC 145 TYR 0.023 0.002 TYRLN 228 ARG 0.010 0.001 ARGLS 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1077 time to evaluate : 8.046 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 116 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6240 (mmm) REVERT: BA 160 VAL cc_start: 0.5214 (p) cc_final: 0.4905 (t) REVERT: L7 180 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7531 (tp-100) REVERT: L8 72 TYR cc_start: 0.8515 (m-80) cc_final: 0.8135 (m-80) REVERT: LC 99 ASP cc_start: 0.8153 (t70) cc_final: 0.7797 (t70) REVERT: LE 88 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6996 (mtm180) REVERT: LF 98 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: LI 53 ASP cc_start: 0.7628 (m-30) cc_final: 0.7343 (m-30) REVERT: LL 46 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: LN 5 LYS cc_start: 0.8095 (mptt) cc_final: 0.7829 (ttmt) REVERT: LN 246 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7137 (mpp-170) REVERT: LN 332 MET cc_start: 0.8171 (ttm) cc_final: 0.7561 (ttm) REVERT: LO 20 LEU cc_start: 0.8653 (mt) cc_final: 0.8398 (tt) REVERT: LO 32 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8516 (mtmt) REVERT: LP 44 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7373 (mmm-85) REVERT: LQ 129 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6394 (mp) REVERT: LV 59 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7641 (mmtm) REVERT: LV 71 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: LW 36 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7789 (tppt) REVERT: NF 13 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7125 (mtp180) REVERT: NL 270 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: NL 381 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6812 (ttm-80) REVERT: NP 34 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: NP 55 LEU cc_start: 0.8540 (mt) cc_final: 0.8294 (mp) REVERT: SA 264 TYR cc_start: 0.8667 (m-80) cc_final: 0.8358 (m-80) REVERT: SB 206 ASP cc_start: 0.7400 (m-30) cc_final: 0.7164 (m-30) REVERT: SE 232 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6477 (tp30) REVERT: SF 3 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7010 (ptp-170) REVERT: SG 11 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: SG 106 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7876 (mm110) REVERT: SG 152 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7788 (mt-10) REVERT: SQ 12 LEU cc_start: 0.8758 (mt) cc_final: 0.8342 (mp) REVERT: SQ 207 MET cc_start: 0.4775 (ppp) cc_final: 0.4319 (ppp) REVERT: SR 48 MET cc_start: 0.7968 (mtm) cc_final: 0.7685 (mtp) REVERT: SR 517 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7305 (ttp-170) REVERT: SR 575 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6729 (ptp-170) REVERT: SV 1 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6969 (ptt) outliers start: 210 outliers final: 95 residues processed: 1186 average time/residue: 2.2696 time to fit residues: 3862.1027 Evaluate side-chains 1141 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1026 time to evaluate : 7.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LN residue 246 ARG Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 113 THR Chi-restraints excluded: chain LQ residue 41 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LT residue 2 SER Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LV residue 71 GLU Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LW residue 36 LYS Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 281 LEU Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NL residue 460 LYS Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 15 LEU Chi-restraints excluded: chain NP residue 34 GLU Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 145 GLU Chi-restraints excluded: chain SA residue 150 LEU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 84 THR Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SF residue 3 ARG Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 ASP Chi-restraints excluded: chain SG residue 11 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 SG residue 106 GLN Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 180 THR Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 109 LYS Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 427 ASP Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 572 ARG Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1092 optimal weight: 0.9980 chunk 831 optimal weight: 2.9990 chunk 574 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 527 optimal weight: 4.9990 chunk 742 optimal weight: 3.9990 chunk 1110 optimal weight: 5.9990 chunk 1175 optimal weight: 9.9990 chunk 580 optimal weight: 0.7980 chunk 1052 optimal weight: 9.9990 chunk 316 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 159 ASN L7 180 GLN L8 75 GLN L8 125 ASN LA 75 GLN LC 36 ASN LD 34 ASN LD 39 GLN ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LF 119 GLN LG 135 ASN LH 93 ASN LM 58 GLN LN 328 ASN LP 18 ASN LQ 52 GLN LQ 107 ASN LU 20 ASN LZ 20 ASN SB 244 HIS SD 63 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SG 106 GLN SK 74 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 245 HIS SV 24 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 160031 Z= 0.276 Angle : 0.702 19.614 233677 Z= 0.377 Chirality : 0.037 0.384 28549 Planarity : 0.007 0.134 15921 Dihedral : 23.000 179.616 68250 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.85 % Allowed : 13.15 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.18 (0.09), residues: 8584 helix: 1.91 (0.09), residues: 3349 sheet: 0.46 (0.15), residues: 1105 loop : 0.01 (0.09), residues: 4130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPL9 120 HIS 0.007 0.001 HISLK 39 PHE 0.016 0.002 PHELC 145 TYR 0.020 0.002 TYRSB 119 ARG 0.010 0.000 ARGSE 