Starting phenix.real_space_refine on Sat Mar 2 05:00:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fla_29272/03_2024/8fla_29272_neut_updated.pdb" } resolution = 2.63 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= 0.192 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 3769 5.49 5 Mg 88 5.21 5 S 296 5.16 5 C 81771 2.51 5 N 28789 2.21 5 O 38589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L9 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 188": "OE1" <-> "OE2" Residue "SI TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153309 Number of models: 1 Model: "" Number of chains: 72 Chain: "BA" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 449 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 126 Chain: "L1" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3278 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 3, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 25, 'rna3p': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "L2" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1535 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 24, 'rna3p_pyr': 32} Link IDs: {'rna2p': 16, 'rna3p': 55} Chain breaks: 4 Chain: "L3" Number of atoms: 73423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3420, 73423 Classifications: {'RNA': 3420} Modifications used: {'rna2p': 6, 'rna2p_pur': 332, 'rna2p_pyr': 213, 'rna3p': 80, 'rna3p_pur': 1514, 'rna3p_pyr': 1257} Link IDs: {'rna2p': 550, 'rna3p': 2869} Chain breaks: 29 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 33 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: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NL" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2666 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 2 Chain: "NP" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "NR" Number of atoms: 1299 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1292 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 152, 1292 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1304 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: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1120 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 141} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "SI" Number of atoms: 1937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1950 Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "SL" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1917 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "SM" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3278 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 380} Chain breaks: 2 Chain: "SQ" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 650 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 260 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: "VB" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "L1" 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: "L3" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Unusual residues: {' MG': 74} Classifications: {'undetermined': 74} Link IDs: {None: 73} 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: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 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 A07OY SG CYSLR 46 86.930 180.146 120.382 1.00 49.27 S ATOM A07PF SG CYSLR 49 85.742 183.290 122.148 1.00 54.28 S ATOM A07WQ SG CYSLR 83 83.652 181.986 119.309 1.00 45.30 S ATOM A07XA SG CYSLR 86 87.059 183.300 118.473 1.00 46.31 S ATOM A0A9M SG CYSLV 12 190.074 112.711 155.318 1.00 30.21 S ATOM A0AAA SG CYSLV 15 193.197 111.734 153.443 1.00 35.18 S ATOM A0ANB SG CYSLV 72 192.137 115.508 153.859 1.00 31.48 S ATOM A0AOC SG CYSLV 77 190.217 113.052 151.623 1.00 35.25 S ATOM A0AYM SG CYSLW 19 95.144 124.860 139.746 1.00 32.08 S ATOM A0AZE SG CYSLW 22 95.832 122.174 142.353 1.00 34.55 S ATOM A0B1X SG CYSLW 34 97.748 125.494 142.390 1.00 29.12 S ATOM A0B2G SG CYSLW 37 98.477 123.002 139.712 1.00 33.26 S ATOM A0BMN SG CYSLX 39 97.703 191.363 128.792 1.00 49.95 S ATOM A0BNA SG CYSLX 42 94.351 193.013 128.556 1.00 50.33 S ATOM A0BQO SG CYSLX 57 94.703 189.937 130.695 1.00 48.54 S ATOM A0BR4 SG CYSLX 60 94.924 189.519 126.961 1.00 49.11 S ATOM A0FJ2 SG CYSNP 63 76.415 198.521 199.234 1.00 54.71 S ATOM A0FJL SG CYSNP 66 74.227 195.309 199.387 1.00 55.97 S ATOM A13TA SG CYSSV 6 65.125 179.597 219.581 1.00 46.46 S ATOM A13U3 SG CYSSV 9 61.502 178.437 219.233 1.00 44.17 S ATOM A13Z7 SG CYSSV 32 64.097 175.910 220.128 1.00 43.99 S ATOM A1401 SG CYSSV 36 64.116 177.342 216.664 1.00 42.75 S Time building chain proxies: 59.85, per 1000 atoms: 0.39 Number of scatterers: 153309 At special positions: 0 Unit cell: (258.352, 240.128, 320.528, 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 296 16.00 P 3769 15.00 Mg 88 11.99 O 38589 8.00 N 28789 7.00 C 81771 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: 58.09 Conformation dependent library (CDL) restraints added in 11.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 500 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 46 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 83 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 49 " 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 19 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 37 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " 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 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 32 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16930 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: 333 helices and 78 sheets defined 47.2% alpha, 11.8% beta 1172 base pairs and 1795 stacking pairs defined. Time for finding SS restraints: 87.29 Creating SS restraints... Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.502A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 4.904A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.532A 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 Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.542A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 4.116A 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: 4.612A 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: 4.281A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.054A 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: 4.016A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.245A 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: 4.201A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 176 removed outlier: 3.514A pdb=" N LYSL6 174 " --> pdb=" O THRL6 170 " (cutoff:3.500A) Processing helix chain 'L6' and resid 177 through 192 Processing helix chain 'L6' and resid 193 through 211 Processing helix chain 'L7' and resid 15 through 30 Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.712A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.657A 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: 3.610A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.733A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.934A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 151 through 190 removed outlier: 3.539A pdb=" N ILEL7 166 " --> pdb=" O GLUL7 162 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.831A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.288A 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: 3.554A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.643A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.853A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.548A pdb=" N GLUL8 126 " --> pdb=" O ILEL8 122 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.924A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.654A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.190A 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: 3.983A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 5.013A 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: 3.710A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.706A 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: 6.215A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.527A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 removed outlier: 3.570A pdb=" N ALALA 35 " --> pdb=" O GLULA 31 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.563A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.175A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.722A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.685A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.663A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.547A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHELB 152 " --> pdb=" O VALLB 148 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 146 through 153' Processing helix chain 'LB' and resid 171 through 176 removed outlier: 5.516A pdb=" N GLULB 175 " --> pdb=" O GLYLB 171 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARGLB 176 " --> pdb=" O ARGLB 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 171 through 176' Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.985A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) removed outlier: 3.502A 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: 3.882A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.586A 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: 4.472A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.214A 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: 3.672A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.810A 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: 3.966A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.592A 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: 6.816A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 4.459A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 removed outlier: 3.608A pdb=" N LEULD 138 " --> pdb=" O ASNLD 134 " (cutoff:3.500A) Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.559A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.759A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLYLE 59 " --> pdb=" O LYSLE 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 54 through 59' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.970A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.145A 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: 4.124A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 Processing helix chain 'LF' and resid 55 through 60 Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.953A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.537A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.244A 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 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 136 removed outlier: 3.835A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.546A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 Processing helix chain 'LH' and resid 