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1049 time to evaluate : 8.123 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 116 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6204 (mmm) REVERT: BA 123 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7377 (ttm-80) REVERT: BA 160 VAL cc_start: 0.5162 (p) cc_final: 0.4820 (t) REVERT: L7 180 GLN cc_start: 0.7830 (tp40) cc_final: 0.7532 (tp-100) REVERT: LB 45 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: LD 3 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7924 (tpp) REVERT: LD 16 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7676 (mpp80) REVERT: LE 88 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6974 (mtm180) REVERT: LE 94 GLU cc_start: 0.7237 (mp0) cc_final: 0.7021 (mp0) REVERT: LF 98 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: LG 99 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: LI 53 ASP cc_start: 0.7636 (m-30) cc_final: 0.7356 (m-30) REVERT: LL 46 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7495 (mtm-85) REVERT: LN 246 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7125 (mpp-170) REVERT: LN 332 MET cc_start: 0.8143 (ttm) cc_final: 0.7577 (ttm) REVERT: LO 32 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8545 (mtmt) REVERT: LP 44 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7404 (mmm-85) REVERT: LQ 129 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6287 (mp) REVERT: LV 59 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7648 (mmtm) REVERT: LV 71 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: LW 36 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7764 (tppt) REVERT: NF 13 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7200 (mtp180) REVERT: NL 270 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: NL 381 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6918 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8521 (mt) cc_final: 0.8287 (mp) REVERT: SA 264 TYR cc_start: 0.8656 (m-80) cc_final: 0.8382 (m-80) REVERT: SB 206 ASP cc_start: 0.7374 (m-30) cc_final: 0.7142 (m-30) REVERT: SE 232 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6483 (tp30) REVERT: SF 3 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7128 (ptp-170) REVERT: SG 11 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: SG 152 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7846 (mt-10) REVERT: SG 183 GLU cc_start: 0.6958 (pp20) cc_final: 0.6654 (pp20) REVERT: SI 106 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.6173 (p0) REVERT: SQ 12 LEU cc_start: 0.8791 (mt) cc_final: 0.8383 (mp) REVERT: SQ 50 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7279 (m110) REVERT: SR 48 MET cc_start: 0.7942 (mtm) cc_final: 0.7629 (mtp) REVERT: SR 575 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6681 (ptp-170) outliers start: 212 outliers final: 101 residues processed: 1153 average time/residue: 2.3325 time to fit residues: 3892.8171 Evaluate side-chains 1141 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1016 time to evaluate : 7.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 17 ASP Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 45 GLN Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 16 ARG Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LN residue 246 ARG Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 32 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 56 ARG Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 113 THR Chi-restraints excluded: chain LQ residue 41 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LV residue 71 GLU Chi-restraints excluded: chain LW residue 36 LYS Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 281 LEU Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 15 LEU Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 145 GLU Chi-restraints excluded: chain SA residue 150 LEU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 84 THR Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SF residue 3 ARG Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 ASP Chi-restraints excluded: chain SG residue 11 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 187 VAL Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 75 LYS Chi-restraints excluded: chain SI residue 106 ASP Chi-restraints excluded: chain SI residue 180 THR Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 56 ILE Chi-restraints excluded: chain SQ residue 109 LYS Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 192 ASP Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 427 ASP Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 978 optimal weight: 0.5980 chunk 667 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 875 optimal weight: 6.9990 chunk 484 optimal weight: 1.9990 chunk 1003 optimal weight: 5.9990 chunk 812 optimal weight: 0.9980 chunk 1 optimal weight: 50.0000 chunk 600 optimal weight: 0.0870 chunk 1055 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 75 GLN L8 125 ASN L9 86 HIS LA 75 GLN LC 36 ASN LD 34 ASN ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 119 GLN LH 93 ASN LJ 78 ASN LM 58 GLN LP 18 ASN LQ 107 ASN LU 20 ASN NF 33 HIS SB 244 HIS ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SK 9 ASN SK 178 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 24 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 160031 Z= 0.178 Angle : 0.664 19.605 233677 Z= 0.362 Chirality : 0.034 0.373 28549 Planarity : 0.007 0.129 15921 Dihedral : 22.960 179.969 68250 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.33 (0.09), residues: 8584 helix: 2.10 (0.09), residues: 3337 sheet: 0.43 (0.15), residues: 1126 loop : 0.07 (0.09), residues: 4121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPL6 18 HIS 0.004 0.001 HISLK 40 PHE 0.014 0.001 PHEL6 192 TYR 0.017 0.001 TYRSB 119 