105 through 117 Processing helix chain 'LH' and resid 145 through 154 removed outlier: 3.590A pdb=" N LYSLH 152 " --> pdb=" O ASPLH 148 " (cutoff:3.500A) Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 4.029A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.183A 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: 4.111A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 removed outlier: 3.517A pdb=" N ILELI 118 " --> pdb=" O ASPLI 114 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 4.057A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.690A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.303A 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: 3.988A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 removed outlier: 4.607A pdb=" N ARGLJ 102 " --> pdb=" O LYSLJ 98 " (cutoff:3.500A) removed outlier: 4.294A 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: 3.645A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.721A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 7 removed outlier: 3.889A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.657A 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: 4.229A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHELK 69 " --> pdb=" O ARGLK 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 64 through 69' Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.348A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.634A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.513A pdb=" N GLYLK 141 " --> pdb=" O ILELK 137 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 5.677A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 99 Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.345A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 11 through 20 removed outlier: 4.523A pdb=" N LYSLM 15 " --> pdb=" O ASNLM 11 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASNLM 19 " --> pdb=" O LYSLM 15 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLYLM 20 " --> pdb=" O TRPLM 16 " (cutoff:3.500A) Processing helix chain 'LM' and resid 36 through 54 removed outlier: 5.046A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.492A 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 102 Proline residue: LM 102 - end of helix Processing helix chain 'LM' and resid 105 through 118 removed outlier: 3.597A pdb=" N ARGLM 117 " --> pdb=" O ALALM 113 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.476A 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: 3.829A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.621A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.167A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.937A 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: 5.010A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLULN 361 " --> pdb=" O ARGLN 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 356 through 361' Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.539A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 removed outlier: 3.536A 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: 3.685A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 57 removed outlier: 3.524A pdb=" N LEULP 46 " --> pdb=" O ALALP 42 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSLP 47 " --> pdb=" O PROLP 43 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.560A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 3.575A pdb=" N LEULQ 85 " --> pdb=" O ASNLQ 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 81 through 90' Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.715A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.712A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.357A 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: 5.853A 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: 3.567A pdb=" N LYSLS 46 " --> pdb=" O SERLS 42 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.056A 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: 3.505A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.595A 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: 3.883A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.505A 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: 4.072A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.354A 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 Processing helix chain 'LV' and resid 35 through 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.892A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.511A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.379A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 19 through 34 removed outlier: 3.991A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 removed outlier: 3.511A pdb=" N GLNLX 92 " --> pdb=" O GLULX 88 " (cutoff:3.500A) Processing helix chain 'LY' and resid 7 through 17 Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.555A pdb=" N ALALY 53 " --> pdb=" O ASPLY 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLULY 54 " --> pdb=" O LYSLY 50 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.265A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.731A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.825A 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 'NK' and resid 12 through 33 removed outlier: 3.531A pdb=" N LYSNK 20 " --> pdb=" O GLUNK 16 " (cutoff:3.500A) Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 removed outlier: 3.663A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARGNK 109 " --> pdb=" O LEUNK 105 " (cutoff:3.500A) Processing helix chain 'NL' and resid 116 through 123 Processing helix chain 'NL' and resid 133 through 138 removed outlier: 3.867A pdb=" N HISNL 137 " --> pdb=" O ASPNL 133 " (cutoff:3.500A) Processing helix chain 'NL' and resid 141 through 159 Processing helix chain 'NL' and resid 162 through 173 Processing helix chain 'NL' and resid 185 through 190 Processing helix chain 'NL' and resid 200 through 205 Proline residue: NL 205 - end of helix Processing helix chain 'NL' and resid 210 through 218 Processing helix chain 'NL' and resid 225 through 230 removed outlier: 3.979A pdb=" N HISNL 229 " --> pdb=" O PRONL 225 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THRNL 230 " --> pdb=" O ALANL 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'NL' and resid 225 through 230' Processing helix chain 'NL' and resid 252 through 280 Processing helix chain 'NL' and resid 289 through 299 Processing helix chain 'NL' and resid 338 through 371 removed outlier: 3.850A pdb=" N LEUNL 368 " --> pdb=" O ARGNL 364 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHENL 369 " --> pdb=" O HISNL 365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGNL 370 " --> pdb=" O GLNNL 366 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEUNL 371 " --> pdb=" O GLUNL 367 " (cutoff:3.500A) Processing helix chain 'NL' and resid 372 through 400 Processing helix chain 'NL' and resid 436 through 449 Processing helix chain 'NL' and resid 470 through 477 removed outlier: 3.758A pdb=" N ILENL 476 " --> pdb=" O ALANL 472 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLNNL 477 " --> pdb=" O PHENL 473 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 21 removed outlier: 4.100A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALANP 21 " --> pdb=" O ARGNP 17 " (cutoff:3.500A) Processing helix chain 'NP' and resid 27 through 36 removed outlier: 3.585A pdb=" N ILENP 31 " --> pdb=" O ASPNP 27 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 83 removed outlier: 3.770A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYSNP 83 " --> pdb=" O HISNP 79 " (cutoff:3.500A) Processing helix chain 'NP' and resid 84 through 94 removed outlier: 3.716A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.587A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'NR' and resid 21 through 62 removed outlier: 3.513A pdb=" N VALNR 51 " --> pdb=" O ARGNR 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUNR 62 " --> pdb=" O PHENR 58 " (cutoff:3.500A) Processing helix chain 'NR' and resid 70 through 98 removed outlier: 3.565A pdb=" N ARGNR 84 " --> pdb=" O ARGNR 80 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N PHENR 85 " --> pdb=" O TYRNR 81 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SERNR 86 " --> pdb=" O LEUNR 82 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SERNR 87 " --> pdb=" O ASNNR 83 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLUNR 88 " --> pdb=" O ARGNR 84 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILENR 98 " --> pdb=" O LEUNR 94 " (cutoff:3.500A) Processing helix chain 'NR' and resid 106 through 126 Processing helix chain 'NR' and resid 136 through 146 Processing helix chain 'NR' and resid 152 through 157 removed outlier: 4.015A pdb=" N ILENR 156 " --> pdb=" O LYSNR 152 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYSNR 157 " --> pdb=" O LEUNR 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'NR' and resid 152 through 157' Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.446A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.904A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.706A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.985A 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: 3.737A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.419A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.091A 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: 3.766A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.685A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 263 removed outlier: 3.566A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.604A 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: 4.097A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.612A 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: 4.509A 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 Processing helix chain 'SB' and resid 29 through 37 removed outlier: 4.071A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.179A 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: 3.626A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.904A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) removed outlier: 3.550A 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 Processing helix chain 'SB' and resid 216 through 224 Processing helix chain 'SB' and resid 225 through 230 removed outlier: 4.528A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 4.716A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLUSB 238 " --> pdb=" O ASPSB 234 " (cutoff:3.500A) Proline residue: SB 251 - end of helix Processing helix chain 'SB' and resid 272 through 280 Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.791A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.804A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.338A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.388A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.656A 