ARG 0.011 0.000 ARGSE 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1057 time to evaluate : 8.068 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: 0.6701 (mmm) cc_final: 0.6279 (mmm) REVERT: BA 160 VAL cc_start: 0.5164 (p) cc_final: 0.4810 (t) REVERT: L7 180 GLN cc_start: 0.7823 (tp40) cc_final: 0.7376 (tp-100) REVERT: L8 72 TYR cc_start: 0.8500 (m-80) cc_final: 0.8075 (m-80) REVERT: LD 3 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8007 (tpp) REVERT: LE 88 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6878 (mtm180) REVERT: LG 99 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: LL 46 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7510 (mtm-85) REVERT: LL 125 MET cc_start: 0.6329 (tmm) cc_final: 0.6089 (pmm) REVERT: LM 114 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8048 (ttpp) REVERT: LN 332 MET cc_start: 0.8107 (ttm) cc_final: 0.7550 (ttm) REVERT: LO 32 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8523 (mtmt) REVERT: LQ 129 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6329 (mp) REVERT: LV 59 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7692 (mmtm) REVERT: LW 36 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7824 (tppt) REVERT: NL 270 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8187 (mtmm) REVERT: NL 381 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6904 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8483 (mt) cc_final: 0.8259 (mp) REVERT: SA 264 TYR cc_start: 0.8620 (m-80) cc_final: 0.8353 (m-80) REVERT: SA 312 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6409 (ttt180) REVERT: SB 206 ASP cc_start: 0.7332 (m-30) cc_final: 0.7081 (m-30) REVERT: SB 225 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: SC 104 THR cc_start: 0.7626 (p) cc_final: 0.7383 (t) REVERT: SG 111 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8774 (tt) REVERT: SG 152 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7803 (mt-10) REVERT: SI 242 TYR cc_start: 0.8762 (t80) cc_final: 0.8550 (t80) REVERT: SQ 12 LEU cc_start: 0.8777 (mt) cc_final: 0.8357 (mp) REVERT: SQ 50 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7249 (m110) REVERT: SR 48 MET cc_start: 0.7925 (mtm) cc_final: 0.7611 (mtp) REVERT: SR 397 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6581 (mtp180) outliers start: 177 outliers final: 86 residues processed: 1143 average time/residue: 2.2935 time to fit residues: 3774.2095 Evaluate side-chains 1119 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1017 time to evaluate : 7.968 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LI residue 99 ILE Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 32 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 56 ARG Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LW residue 36 LYS Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 281 LEU Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 15 LEU Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 312 ARG Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 225 GLN Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SF residue 228 ASP Chi-restraints excluded: chain SG residue 41 ILE Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 111 LEU Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 397 ARG Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 427 ASP Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 24 ASN Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 395 optimal weight: 5.9990 chunk 1058 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 690 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 1176 optimal weight: 0.9980 chunk 976 optimal weight: 3.9990 chunk 544 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 617 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 75 GLN L8 125 ASN LA 75 GLN LC 36 ASN LD 34 ASN ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LF 116 GLN LF 119 GLN LG 135 ASN LH 93 ASN LM 58 GLN LN 258 HIS LP 18 ASN SD 63 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SK 74 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 160031 Z= 0.316 Angle : 0.717 19.557 233677 Z= 0.382 Chirality : 0.038 0.388 28549 Planarity : 0.007 0.136 15921 Dihedral : 22.955 179.626 68250 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.70 % Allowed : 14.84 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.15 (0.09), residues: 8584 helix: 1.93 (0.09), residues: 3358 sheet: 0.36 (0.15), residues: 1112 loop : -0.05 (0.09), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPL9 120 HIS 0.007 0.001 HISLK 39 PHE 0.019 0.002 PHESB 160 TYR 0.022 0.002 TYRSB 119 ARG 0.017 0.001 ARGNP 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1044 time to evaluate : 8.294 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 116 MET cc_start: 0.6650 (mmm) cc_final: 0.6166 (mmm) REVERT: BA 160 VAL cc_start: 0.5272 (p) cc_final: 0.4848 (t) REVERT: L6 125 ILE cc_start: 0.8423 (mt) cc_final: 0.8222 (mt) REVERT: L7 180 GLN cc_start: 0.7813 (tp40) cc_final: 0.7510 (tp-100) REVERT: L8 72 TYR cc_start: 0.8514 (m-80) cc_final: 0.8090 (m-80) REVERT: LD 3 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8173 (tpp) REVERT: LD 16 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7642 (mpp80) REVERT: LE 88 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6891 (mtm180) REVERT: LF 98 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: LG 99 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: LJ 109 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: LK 58 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8470 (ptm) REVERT: LL 46 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: LL 125 MET cc_start: 0.6166 (tmm) cc_final: 0.5431 (pmm) REVERT: LM 114 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8012 (ttpp) REVERT: LN 332 