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: 3.590A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.590A 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: 4.268A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.692A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.290A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.546A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.683A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 5.034A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.524A pdb=" N GLNSE 94 " --> pdb=" O GLNSE 90 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 122 removed outlier: 5.477A pdb=" N ALASE 122 " --> pdb=" O ALASE 118 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 164 through 178 removed outlier: 5.137A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.961A 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: 3.810A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 4.746A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.787A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.240A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.419A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.653A 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: 3.741A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.722A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.112A 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 'SF' and resid 173 through 178 removed outlier: 3.812A pdb=" N LYSSF 177 " --> pdb=" O ARGSF 174 " (cutoff:3.500A) Proline residue: SF 178 - end of helix Processing helix chain 'SG' and resid 63 through 86 removed outlier: 4.158A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 4.136A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.527A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.920A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.832A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 Processing helix chain 'SH' and resid 154 through 180 Processing helix chain 'SI' and resid 23 through 53 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.581A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.830A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.623A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.358A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.914A 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 246 through 255 removed outlier: 3.904A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.073A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.643A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.033A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.701A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.547A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 4.205A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 51 removed outlier: 5.814A pdb=" N LYSSL 51 " --> pdb=" O CYSSL 47 " (cutoff:3.500A) Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.835A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 5.233A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUSL 165 " --> pdb=" O ILESL 161 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 4.149A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 241 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.778A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 12 through 18 removed outlier: 6.143A 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: 3.673A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 4.292A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Proline residue: SM 77 - end of helix Processing helix chain 'SM' and resid 78 through 99 Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 148 removed outlier: 3.734A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEUSM 143 " --> pdb=" O SERSM 139 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 4.308A 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: 3.783A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 267 through 279 removed outlier: 4.651A pdb=" N CYSSM 272 " --> pdb=" O ASPSM 268 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N METSM 273 " --> pdb=" O SERSM 269 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.596A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.807A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.314A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.467A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 20 through 37 removed outlier: 3.542A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 4.157A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.980A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 3.538A pdb=" N VALSQ 112 " --> pdb=" O THRSQ 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASNSQ 113 " --> pdb=" O LYSSQ 109 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLUSQ 114 " --> pdb=" O GLUSQ 110 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRPSQ 115 " --> pdb=" O GLUSQ 111 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 70 removed outlier: 3.607A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Proline residue: SR 70 - end of helix Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.962A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 146 removed outlier: 3.687A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) Processing helix chain 'SR' and resid 147 through 162 removed outlier: 3.776A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Proline residue: SR 162 - end of helix Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.642A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALSR 188 " --> pdb=" O PHESR 184 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.621A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.058A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 removed outlier: 3.518A pdb=" N PHESR 272 " --> pdb=" O GLNSR 268 " (cutoff:3.500A) Proline residue: SR 277 - end of helix removed outlier: 3.898A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.672A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.644A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.511A pdb=" N GLYSR 350 " --> pdb=" O THRSR 346 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 3.865A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.264A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.202A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.002A 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: 3.973A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) removed outlier: 6.218A 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: 3.715A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.381A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILESR 480 " --> pdb=" O GLUSR 476 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 3.835A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 5.228A 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: 3.617A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.811A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.197A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.636A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N METSR 600 " --> pdb=" O ALASR 596 " (cutoff:3.500A) Processing helix chain 'SR' and resid 618 through 623 Processing helix chain 'SV' and resid 33 through 43 removed outlier: 3.599A pdb=" N LYSSV 43 " --> pdb=" O ASNSV 39 " (cutoff:3.500A) Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.532A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.477A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.781A 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: 3.585A pdb=" N ARGSV 95 " --> pdb=" O ASPSV 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSSV 125 " --> pdb=" O VALSV 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VALSV 127 " --> pdb=" O ASPSV 123 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) Processing helix chain 'VB' and resid 41 through 73 removed outlier: 3.865A pdb=" N LEUVB 49 " --> pdb=" O GLNVB 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYSVB 50 " --> pdb=" O GLNVB 46 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'L5' and resid 48 through 51 removed outlier: 3.662A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASNL5 23 " --> pdb=" O ASPL5 129 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L5' and resid 92 through 95 Processing sheet with id= 3, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 4, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 5, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.558A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.590A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.260A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.613A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.416A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.498A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 124 through 131 removed outlier: 3.984A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 13, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.657A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.224A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.728A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LE' and resid 39 through 42 removed outlier: 3.973A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 18, first strand: chain 'LF' and resid 61 through 65 removed outlier: 6.013A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LG' and resid 36 through 39 removed outlier: 4.854A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.915A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 82 through 85 removed outlier: 4.362A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.859A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.681A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LI' and resid 72 through 75 Processing sheet with id= 25, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.504A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.181A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.151A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 29, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.379A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LN' and resid 45 through 50 removed outlier: 4.696A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 53 through 59 Processing sheet with id= 32, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.673A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LN' and resid 179 through 184 removed outlier: 5.080A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.781A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.386A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.901A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 38, first strand: chain 'LR' and resid 20 through 24 Processing sheet with id= 39, first strand: chain 'LT' and resid 46 through 49 removed outlier: 4.934A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARGLT 76 " --> pdb=" O ARGLT 85 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.769A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.550A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.550A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LY' and resid 2 through 5 removed outlier: 4.851A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'NR' and resid 128 through 131 removed outlier: 3.636A pdb=" N ILENR 161 " --> pdb=" O LEUNR 129 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SA' and resid 6 through 10 removed outlier: 5.006A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.560A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.576A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SC' and resid 91 through 95 Processing sheet with id= 49, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.443A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLYSC 177 " --> pdb=" O PROSC 185 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.531A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SE' and resid 180 through 185 removed outlier: 3.511A pdb=" N HISSE 159 " --> pdb=" O ILESE 184 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.791A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SF' and resid 110 through 114 removed outlier: 3.974A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SERSF 138 " --> pdb=" O ARGSF 147 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.366A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.574A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 58, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.892A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.705A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYSSG 91 " --> pdb=" O SERSG 182 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SG' and resid 87 through 91 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'SH' and resid 72 through 77 removed outlier: 4.097A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SI' and resid 147 through 151 removed outlier: 4.274A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 64, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 65, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 66, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 67, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 68, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.124A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SL' and resid 127 through 130 removed outlier: 3.563A pdb=" N GLNSL 128 " --> pdb=" O ILESL 95 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SL' and resid 210 through 217 removed outlier: 5.890A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.523A 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: 6.778A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THRSQ 203 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.586A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.204A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.579A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.310A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'SV' and resid 18 through 23 removed outlier: 3.750A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) 3037 hydrogen bonds defined for protein. 9031 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3099 hydrogen bonds 5282 hydrogen bond angles 0 basepair planarities 1172 basepair parallelities 1795 stacking parallelities Total time for adding SS restraints: 299.94 Time building geometry restraints manager: 63.29 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: 16768 1.31 - 1.44: 66086 1.44 - 1.56: 73213 1.56 - 1.69: 7519 1.69 - 1.81: 472 Bond restraints: 164058 Sorted by residual: bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.553 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C2' A2ML31524 " pdb=" C1' A2ML31524 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.53e+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' A2ML32401 " pdb=" C1' A2ML32401 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML33867 " pdb=" C1' A2ML33867 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 164053 not shown) Histogram of bond angle deviations from ideal: 87.97 - 98.26: 14 98.26 - 108.56: 43463 108.56 - 118.85: 110976 118.85 - 129.14: 81821 129.14 - 139.43: 3267 Bond angle restraints: 239541 Sorted by residual: angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 127.90 -39.40 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 126.97 -38.47 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C1' A2ML31871 " pdb=" N9 A2ML31871 " pdb=" C8 A2ML31871 " ideal model delta sigma weight residual 88.50 126.97 -38.47 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 88.50 126.55 -38.05 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C1' A2ML3 398 " pdb=" N9 A2ML3 398 " pdb=" C8 A2ML3 398 " ideal model delta sigma weight residual 88.50 126.46 -37.96 3.00e+00 1.11e-01 1.60e+02 ... (remaining 239536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 95354 35.60 - 71.21: 8877 71.21 - 106.81: 1395 106.81 - 142.41: 19 142.41 - 178.02: 15 Dihedral angle restraints: 105660 sinusoidal: 79502 harmonic: 26158 Sorted by residual: dihedral pdb=" C4' GL31853 " pdb=" C3' GL31853 " pdb=" C2' GL31853 " pdb=" C1' GL31853 " ideal model delta sinusoidal sigma weight residual -35.00 35.61 -70.61 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C4' CL3 502 " pdb=" C3' CL3 502 " pdb=" C2' CL3 502 " pdb=" C1' CL3 502 " ideal model delta sinusoidal sigma weight residual -35.00 34.15 -69.15 1 8.00e+00 1.56e-02 9.66e+01 dihedral pdb=" C5' GL31853 " pdb=" C4' GL31853 " pdb=" C3' GL31853 " pdb=" O3' GL31853 " ideal model delta sinusoidal sigma weight residual 147.00 78.67 68.33 1 8.00e+00 1.56e-02 9.46e+01 ... (remaining 105657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 28193 0.082 - 0.163: 1040 0.163 - 0.245: 51 0.245 - 0.327: 2 0.327 - 0.408: 20 Chirality restraints: 29306 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 -2.80 0.41 2.00e-01 2.50e+01 4.17e+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 -2.79 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C2' A2ML33825 " pdb=" C3' A2ML33825 " pdb=" O2' A2ML33825 " pdb=" C1' A2ML33825 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 29303 not shown) Planarity restraints: 16365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.050 2.00e-02 2.50e+03 6.11e-01 8.39e+03 pdb=" C4' OMGL34494 " -0.462 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.737 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.589 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.617 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.210 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.930 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.197 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.960 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL33887 " 0.011 2.00e-02 2.50e+03 6.02e-01 8.15e+03 pdb=" C4' OMCL33887 " 0.474 2.00e-02 2.50e+03 pdb=" O4' OMCL33887 " 0.836 2.00e-02 2.50e+03 pdb=" C3' OMCL33887 " -0.574 2.00e-02 2.50e+03 pdb=" O3' OMCL33887 " -0.542 2.00e-02 2.50e+03 pdb=" C2' OMCL33887 " -0.264 2.00e-02 2.50e+03 pdb=" O2' OMCL33887 " 0.831 2.00e-02 2.50e+03 pdb=" C1' OMCL33887 " 0.184 2.00e-02 2.50e+03 pdb=" N1 OMCL33887 " -0.958 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.887 2.00e-02 2.50e+03 5.99e-01 8.07e+03 pdb=" C4' OMGL34228 " -0.217 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.679 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.193 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.955 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.618 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.636 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.441 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.042 2.00e-02 2.50e+03 ... (remaining 16362 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 1121 2.59 - 3.22: 134989 3.22 - 3.86: 340490 3.86 - 4.50: 477855 4.50 - 5.14: 649171 Nonbonded interactions: 1603626 Sorted by model distance: nonbonded pdb=" OP2 AL31917 " pdb="MG MGL35123 " model vdw 1.946 2.170 nonbonded pdb=" OP1 CL31676 " pdb="MG MGL35154 " model vdw 1.948 2.170 nonbonded pdb=" O2' CL31480 " pdb=" OP2 GL31482 " model vdw 1.971 2.440 nonbonded pdb=" O1B GDPSR1001 " pdb="MG MGSR1003 " model vdw 1.989 2.170 nonbonded pdb=" OP2 AL34479 " pdb="MG MGL35130 " model vdw 1.992 2.170 ... (remaining 1603621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.750 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: 0.110 Extract box with map and model: 26.590 Check model and map are aligned: 1.760 Set scattering table: 1.080 Process input model: 647.440 Find NCS groups from input model: 4.060 Set up NCS constraints: 0.520 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: 0.040 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 700.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 0.248 164058 Z= 0.393 Angle : 0.736 39.397 239541 Z= 0.316 Chirality : 0.035 0.408 29306 Planarity : 0.025 0.611 16365 Dihedral : 21.912 178.016 88730 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.22 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % 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: 1.16 (0.09), residues: 8861 helix: 1.51 (0.09), residues: 3471 sheet: 0.64 (0.15), residues: 1129 loop : 0.30 (0.09), residues: 4261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPSV 86 HIS 0.007 0.001 HISSK 118 PHE 0.017 0.001 PHELN 150 TYR 0.015 0.001 TYRL5 131 ARG 0.008 0.001 ARGLW 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1727 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1727 time to evaluate : 8.304 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: L6 184 MET cc_start: 0.7882 (mtp) cc_final: 0.7682 (mtp) REVERT: L9 118 SER cc_start: 0.8010 (p) cc_final: 0.7787 (p) REVERT: LA 104 LEU cc_start: 0.8679 (tp) cc_final: 0.8463 (mt) REVERT: LD 28 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6695 (mm-30) REVERT: LG 99 GLU cc_start: 0.7739 (tt0) cc_final: 0.7532 (tt0) REVERT: LI 43 ASN cc_start: 0.8144 (t0) cc_final: 0.7866 (t0) REVERT: LS 111 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7592 (mt-10) REVERT: LX 47 MET cc_start: 0.8618 (tpp) cc_final: 0.8184 (tpt) REVERT: NL 124 ASN cc_start: 0.8663 (t0) cc_final: 0.8434 (t0) REVERT: NR 100 ASP cc_start: 0.7109 (m-30) cc_final: 0.6655 (p0) REVERT: SB 236 MET cc_start: 0.8644 (mtp) cc_final: 0.8275 (mtm) REVERT: SH 95 SER cc_start: 0.8739 (t) cc_final: 0.7919 (m) REVERT: SH 151 ARG cc_start: 0.6389 (ptm160) cc_final: 0.5862 (pmt170) REVERT: SI 166 GLN cc_start: 0.8450 (mt0) cc_final: 0.8169 (mt0) REVERT: SK 123 ARG cc_start: 0.7270 (mmm-85) cc_final: 0.6670 (mmm-85) REVERT: SL 153 ASP cc_start: 0.7151 (m-30) cc_final: 0.6770 (m-30) REVERT: SQ 3 LYS cc_start: 0.6845 (mttt) cc_final: 0.6564 (mmtm) REVERT: SQ 5 LYS cc_start: 0.5756 (mmmt) cc_final: 0.5496 (pttm) REVERT: SR 346 THR cc_start: 0.8278 (p) cc_final: 0.8056 (p) REVERT: VB 6 ARG cc_start: 0.6209 (mtm180) cc_final: 0.5972 (mpp-170) REVERT: VB 7 LYS cc_start: 0.6994 (mmtm) cc_final: 0.6755 (mmpt) outliers start: 0 outliers final: 6 residues processed: 1727 average time/residue: 2.3950 time to fit residues: 5828.2404 Evaluate side-chains 1117 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1111 time to evaluate : 8.