MET cc_start: 0.8132 (ttm) cc_final: 0.7678 (ttm) REVERT: LO 32 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: LP 44 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7375 (mmm-85) REVERT: LQ 129 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6540 (mp) REVERT: LV 59 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7649 (mmtm) REVERT: LW 36 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7779 (tppt) REVERT: NF 13 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7033 (mtp180) REVERT: NL 270 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (mtmm) REVERT: NL 381 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6861 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8458 (mt) cc_final: 0.8217 (mp) REVERT: SA 264 TYR cc_start: 0.8692 (m-80) cc_final: 0.8381 (m-80) REVERT: SA 312 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6485 (ttt180) REVERT: SB 206 ASP cc_start: 0.7379 (m-30) cc_final: 0.7132 (m-30) REVERT: SB 225 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: SE 232 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6474 (tp30) REVERT: SG 152 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7862 (mt-10) REVERT: SG 183 GLU cc_start: 0.7029 (pp20) cc_final: 0.6698 (pp20) REVERT: SI 242 TYR cc_start: 0.8896 (t80) cc_final: 0.8680 (t80) REVERT: SQ 12 LEU cc_start: 0.8805 (mt) cc_final: 0.8360 (mp) REVERT: SQ 50 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7281 (m110) REVERT: SQ 216 GLN cc_start: 0.6827 (pm20) cc_final: 0.5604 (pt0) REVERT: SR 48 MET cc_start: 0.7967 (mtm) cc_final: 0.7670 (mtp) REVERT: SR 397 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6594 (mtp180) outliers start: 201 outliers final: 113 residues processed: 1148 average time/residue: 2.2199 time to fit residues: 3670.4959 Evaluate side-chains 1157 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1022 time to evaluate : 7.872 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 79 THR Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 16 ARG Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LJ residue 109 LYS Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 32 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 56 ARG Chi-restraints excluded: chain LO residue 60 ILE Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 113 THR Chi-restraints excluded: chain LQ residue 41 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LW residue 36 LYS Chi-restraints excluded: chain LX residue 40 SER Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 145 GLU Chi-restraints excluded: chain SA residue 312 ARG Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 225 GLN Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 84 THR Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 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 70 THR Chi-restraints excluded: chain SI residue 75 LYS Chi-restraints excluded: chain SI residue 139 MET Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 397 ARG Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 427 ASP Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1134 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 670 optimal weight: 0.8980 chunk 859 optimal weight: 4.9990 chunk 665 optimal weight: 4.9990 chunk 990 optimal weight: 0.0060 chunk 656 optimal weight: 8.9990 chunk 1172 optimal weight: 10.0000 chunk 733 optimal weight: 3.9990 chunk 714 optimal weight: 0.8980 chunk 541 optimal weight: 2.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 67 HIS L8 75 GLN L8 125 ASN LA 75 GLN LC 36 ASN LD 34 ASN ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LF 116 GLN LF 119 GLN LG 135 ASN LH 93 ASN LM 58 GLN LP 18 ASN ** LP 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 52 GLN SA 276 ASN SC 191 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 100 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SK 93 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 24 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 160031 Z= 0.199 Angle : 0.676 19.388 233677 Z= 0.366 Chirality : 0.034 0.376 28549 Planarity : 0.007 0.131 15921 Dihedral : 22.948 179.857 68250 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.47 % Allowed : 15.46 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 8584 helix: 2.05 (0.09), residues: 3350 sheet: 0.35 (0.15), residues: 1133 loop : 0.01 (0.09), residues: 4101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPL9 120 HIS 0.005 0.001 HISSK 118 PHE 0.015 0.001 PHELF 42 TYR 0.018 0.001 TYRSB 119 ARG 0.011 0.000 ARGNL 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1040 time to evaluate : 8.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 116 MET cc_start: 0.6764 (mmm) cc_final: 0.6335 (mmm) REVERT: BA 160 VAL cc_start: 0.5209 (OUTLIER) cc_final: 0.4759 (t) REVERT: L7 180 GLN cc_start: 0.7826 (tp40) cc_final: 0.7561 (tp-100) REVERT: L8 72 TYR cc_start: 0.8515 (m-80) cc_final: 0.8085 (m-80) REVERT: LD 3 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8020 (ttp) REVERT: LD 16 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7658 (mpp80) REVERT: LE 88 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6941 (mtm180) REVERT: LG 99 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: LJ 109 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7985 (ttmt) REVERT: LK 58 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (ptm) REVERT: LL 46 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7428 (mtm-85) REVERT: LL 125 MET cc_start: 0.6298 (tmm) cc_final: 0.5531 (pmm) REVERT: LM 114 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7995 (ttpp) REVERT: LN 332 MET cc_start: 0.8114 (ttm) cc_final: 0.7591 (ttm) REVERT: LO 32 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8553 (mtmt) REVERT: LP 44 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6917 (mmm-85) REVERT: LQ 129 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6487 (mp) REVERT: LV 59 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7718 (mmtm) REVERT: LW 36 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7838 (tppt) REVERT: LX 85 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7385 (ttm110) REVERT: LY 29 LYS cc_start: 0.8300 (mptt) cc_final: 0.8096 (mmtm) REVERT: NL 270 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8222 (mtmm) REVERT: NL 381 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6855 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8474 (mt) cc_final: 0.8259 (mp) REVERT: SA 264 TYR cc_start: 0.8630 (m-80) cc_final: 0.8334 (m-80) REVERT: SB 206 ASP cc_start: 0.7363 (m-30) cc_final: 0.7119 (m-30) REVERT: SB 225 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: SG 152 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7864 (mt-10) REVERT: SQ 12 LEU cc_start: 0.8795 (mt) cc_final: 0.8348 (mp) REVERT: SQ 50 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7364 (m110) REVERT: SQ 216 GLN cc_start: 0.6726 (pm20) cc_final: 0.5988 (pt0) REVERT: SR 48 MET cc_start: 0.7930 (mtm) cc_final: 0.7689 (mtp) REVERT: SR 397 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6583 (mtp180) REVERT: SR 634 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6875 (ttp-110) outliers start: 184 outliers final: 106 residues processed: 1139 average time/residue: 2.2221 time to fit residues: 3652.8557 Evaluate side-chains 1149 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1023 time to evaluate : 7.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG 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 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 17 ASP Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 16 ARG Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 1 MET Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LJ residue 109 LYS Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 299 ILE Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 32 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 113 THR Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LW residue 36 LYS Chi-restraints excluded: chain LX residue 40 SER Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 339 GLU Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 145 GLU Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 225 GLN Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 148 THR Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 84 THR Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 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 187 VAL Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 15 THR Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 397 ARG Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SR residue 634 ARG Chi-restraints excluded: chain SV residue 98 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 725 optimal weight: 6.9990 chunk 468 optimal weight: 0.8980 chunk 699 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 745 optimal weight: 7.9990 chunk 798 optimal weight: 4.9990 chunk 579 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 921 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 75 GLN L8 125 ASN LA 75 GLN LC 36 ASN LD 34 ASN ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LH 93 ASN LM 58 GLN LP 18 ASN ** LP 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 52 GLN NL 436 ASN SB 275 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 100 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SK 74 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 354 ASN SV 24 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 160031 Z= 0.422 Angle : 0.772 19.433 233677 Z= 0.405 Chirality : 0.041 0.395 28549 Planarity : 0.008 0.141 15921 Dihedral : 22.990 179.302 68250 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.63 % Allowed : 15.60 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.92 (0.09), residues: 8584 helix: 1.74 (0.09), residues: 3360 sheet: 0.30 (0.15), residues: 1086 loop : -0.19 (0.09), residues: 4138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPL9 120 HIS 0.009 0.001 HISSD 58 PHE 0.021 0.002 PHELC 145 TYR 0.026 0.002 TYRSB 119 ARG 0.012 0.001 ARGNL 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1024 time to evaluate : 8.292 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: 0.6785 (mmm) cc_final: 0.6313 (mmm) REVERT: BA 160 VAL cc_start: 0.5249 (OUTLIER) cc_final: 0.4782 (t) REVERT: L7 180 GLN cc_start: 0.7894 (tp40) cc_final: 0.7653 (tp-100) REVERT: LD 3 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8098 (tpp) REVERT: LD 16 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7599 (mpp80) REVERT: LE 88 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7010 (mtm180) REVERT: LF 98 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: LG 99 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: LK 58 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8552 (ptm) REVERT: LL 46 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7462 (mtm-85) REVERT: LM 114 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8045 (ttpp) REVERT: LN 332 MET cc_start: 0.8139 (ttm) cc_final: 0.7734 (ttm) REVERT: LO 32 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8605 (mtmt) REVERT: LP 44 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7495 (mmm-85) REVERT: LV 59 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7657 (mmtm) REVERT: LW 36 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7827 (tppt) REVERT: LX 85 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7360 (ttm170) REVERT: NF 13 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7100 (mtp180) REVERT: NL 270 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8299 (mtmm) REVERT: NL 381 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6924 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8535 (mt) cc_final: 0.8300 (mp) REVERT: SA 264 TYR cc_start: 0.8744 (m-80) cc_final: 0.8472 (m-80) REVERT: SB 206 ASP cc_start: 0.7390 (m-30) cc_final: 0.7147 (m-30) REVERT: SB 225 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: SG 152 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7830 (mt-10) REVERT: SG 183 GLU cc_start: 0.7044 (pp20) cc_final: 0.6739 (pp20) REVERT: SM 273 MET cc_start: 0.8033 (mmm) cc_final: 0.7818 (mmp) REVERT: SQ 12 LEU cc_start: 0.8885 (mt) cc_final: 0.8403 (mp) REVERT: SQ 50 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7404 (m110) REVERT: SQ 149 MET cc_start: 0.7923 (mmm) cc_final: 0.7659 (tpp) REVERT: SQ 216 GLN cc_start: 0.7039 (pm20) cc_final: 0.5948 (pt0) REVERT: SR 48 MET cc_start: 0.7956 (mtm) cc_final: 0.7735 (mtp) REVERT: SR 397 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6590 (mtp180) REVERT: SR 575 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7303 (ptp-170) REVERT: SV 129 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7400 (mp10) outliers start: 196 outliers final: 119 residues processed: 1129 average time/residue: 2.3424 time to fit residues: 3808.5492 Evaluate side-chains 1152 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1013 time to evaluate : 7.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG 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 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L7 residue 183 LYS Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 16 ARG Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LE residue 125 TRP Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 113 THR Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LW residue 36 LYS Chi-restraints excluded: chain LX residue 40 SER Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 339 GLU Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 145 GLU Chi-restraints excluded: chain SB residue 225 GLN Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 84 THR Chi-restraints excluded: chain SE residue 115 LEU Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 ASP Chi-restraints excluded: chain SG residue 37 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 187 VAL Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 15 THR Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 397 ARG Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 24 ASN Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 129 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1066 optimal weight: 5.9990 chunk 1122 optimal weight: 4.9990 chunk 1024 optimal weight: 5.9990 chunk 1092 optimal weight: 1.9990 chunk 657 optimal weight: 2.9990 chunk 475 optimal weight: 1.9990 chunk 857 optimal weight: 8.9990 chunk 335 optimal weight: 2.9990 chunk 986 optimal weight: 3.9990 chunk 1032 optimal weight: 2.9990 chunk 1088 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 67 HIS L8 75 GLN L8 125 ASN LA 75 GLN LC 36 ASN LD 34 ASN ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LH 93 ASN LM 58 GLN ** LP 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NL 436 ASN SA 276 ASN SB 275 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 100 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SK 74 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 106 ASN SV 24 ASN SV 122 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 160031 Z= 0.268 Angle : 0.709 19.481 233677 Z= 0.381 Chirality : 0.037 0.383 28549 Planarity : 0.007 0.134 15921 Dihedral : 22.983 179.502 68250 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.28 % Allowed : 16.44 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 0.97 (0.09), residues: 8584 helix: 1.82 (0.09), residues: 3369 sheet: 0.25 (0.15), residues: 1098 loop : -0.17 (0.09), residues: 4117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPL9 120 HIS 0.006 0.001 HISSK 118 PHE 0.020 0.002 PHELF 42 TYR 0.022 0.002 TYRSC 69 ARG 0.013 0.000 ARGNL 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1028 time to evaluate : 7.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 160 VAL cc_start: 0.4995 (OUTLIER) cc_final: 0.4590 (t) REVERT: L7 32 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8243 (mtmm) REVERT: L7 180 GLN cc_start: 0.7841 (tp40) cc_final: 0.7614 (tp-100) REVERT: L8 96 GLU cc_start: 0.7279 (tp30) cc_final: 0.6962 (tp30) REVERT: L8 99 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7102 (mt-10) REVERT: LD 3 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8182 (ttp) REVERT: LD 16 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7617 (mpp80) REVERT: LE 88 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6968 (mtm180) REVERT: LG 99 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: LK 58 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (ptm) REVERT: LL 46 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7450 (mtm-85) REVERT: LM 114 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8002 (ttpp) REVERT: LN 332 MET cc_start: 0.8112 (ttm) cc_final: 0.7666 (ttm) REVERT: LO 32 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8587 (mtmt) REVERT: LP 44 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7366 (mmm-85) REVERT: LQ 129 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6591 (mp) REVERT: LV 59 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7667 (mmtm) REVERT: LY 29 LYS cc_start: 0.8289 (mptt) cc_final: 0.8077 (mmtm) REVERT: NF 13 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7065 (mtp180) REVERT: NL 270 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: NL 381 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6914 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8558 (mt) cc_final: 0.8346 (mp) REVERT: SA 264 TYR cc_start: 0.8678 (m-80) cc_final: 0.8410 (m-80) REVERT: SB 206 ASP cc_start: 0.7368 (m-30) cc_final: 0.7122 (m-30) REVERT: SB 225 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: SE 232 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: SG 152 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7871 (mt-10) REVERT: SM 273 MET cc_start: 0.7975 (mmm) cc_final: 0.7756 (mmp) REVERT: SQ 12 LEU cc_start: 0.8900 (mt) cc_final: 0.8441 (mp) REVERT: SQ 50 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7371 (m110) REVERT: SQ 216 GLN cc_start: 0.6836 (pm20) cc_final: 0.6270 (pm20) REVERT: SR 48 MET cc_start: 0.7968 (mtm) cc_final: 0.7732 (mtp) REVERT: SR 397 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6579 (mtp180) REVERT: SR 575 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7396 (ptp-170) REVERT: SR 634 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6963 (ttp-110) REVERT: SV 129 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7361 (mp10) outliers start: 170 outliers final: 120 residues processed: 1122 average time/residue: 2.2338 time to fit residues: 3607.1556 Evaluate side-chains 1160 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1017 time to evaluate : 7.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG 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 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 32 LYS Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L7 residue 183 LYS Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 20 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 50 ASP Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 16 ARG Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LE residue 125 TRP Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 99 GLU Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 101 ASP Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 1 MET Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 32 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 113 THR Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LX residue 40 SER Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 145 GLU Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 225 GLN Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 84 THR Chi-restraints excluded: chain SE residue 115 LEU Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 ASP Chi-restraints excluded: chain SG residue 37 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 187 VAL Chi-restraints excluded: chain SH residue 70 THR Chi-restraints excluded: chain SI residue 139 MET Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 15 THR Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 397 ARG Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SR residue 634 ARG Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 129 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 717 optimal weight: 2.9990 chunk 1154 optimal weight: 5.9990 chunk 704 optimal weight: 0.9990 chunk 547 optimal weight: 1.9990 chunk 802 optimal weight: 3.9990 chunk 1211 optimal weight: 4.9990 chunk 1115 optimal weight: 6.9990 chunk 964 optimal weight: 0.0570 chunk 100 optimal weight: 20.0000 chunk 745 optimal weight: 1.9990 chunk 591 optimal weight: 0.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 44 GLN L8 75 GLN L8 125 ASN LA 75 GLN LC 36 ASN ** LD 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LF 119 GLN LH 93 ASN LK 120 GLN LM 58 GLN LP 69 ASN NL 436 ASN SB 275 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 100 HIS ** SE 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 106 ASN SV 24 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 160031 Z= 0.160 Angle : 0.678 19.627 233677 Z= 0.370 Chirality : 0.034 0.372 28549 Planarity : 0.007 0.128 15921 Dihedral : 22.969 179.938 68250 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.87 % Allowed : 16.87 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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: 1.14 (0.09), residues: 8584 helix: 1.99 (0.09), residues: 3351 sheet: 0.26 (0.15), residues: 1119 loop : -0.08 (0.09), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPL9 120 HIS 0.004 0.001 HISSK 118 PHE 0.019 0.001 PHEL6 192 TYR 0.034 0.001 TYRSC 69 ARG 0.014 0.000 ARGNL 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1044 time to evaluate : 8.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 114 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6574 (mtm-85) REVERT: BA 116 MET cc_start: 0.7031 (mmm) cc_final: 0.6671 (mmm) REVERT: BA 160 VAL cc_start: 0.4979 (OUTLIER) cc_final: 0.4573 (t) REVERT: L8 96 GLU cc_start: 0.7277 (tp30) cc_final: 0.6957 (tp30) REVERT: L8 99 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7084 (mt-10) REVERT: LD 3 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8127 (ttp) REVERT: LD 16 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7636 (mpp80) REVERT: LD 28 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6803 (mm-30) REVERT: LE 88 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7036 (mtm180) REVERT: LK 58 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8596 (ptm) REVERT: LL 46 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7425 (mtm-85) REVERT: LL 125 MET cc_start: 0.6063 (tmm) cc_final: 0.5454 (pmm) REVERT: LM 114 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7973 (ttpp) REVERT: LN 332 MET cc_start: 0.8118 (ttm) cc_final: 0.7631 (ttm) REVERT: LO 32 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8553 (mtmt) REVERT: LP 44 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6936 (mmm-85) REVERT: LQ 129 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6608 (mp) REVERT: LV 59 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7711 (mmtm) REVERT: NF 13 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7031 (mtp180) REVERT: NL 270 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (mtmm) REVERT: NL 381 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6855 (ttm-80) REVERT: NP 55 LEU cc_start: 0.8530 (mt) cc_final: 0.8321 (mp) REVERT: SA 264 TYR cc_start: 0.8658 (m-80) cc_final: 0.8369 (m-80) REVERT: SB 206 ASP cc_start: 0.7373 (m-30) cc_final: 0.7140 (m-30) REVERT: SB 225 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: SG 152 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7831 (mt-10) REVERT: SM 273 MET cc_start: 0.7936 (mmm) cc_final: 0.7707 (mmp) REVERT: SQ 12 LEU cc_start: 0.8854 (mt) cc_final: 0.8392 (mp) REVERT: SQ 50 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7338 (m110) REVERT: SQ 216 GLN cc_start: 0.6980 (pm20) cc_final: 0.6504 (pm20) REVERT: SR 48 MET cc_start: 0.7956 (mtm) cc_final: 0.7713 (mtp) REVERT: SR 397 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6571 (mtp180) REVERT: SV 129 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7388 (mp10) outliers start: 139 outliers final: 102 residues processed: 1120 average time/residue: 2.2563 time to fit residues: 3642.8036 Evaluate side-chains 1144 residues out of total 7552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1023 time to evaluate : 6.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG 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 102 THR Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 122 SER Chi-restraints excluded: chain L6 residue 146 LEU Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 179 LYS Chi-restraints excluded: chain L7 residue 183 LYS Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 151 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 180 ARG Chi-restraints excluded: chain LC residue 62 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 16 ARG Chi-restraints excluded: chain LD residue 111 GLU Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LE residue 125 TRP Chi-restraints excluded: chain LF residue 35 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 45 THR Chi-restraints excluded: chain LH residue 101 ASP Chi-restraints excluded: chain LH residue 143 ASP Chi-restraints excluded: chain LI residue 1 MET Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 46 ARG Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 65 MET Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 32 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 44 ARG Chi-restraints excluded: chain LP residue 69 ASN Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 3 GLN Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 29 SER Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 59 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 81 ILE Chi-restraints excluded: chain LV residue 2 VAL Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 75 SER Chi-restraints excluded: chain LY residue 23 VAL Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 39 SER Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NF residue 13 ARG Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NL residue 199 ASP Chi-restraints excluded: chain NL residue 270 LYS Chi-restraints excluded: chain NL residue 381 ARG Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 108 MET Chi-restraints excluded: chain SA residue 65 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 225 GLN Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SF residue 118 GLU Chi-restraints excluded: chain SF residue 223 SER Chi-restraints excluded: chain SF residue 228 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 70 THR Chi-restraints excluded: chain SI residue 139 MET Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 58 ILE Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SQ residue 15 THR Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 17 ASP Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 397 ARG Chi-restraints excluded: chain SR residue 415 LYS Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 600 MET Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SV residue 129 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 766 optimal weight: 0.9990 chunk 1027 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 889 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 966 optimal weight: 0.9990 chunk 404 optimal weight: 2.9990 chunk 992 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 75 GLN L8 125 ASN LA 75 GLN LB 45 GLN LC 36 ASN ** LD 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LF 119 GLN LH 93 ASN LM 58 GLN LZ 20 ASN NL 436 ASN SA 276 ASN SB 275 GLN ** SE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 100 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 106 GLN SK 74 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 106 ASN ** SQ 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 24 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065099 restraints weight = 307129.690| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.16 r_work: 0.2870 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 160031 Z= 0.210 Angle : 0.700 59.199 233677 Z= 0.385 Chirality : 0.035 0.375 28549 Planarity : 0.007 0.128 15921 Dihedral : 22.967 179.867 68250 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.88 % Allowed : 17.10 % Favored : 81.02 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.31 % 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: 8584 helix: 1.98 (0.09), residues: 3351 sheet: 0.25 (0.15), residues: 1129 loop : -0.08 (0.09), residues: 4104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.005 0.001 HISSK 118 PHE 0.017 0.001 PHEL6 192 TYR 0.029 0.001 TYRSC 69 ARG 0.011 0.000 ARGNL 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 56853.96 seconds wall clock time: 984 minutes 38.47 seconds (59078.47 seconds total)