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 128 LEU Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LY residue 30 ASP Chi-restraints excluded: chain SR residue 446 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 1058 optimal weight: 0.8980 chunk 949 optimal weight: 7.9990 chunk 526 optimal weight: 8.9990 chunk 324 optimal weight: 4.9990 chunk 640 optimal weight: 7.9990 chunk 507 optimal weight: 5.9990 chunk 982 optimal weight: 6.9990 chunk 380 optimal weight: 4.9990 chunk 597 optimal weight: 9.9990 chunk 730 optimal weight: 4.9990 chunk 1137 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 42 GLN L5 112 HIS L6 67 HIS L6 104 ASN L7 90 HIS L8 69 HIS L8 70 GLN L8 78 GLN L8 125 ASN L9 182 HIS LA 25 HIS LA 93 HIS LB 21 GLN LB 160 HIS LC 122 HIS LC 125 GLN LD 58 HIS LD 143 HIS LE 58 HIS LE 127 GLN LF 50 ASN LH 93 ASN LI 86 GLN LI 96 HIS LK 25 HIS LK 85 GLN LK 89 ASN LL 83 ASN LM 11 ASN LM 19 ASN LM 49 HIS ** LM 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 101 HIS LN 42 HIS LN 186 ASN LN 213 GLN LN 322 HIS LN 328 ASN LO 33 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 20 GLN LS 101 ASN LU 20 ASN NL 340 GLN NL 341 GLN NL 365 HIS NP 13 HIS NP 18 GLN NP 75 ASN NR 115 GLN NR 122 GLN NR 155 ASN SC 136 HIS ** SC 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 190 HIS SE 141 ASN SE 149 ASN SE 208 ASN SF 97 ASN SG 39 ASN SG 40 HIS SI 39 GLN SI 153 ASN SI 225 HIS SK 83 HIS SK 93 GLN SK 178 GLN SL 119 ASN SL 128 GLN SL 195 ASN SL 204 ASN SM 46 HIS SM 55 ASN SM 110 ASN SM 170 HIS SM 211 HIS SM 243 ASN SM 245 HIS SM 418 GLN SR 108 ASN SR 157 HIS SR 209 HIS SR 504 GLN SV 17 HIS SV 39 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 164058 Z= 0.420 Angle : 0.803 20.641 239541 Z= 0.419 Chirality : 0.042 0.366 29306 Planarity : 0.008 0.138 16365 Dihedral : 23.078 179.292 69877 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.15 % Allowed : 10.68 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8861 helix: 1.68 (0.09), residues: 3564 sheet: 0.44 (0.15), residues: 1104 loop : -0.01 (0.09), residues: 4193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPSF 196 HIS 0.012 0.002 HISSK 118 PHE 0.027 0.002 PHESR 18 TYR 0.030 0.002 TYRSB 119 ARG 0.009 0.001 ARGL7 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1163 time to evaluate : 8.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 17 ASP cc_start: 0.7234 (t0) cc_final: 0.7033 (t0) REVERT: L6 197 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7933 (tttm) REVERT: L8 118 MET cc_start: 0.7206 (mmm) cc_final: 0.6916 (mmm) REVERT: L9 118 SER cc_start: 0.8252 (p) cc_final: 0.8025 (p) REVERT: LB 93 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: LB 168 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7657 (ptp90) REVERT: LE 69 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: LE 136 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: LF 31 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: LG 99 GLU cc_start: 0.7702 (tt0) cc_final: 0.7501 (tt0) REVERT: LG 100 ASP cc_start: 0.8561 (p0) cc_final: 0.8337 (p0) REVERT: LI 35 SER cc_start: 0.8294 (p) cc_final: 0.7337 (m) REVERT: LI 43 ASN cc_start: 0.8239 (t0) cc_final: 0.7919 (t0) REVERT: LL 28 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: LL 66 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6521 (ttm-80) REVERT: LN 213 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6986 (tm130) REVERT: LS 107 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7591 (mm-40) REVERT: LX 24 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8445 (ttmm) REVERT: LX 48 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7507 (mtpm) REVERT: NR 100 ASP cc_start: 0.6860 (m-30) cc_final: 0.6657 (p0) REVERT: NR 146 TRP cc_start: 0.8120 (t60) cc_final: 0.7825 (t60) REVERT: SA 35 ASP cc_start: 0.8053 (p0) cc_final: 0.7677 (p0) REVERT: SB 271 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: SC 135 GLN cc_start: 0.8458 (mt0) cc_final: 0.8073 (mt0) REVERT: SH 96 GLU cc_start: 0.7646 (tt0) cc_final: 0.7345 (mt-10) REVERT: SH 151 ARG cc_start: 0.6464 (ptm160) cc_final: 0.5841 (pmt170) REVERT: SK 67 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7153 (ptp90) REVERT: SQ 3 LYS cc_start: 0.6849 (mttt) cc_final: 0.6381 (mppt) REVERT: SQ 5 LYS cc_start: 0.5988 (mmmt) cc_final: 0.5509 (pttp) REVERT: SR 255 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7477 (mtp) REVERT: SR 490 LYS cc_start: 0.8417 (tppp) cc_final: 0.8110 (tppp) REVERT: SR 575 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.5396 (ptp-170) outliers start: 240 outliers final: 111 residues processed: 1292 average time/residue: 2.2100 time to fit residues: 4137.4089 Evaluate side-chains 1168 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1042 time to evaluate : 8.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 4 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 139 SER Chi-restraints excluded: chain L6 residue 148 THR Chi-restraints excluded: chain L6 residue 197 LYS Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 10 ASN Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 93 GLN Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LF residue 31 ASP Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 95 ASN Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 33 LYS Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 66 ARG Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LM residue 30 GLU Chi-restraints excluded: chain LN residue 213 GLN Chi-restraints excluded: chain LN residue 304 SER Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LR residue 96 LEU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 54 LYS Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 39 SER Chi-restraints excluded: chain NL residue 293 THR Chi-restraints excluded: chain NL residue 297 LEU Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain SA residue 146 GLU Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 271 MET Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 64 SER Chi-restraints excluded: chain SC residue 120 ASP Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 127 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 273 SER Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SG residue 182 SER Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 93 GLN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 573 THR Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SV residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 632 optimal weight: 0.9990 chunk 353 optimal weight: 7.9990 chunk 947 optimal weight: 0.7980 chunk 774 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 1139 optimal weight: 5.9990 chunk 1231 optimal weight: 0.9990 chunk 1015 optimal weight: 4.9990 chunk 1130 optimal weight: 1.9990 chunk 388 optimal weight: 7.9990 chunk 914 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L8 70 GLN L8 125 ASN L9 86 HIS LB 21 GLN LC 125 GLN ** LE 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 41 GLN LI 86 GLN LK 89 ASN LL 83 ASN LM 11 ASN LM 19 ASN LN 213 GLN LN 328 ASN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 101 ASN LU 20 ASN NP 18 GLN NR 96 ASN NR 122 GLN SA 215 ASN SA 276 ASN SD 151 ASN SE 112 GLN SE 149 ASN SI 153 ASN SL 119 ASN SL 204 ASN SM 170 HIS SM 211 HIS SM 245 HIS SM 320 GLN SM 418 GLN SR 612 HIS SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 164058 Z= 0.157 Angle : 0.664 19.930 239541 Z= 0.364 Chirality : 0.033 0.332 29306 Planarity : 0.006 0.126 16365 Dihedral : 22.985 179.747 69867 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.69 % Allowed : 12.99 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.09), residues: 8861 helix: 2.06 (0.09), residues: 3563 sheet: 0.44 (0.15), residues: 1114 loop : 0.10 (0.09), residues: 4184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLN 196 HIS 0.008 0.001 HISSK 118 PHE 0.028 0.001 PHESD 37 TYR 0.020 0.001 TYRSC 216 ARG 0.009 0.000 ARGLT 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1128 time to evaluate : 8.419 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: L6 69 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7842 (mmtt) REVERT: L6 184 MET cc_start: 0.7828 (mtp) cc_final: 0.7437 (mtp) REVERT: L9 118 SER cc_start: 0.8096 (p) cc_final: 0.7865 (p) REVERT: LB 6 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8480 (ttt-90) REVERT: LB 14 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6983 (mtm-85) REVERT: LB 168 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7701 (ptp90) REVERT: LC 164 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7890 (tppt) REVERT: LE 136 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7597 (mtp180) REVERT: LE 157 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: LF 31 ASP cc_start: 0.7541 (m-30) cc_final: 0.7299 (m-30) REVERT: LG 100 ASP cc_start: 0.8596 (p0) cc_final: 0.8346 (p0) REVERT: LI 43 ASN cc_start: 0.8182 (t0) cc_final: 0.7758 (t0) REVERT: LL 28 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: LM 40 LEU cc_start: 0.8603 (mt) cc_final: 0.8402 (tp) REVERT: LR 99 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7689 (mm-30) REVERT: LS 107 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7417 (tm-30) REVERT: LX 24 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8373 (ttmm) REVERT: NR 146 TRP cc_start: 0.7934 (t60) cc_final: 0.7615 (t60) REVERT: SA 35 ASP cc_start: 0.7987 (p0) cc_final: 0.7578 (p0) REVERT: SB 15 ARG cc_start: 0.8012 (ptp90) cc_final: 0.7737 (ptp90) REVERT: SB 73 MET cc_start: 0.8222 (mmt) cc_final: 0.7954 (mmt) REVERT: SC 115 TYR cc_start: 0.8544 (t80) cc_final: 0.8327 (t80) REVERT: SC 135 GLN cc_start: 0.8442 (mt0) cc_final: 0.8109 (mt0) REVERT: SG 128 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.6573 (mmt) REVERT: SG 143 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6754 (mt-10) REVERT: SH 42 LEU cc_start: 0.7870 (mp) cc_final: 0.7568 (mp) REVERT: SH 96 GLU cc_start: 0.7479 (tt0) cc_final: 0.7209 (mt-10) REVERT: SH 151 ARG cc_start: 0.6503 (ptm160) cc_final: 0.5903 (pmt170) REVERT: SK 67 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7139 (ptp90) REVERT: SL 101 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: SQ 3 LYS cc_start: 0.6830 (mttt) cc_final: 0.6379 (mppt) REVERT: SQ 5 LYS cc_start: 0.5876 (mmmt) cc_final: 0.5415 (pttm) REVERT: SR 4 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.5212 (m-80) REVERT: SR 83 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7882 (mtm) REVERT: SR 115 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.7173 (ttt90) REVERT: SR 572 ARG cc_start: 0.5958 (mmp80) cc_final: 0.5508 (mpt180) REVERT: SR 575 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7599 (ptp-170) REVERT: SR 599 LYS cc_start: 0.7475 (mttt) cc_final: 0.7247 (mptt) outliers start: 205 outliers final: 73 residues processed: 1237 average time/residue: 2.1918 time to fit residues: 3948.8525 Evaluate side-chains 1133 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1045 time to evaluate : 8.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 6 ARG Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 164 LYS Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 33 LYS Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 44 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 49 ASP Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 273 SER Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 252 LYS Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 182 SER Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 458 GLU Chi-restraints excluded: chain SR residue 575 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 1126 optimal weight: 3.9990 chunk 857 optimal weight: 8.9990 chunk 591 optimal weight: 0.0980 chunk 126 optimal weight: 7.9990 chunk 544 optimal weight: 2.9990 chunk 765 optimal weight: 9.9990 chunk 1144 optimal weight: 0.9990 chunk 1211 optimal weight: 30.0000 chunk 597 optimal weight: 5.9990 chunk 1084 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 188 ASN L8 70 GLN L8 125 ASN LA 93 HIS LB 21 GLN LC 125 GLN ** LE 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 41 GLN LF 50 ASN LF 95 ASN LI 86 GLN LK 93 ASN LM 11 ASN LN 175 GLN LN 328 ASN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 101 ASN LU 20 ASN NK 82 ASN NP 18 GLN NR 56 GLN NR 60 ASN NR 122 GLN NR 155 ASN SA 61 GLN ** SC 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 211 HIS SC 250 GLN SD 63 GLN SD 151 ASN SE 112 GLN SE 149 ASN SI 33 GLN SK 93 GLN SL 119 ASN SL 121 HIS SL 204 ASN SM 170 HIS SM 211 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 164058 Z= 0.284 Angle : 0.699 20.178 239541 Z= 0.376 Chirality : 0.036 0.349 29306 Planarity : 0.007 0.135 16365 Dihedral : 22.945 179.823 69867 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.32 % Allowed : 14.14 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8861 helix: 1.98 (0.09), residues: 3574 sheet: 0.39 (0.15), residues: 1110 loop : 0.03 (0.09), residues: 4177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPLN 196 HIS 0.009 0.001 HISSK 118 PHE 0.028 0.002 PHELP 52 TYR 0.024 0.002 TYRSB 119 ARG 0.009 0.001 ARGLT 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1072 time to evaluate : 8.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 184 MET cc_start: 0.7821 (mtp) cc_final: 0.7409 (mtp) REVERT: L7 71 TYR cc_start: 0.8232 (m-10) cc_final: 0.7986 (m-80) REVERT: L7 144 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: LB 6 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8547 (ttt-90) REVERT: LB 14 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7067 (mtm-85) REVERT: LB 168 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7724 (ptp90) REVERT: LC 164 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7909 (tppt) REVERT: LE 69 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: LE 118 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: LE 136 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7673 (mtp180) REVERT: LE 157 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: LG 100 ASP cc_start: 0.8616 (p0) cc_final: 0.8388 (p0) REVERT: LI 43 ASN cc_start: 0.8167 (t0) cc_final: 0.7715 (t0) REVERT: LL 28 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: LM 40 LEU cc_start: 0.8665 (mt) cc_final: 0.8463 (tp) REVERT: LO 94 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8126 (pt) REVERT: LR 99 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7866 (mm-30) REVERT: LS 107 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7444 (tm-30) REVERT: LV 59 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7899 (tttp) REVERT: LX 45 THR cc_start: 0.8956 (m) cc_final: 0.8716 (p) REVERT: NR 72 LYS cc_start: 0.7464 (ttpp) cc_final: 0.7220 (ttmm) REVERT: NR 100 ASP cc_start: 0.5966 (p0) cc_final: 0.5561 (m-30) REVERT: NR 133 ASP cc_start: 0.7778 (t70) cc_final: 0.7525 (t70) REVERT: NR 146 TRP cc_start: 0.7998 (t60) cc_final: 0.7671 (t60) REVERT: SA 35 ASP cc_start: 0.8111 (p0) cc_final: 0.7683 (p0) REVERT: SB 15 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7631 (ptt-90) REVERT: SC 115 TYR cc_start: 0.8692 (t80) cc_final: 0.8488 (t80) REVERT: SC 135 GLN cc_start: 0.8432 (mt0) cc_final: 0.8050 (mt0) REVERT: SD 68 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: SG 128 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6517 (mmt) REVERT: SG 140 GLN cc_start: 0.6496 (pm20) cc_final: 0.5772 (pm20) REVERT: SH 42 LEU cc_start: 0.7879 (mp) cc_final: 0.7581 (mp) REVERT: SH 96 GLU cc_start: 0.7650 (tt0) cc_final: 0.7414 (mt-10) REVERT: SH 151 ARG cc_start: 0.6630 (ptm160) cc_final: 0.5969 (pmt170) REVERT: SI 153 ASN cc_start: 0.7145 (m110) cc_final: 0.6935 (m-40) REVERT: SK 67 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7167 (ptp90) REVERT: SK 223 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7764 (mmtp) REVERT: SQ 3 LYS cc_start: 0.6859 (mttt) cc_final: 0.6413 (mppt) REVERT: SQ 5 LYS cc_start: 0.6039 (mmmt) cc_final: 0.5478 (pttm) REVERT: SR 4 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.5203 (m-80) REVERT: SR 83 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7871 (mtm) REVERT: SR 255 MET cc_start: 0.7744 (mmt) cc_final: 0.7305 (mtp) REVERT: SR 523 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7062 (tp30) REVERT: SR 575 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.5297 (ptp-170) outliers start: 253 outliers final: 140 residues processed: 1203 average time/residue: 2.1491 time to fit residues: 3778.5017 Evaluate side-chains 1186 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1027 time to evaluate : 8.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 74 VAL Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 4 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 148 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 27 CYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 6 ARG Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 161 ARG Chi-restraints excluded: chain LC residue 164 LYS Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 112 SER Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 97 LYS Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 118 GLU Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 53 ASP Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 33 LYS Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 30 GLU Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LR residue 96 LEU Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 44 LEU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 91 SER Chi-restraints excluded: chain LV residue 59 LYS Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 33 THR Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LX residue 89 LEU Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NL residue 334 THR Chi-restraints excluded: chain NL residue 371 LEU Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 92 LEU Chi-restraints excluded: chain NP residue 93 SER Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 273 SER Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 206 ASN Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 252 LYS Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SH residue 125 LYS Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 63 CYS Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SK residue 223 LYS Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 275 LYS Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 1008 optimal weight: 9.9990 chunk 687 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 901 optimal weight: 7.9990 chunk 499 optimal weight: 0.5980 chunk 1033 optimal weight: 5.9990 chunk 837 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 618 optimal weight: 0.8980 chunk 1087 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 167 GLN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 70 GLN L8 125 ASN LA 93 HIS LB 21 GLN LC 37 HIS LC 125 GLN ** LE 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 41 GLN LF 50 ASN LI 43 ASN LI 86 GLN LI 127 GLN LK 93 ASN LL 83 ASN LM 11 ASN LN 175 GLN ** LN 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 52 GLN LS 101 ASN LU 20 ASN NP 18 GLN NR 56 GLN NR 122 GLN SD 151 ASN SE 149 ASN SI 50 GLN SI 153 ASN SK 93 GLN SL 119 ASN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 204 ASN SM 170 HIS SM 245 HIS SM 320 GLN SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 164058 Z= 0.171 Angle : 0.659 19.845 239541 Z= 0.361 Chirality : 0.033 0.334 29306 Planarity : 0.007 0.129 16365 Dihedral : 22.923 179.758 69865 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.88 % Allowed : 14.95 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % 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: 8861 helix: 2.09 (0.09), residues: 3563 sheet: 0.43 (0.15), residues: 1115 loop : 0.06 (0.09), residues: 4183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLN 196 HIS 0.006 0.001 HISSK 118 PHE 0.028 0.001 PHESL 113 TYR 0.019 0.001 TYRNP 111 ARG 0.011 0.000 ARGLT 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1079 time to evaluate : 8.782 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: L6 184 MET cc_start: 0.7781 (mtp) cc_final: 0.7513 (mtp) REVERT: L7 144 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: LB 168 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7708 (ptp90) REVERT: LC 164 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7878 (tppt) REVERT: LD 140 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: LE 69 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7735 (mp-120) REVERT: LE 118 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: LE 136 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7628 (mtp180) REVERT: LE 157 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: LF 95 ASN cc_start: 0.8037 (t0) cc_final: 0.7780 (t0) REVERT: LI 43 ASN cc_start: 0.8117 (t0) cc_final: 0.7647 (t0) REVERT: LL 28 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7052 (pp20) REVERT: LN 148 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6432 (ttmm) REVERT: LO 94 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8116 (pt) REVERT: LQ 55 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7174 (mtt) REVERT: LR 99 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7921 (mm-30) REVERT: LS 3 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6780 (ttmm) REVERT: LS 107 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7364 (tm-30) REVERT: LS 111 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7410 (mt-10) REVERT: LX 45 THR cc_start: 0.8955 (m) cc_final: 0.8747 (p) REVERT: LY 56 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9058 (tp) REVERT: NR 72 LYS cc_start: 0.7313 (ttpp) cc_final: 0.7099 (ttmm) REVERT: NR 100 ASP cc_start: 0.5895 (p0) cc_final: 0.5556 (m-30) REVERT: NR 146 TRP cc_start: 0.7964 (t60) cc_final: 0.7651 (t60) REVERT: SA 35 ASP cc_start: 0.8083 (p0) cc_final: 0.7664 (p0) REVERT: SB 15 ARG cc_start: 0.8025 (ptp90) cc_final: 0.7677 (ptt-90) REVERT: SC 135 GLN cc_start: 0.8466 (mt0) cc_final: 0.8206 (mt0) REVERT: SD 68 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: SF 95 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: SG 86 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6798 (mt) REVERT: SH 42 LEU cc_start: 0.7831 (mp) cc_final: 0.7553 (mp) REVERT: SH 96 GLU cc_start: 0.7543 (tt0) cc_final: 0.7292 (mt-10) REVERT: SH 151 ARG cc_start: 0.6678 (ptm160) cc_final: 0.6056 (pmt170) REVERT: SK 67 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7168 (ptp90) REVERT: SQ 3 LYS cc_start: 0.6855 (mttt) cc_final: 0.6417 (mppt) REVERT: SQ 5 LYS cc_start: 0.5996 (mmmt) cc_final: 0.5447 (pttm) REVERT: SR 4 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: SR 83 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: SR 115 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.7217 (ttt90) REVERT: SR 255 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7361 (mtp) REVERT: SR 523 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7005 (tp30) REVERT: SR 575 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7588 (ptp-170) REVERT: SR 599 LYS cc_start: 0.7472 (mttt) cc_final: 0.7233 (mptt) outliers start: 219 outliers final: 123 residues processed: 1190 average time/residue: 2.1731 time to fit residues: 3771.8291 Evaluate side-chains 1186 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1041 time to evaluate : 8.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 34 THR Chi-restraints excluded: chain L5 residue 47 THR Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 115 ARG Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 161 ARG Chi-restraints excluded: chain LC residue 164 LYS Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 97 LYS Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 118 GLU Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 30 GLU Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LN residue 148 LYS Chi-restraints excluded: chain LN residue 279 GLU Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 55 MET Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 3 LYS Chi-restraints excluded: chain LS residue 44 LEU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 54 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain LZ residue 8 ARG Chi-restraints excluded: chain NL residue 371 LEU Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 273 SER Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 252 LYS Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 95 GLN Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SH residue 125 LYS Chi-restraints excluded: chain SI residue 110 LEU Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 63 CYS Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 239 GLU Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 265 LEU Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 590 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 407 optimal weight: 0.8980 chunk 1090 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 711 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 1212 optimal weight: 0.0770 chunk 1006 optimal weight: 10.0000 chunk 561 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 401 optimal weight: 6.9990 chunk 636 optimal weight: 5.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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 70 GLN LA 93 HIS LB 21 GLN LC 125 GLN ** LE 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 41 GLN LF 50 ASN LI 86 GLN LK 93 ASN LL 83 ASN LN 175 GLN ** LN 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 52 GLN LS 101 ASN LU 20 ASN NK 99 GLN NP 18 GLN NR 56 GLN NR 122 GLN ** SC 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 151 ASN SE 112 GLN SE 149 ASN SK 93 GLN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 218 HIS SM 170 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 164058 Z= 0.244 Angle : 0.682 19.989 239541 Z= 0.369 Chirality : 0.035 0.343 29306 Planarity : 0.007 0.133 16365 Dihedral : 22.897 179.655 69865 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.09 % Allowed : 15.66 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 8861 helix: 2.03 (0.09), residues: 3570 sheet: 0.34 (0.15), residues: 1120 loop : 0.03 (0.09), residues: 4171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPLN 196 HIS 0.008 0.001 HISSK 118 PHE 0.029 0.002 PHELP 52 TYR 0.022 0.002 TYRSB 119 ARG 0.012 0.000 ARGLT 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1070 time to evaluate : 8.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 69 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7913 (mmtt) REVERT: L6 184 MET cc_start: 0.7811 (mtp) cc_final: 0.7499 (mtp) REVERT: L7 144 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: LB 168 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7724 (ptp90) REVERT: LD 140 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: LE 69 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: LE 117 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7592 (mtpt) REVERT: LE 136 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7633 (mtp180) REVERT: LE 157 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: LF 95 ASN cc_start: 0.8257 (t0) cc_final: 0.8014 (t0) REVERT: LG 73 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: LI 43 ASN cc_start: 0.8165 (t0) cc_final: 0.7668 (t0) REVERT: LL 28 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7058 (pp20) REVERT: LL 66 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6461 (ttm-80) REVERT: LN 148 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6464 (ttmm) REVERT: LO 94 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8127 (pt) REVERT: LS 3 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6777 (ttmm) REVERT: LS 107 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7654 (mm-40) REVERT: LX 45 THR cc_start: 0.8946 (m) cc_final: 0.8742 (p) REVERT: LY 21 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.8002 (mttm) REVERT: NK 80 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7051 (pttm) REVERT: NP 95 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: NR 72 LYS cc_start: 0.7519 (ttpp) cc_final: 0.7215 (ttmm) REVERT: NR 100 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5587 (m-30) REVERT: NR 146 TRP cc_start: 0.7985 (t60) cc_final: 0.7712 (t60) REVERT: SA 35 ASP cc_start: 0.8137 (p0) cc_final: 0.7712 (p0) REVERT: SB 15 ARG cc_start: 0.8021 (ptp90) cc_final: 0.7699 (ptt-90) REVERT: SC 135 GLN cc_start: 0.8454 (mt0) cc_final: 0.8156 (mt0) REVERT: SD 68 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: SD 220 MET cc_start: 0.7482 (mtm) cc_final: 0.7183 (mtp) REVERT: SF 95 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: SG 86 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6769 (mt) REVERT: SG 143 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6734 (mt-10) REVERT: SH 42 LEU cc_start: 0.7851 (mp) cc_final: 0.7589 (mp) REVERT: SH 96 GLU cc_start: 0.7598 (tt0) cc_final: 0.7370 (mt-10) REVERT: SH 151 ARG cc_start: 0.6709 (ptm160) cc_final: 0.6054 (pmt170) REVERT: SK 67 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7151 (ptp90) REVERT: SK 75 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: SL 221 MET cc_start: 0.6690 (mtp) cc_final: 0.6000 (mtm) REVERT: SQ 3 LYS cc_start: 0.6870 (mttt) cc_final: 0.6446 (mppt) REVERT: SQ 5 LYS cc_start: 0.6030 (mmmt) cc_final: 0.5503 (pttm) REVERT: SR 4 TYR cc_start: 0.5402 (OUTLIER) cc_final: 0.5137 (m-80) REVERT: SR 83 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7901 (mtm) REVERT: SR 115 ARG cc_start: 0.7524 (mtp-110) cc_final: 0.7307 (ttt90) REVERT: SR 255 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7439 (mtp) REVERT: SR 523 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7040 (tp30) REVERT: SR 575 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7610 (ptp-170) outliers start: 235 outliers final: 148 residues processed: 1192 average time/residue: 2.1905 time to fit residues: 3807.5874 Evaluate side-chains 1209 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1035 time to evaluate : 8.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 34 THR Chi-restraints excluded: chain L5 residue 47 THR Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 93 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 27 CYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 98 LEU Chi-restraints excluded: chain LB residue 114 LEU Chi-restraints excluded: chain LB residue 115 ARG Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 161 ARG Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 99 MET Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 97 LYS Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 117 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 62 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 53 ASP Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 33 LYS Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 66 ARG Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 30 GLU Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LN residue 148 LYS Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 101 ASP Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 3 LYS Chi-restraints excluded: chain LS residue 44 LEU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 33 THR Chi-restraints excluded: chain LW residue 54 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 21 LYS Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 80 LYS Chi-restraints excluded: chain NL residue 118 VAL Chi-restraints excluded: chain NL residue 334 THR Chi-restraints excluded: chain NL residue 371 LEU Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 93 SER Chi-restraints excluded: chain NP residue 95 GLU Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain NR residue 100 ASP Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 273 SER Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 206 ASN Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 252 LYS Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 95 GLN Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SH residue 125 LYS Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 63 CYS Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 239 GLU Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 275 LYS Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 265 LEU Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 1168 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 690 optimal weight: 2.9990 chunk 885 optimal weight: 10.0000 chunk 685 optimal weight: 0.9980 chunk 1020 optimal weight: 0.2980 chunk 676 optimal weight: 4.9990 chunk 1207 optimal weight: 9.9990 chunk 755 optimal weight: 2.9990 chunk 736 optimal weight: 0.7980 chunk 557 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 70 GLN LA 21 ASN LA 93 HIS LB 21 GLN LC 125 GLN LF 41 GLN LF 50 ASN LK 93 ASN LM 11 ASN LN 175 GLN LN 328 ASN LP 18 ASN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 101 ASN LU 20 ASN NK 99 GLN NP 18 GLN NR 56 GLN NR 122 GLN SD 151 ASN SE 112 GLN SE 149 ASN SK 93 GLN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 164058 Z= 0.154 Angle : 0.662 19.787 239541 Z= 0.362 Chirality : 0.033 0.334 29306 Planarity : 0.007 0.128 16365 Dihedral : 22.914 179.799 69865 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.92 % Allowed : 16.11 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.09), residues: 8861 helix: 2.10 (0.09), residues: 3569 sheet: 0.38 (0.15), residues: 1118 loop : 0.08 (0.09), residues: 4174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLN 196 HIS 0.007 0.001 HISLV 21 PHE 0.032 0.001 PHELF 42 TYR 0.023 0.001 TYRNP 111 ARG 0.019 0.000 ARGSV 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1051 time to evaluate : 7.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 69 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7905 (mmtt) REVERT: L6 184 MET cc_start: 0.7793 (mtp) cc_final: 0.7470 (mtp) REVERT: L7 144 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: L8 78 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: LA 126 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7433 (ttp80) REVERT: LB 168 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7680 (ptp90) REVERT: LE 69 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7726 (mp-120) REVERT: LE 117 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7604 (mtpt) REVERT: LE 136 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7628 (mtp180) REVERT: LF 95 ASN cc_start: 0.8198 (t0) cc_final: 0.7967 (t0) REVERT: LI 43 ASN cc_start: 0.8176 (t0) cc_final: 0.7664 (t0) REVERT: LL 28 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: LO 94 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8154 (pt) REVERT: LS 3 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6793 (ttmm) REVERT: LS 107 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7593 (tm-30) REVERT: LS 111 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7495 (mt-10) REVERT: NK 80 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7179 (pttm) REVERT: NP 95 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: NR 72 LYS cc_start: 0.7507 (ttpp) cc_final: 0.7212 (ttmm) REVERT: NR 100 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.5573 (m-30) REVERT: NR 146 TRP cc_start: 0.7962 (t60) cc_final: 0.7669 (t60) REVERT: SA 35 ASP cc_start: 0.8115 (p0) cc_final: 0.7704 (p0) REVERT: SB 15 ARG cc_start: 0.8009 (ptp90) cc_final: 0.7698 (ptt-90) REVERT: SC 135 GLN cc_start: 0.8380 (mt0) cc_final: 0.8118 (mt0) REVERT: SD 220 MET cc_start: 0.7485 (mtm) cc_final: 0.7148 (mtp) REVERT: SF 95 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: SG 86 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6761 (mt) REVERT: SH 42 LEU cc_start: 0.7833 (mp) cc_final: 0.7581 (mp) REVERT: SH 151 ARG cc_start: 0.6692 (ptm160) cc_final: 0.6050 (pmt170) REVERT: SK 67 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7169 (ptp90) REVERT: SK 223 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7544 (mmtp) REVERT: SL 221 MET cc_start: 0.6763 (mtp) cc_final: 0.6079 (mtm) REVERT: SQ 3 LYS cc_start: 0.6855 (mttt) cc_final: 0.6436 (mppt) REVERT: SQ 5 LYS cc_start: 0.5786 (mmmt) cc_final: 0.5329 (pttm) REVERT: SR 4 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.5114 (m-80) REVERT: SR 83 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7898 (mtm) REVERT: SR 255 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7383 (mtp) REVERT: SR 523 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7027 (tp30) REVERT: SR 575 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7592 (ptp-170) REVERT: SR 599 LYS cc_start: 0.7512 (mttt) cc_final: 0.7273 (mptt) REVERT: SV 118 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8338 (mp) outliers start: 222 outliers final: 126 residues processed: 1174 average time/residue: 2.2030 time to fit residues: 3799.8177 Evaluate side-chains 1168 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1019 time to evaluate : 8.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 34 THR Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 148 THR Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 126 ARG Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 98 LEU Chi-restraints excluded: chain LB residue 114 LEU Chi-restraints excluded: chain LB residue 115 ARG Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 161 ARG Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 140 GLU Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 117 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 35 SER Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LN residue 279 GLU Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 101 ASP Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 3 LYS Chi-restraints excluded: chain LS residue 44 LEU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LZ residue 8 ARG Chi-restraints excluded: chain NK residue 80 LYS Chi-restraints excluded: chain NL residue 371 LEU Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 95 GLU Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain NR residue 100 ASP Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SD residue 206 ASN Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 252 LYS Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 95 GLN Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 63 CYS Chi-restraints excluded: chain SK residue 67 ARG Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 93 GLN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SK residue 223 LYS Chi-restraints excluded: chain SL residue 31 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SL residue 239 GLU Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 275 LYS Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 265 LEU Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SV residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 747 optimal weight: 9.9990 chunk 482 optimal weight: 7.9990 chunk 721 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 767 optimal weight: 4.9990 chunk 822 optimal weight: 0.6980 chunk 597 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 949 optimal weight: 3.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 97 ASN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 70 GLN LA 93 HIS LB 21 GLN LC 125 GLN LF 27 HIS LF 41 GLN LK 93 ASN LL 83 ASN LL 121 GLN LM 11 ASN LN 328 ASN LP 18 ASN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 52 GLN LS 101 ASN LU 20 ASN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 56 GLN NR 96 ASN NR 122 GLN SB 138 GLN ** SC 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SD 151 ASN SE 112 GLN SE 149 ASN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SR 486 GLN SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 164058 Z= 0.391 Angle : 0.752 20.275 239541 Z= 0.398 Chirality : 0.040 0.369 29306 Planarity : 0.008 0.141 16365 Dihedral : 22.928 179.635 69865 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.11 % Allowed : 16.25 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % 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: 1.05 (0.09), residues: 8861 helix: 1.85 (0.09), residues: 3571 sheet: 0.25 (0.15), residues: 1111 loop : -0.12 (0.09), residues: 4179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPSD 142 HIS 0.010 0.001 HISSK 118 PHE 0.034 0.002 PHELP 52 TYR 0.027 0.002 TYRSB 119 ARG 0.014 0.001 ARGLT 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1030 time to evaluate : 8.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 184 MET cc_start: 0.7871 (mtp) cc_final: 0.7521 (mtp) REVERT: L7 144 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: L7 178 ARG cc_start: 0.8573 (ttt90) cc_final: 0.8052 (ttt90) REVERT: LB 168 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7764 (ptp90) REVERT: LD 149 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8353 (mptt) REVERT: LE 69 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: LE 117 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7626 (mtpt) REVERT: LE 118 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: LE 136 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: LF 95 ASN cc_start: 0.8367 (t0) cc_final: 0.8133 (t0) REVERT: LG 73 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7257 (mtm-85) REVERT: LI 43 ASN cc_start: 0.8255 (t0) cc_final: 0.7764 (t0) REVERT: LL 28 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7072 (pp20) REVERT: LN 148 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6517 (ttmm) REVERT: LO 94 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8128 (pt) REVERT: LS 3 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6807 (ttmm) REVERT: LS 107 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7516 (tm-30) REVERT: LX 48 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7661 (mtpm) REVERT: NK 80 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6947 (pttm) REVERT: NP 95 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: NR 72 LYS cc_start: 0.7569 (ttpp) cc_final: 0.7235 (ttmm) REVERT: NR 83 ASN cc_start: 0.7100 (t0) cc_final: 0.6886 (t0) REVERT: NR 146 TRP cc_start: 0.8038 (t60) cc_final: 0.7779 (t60) REVERT: SB 15 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7668 (ptt-90) REVERT: SD 220 MET cc_start: 0.7548 (mtm) cc_final: 0.7294 (mtp) REVERT: SF 95 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: SG 86 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6863 (mt) REVERT: SH 42 LEU cc_start: 0.7986 (mp) cc_final: 0.7717 (mp) REVERT: SH 151 ARG cc_start: 0.6775 (ptm160) cc_final: 0.6125 (pmt170) REVERT: SK 223 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7763 (mmtp) REVERT: SK 237 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6546 (ttp-170) REVERT: SQ 3 LYS cc_start: 0.6878 (mttt) cc_final: 0.6459 (mppt) REVERT: SQ 5 LYS cc_start: 0.6209 (mmmt) cc_final: 0.5671 (pttm) REVERT: SR 4 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.5136 (m-80) REVERT: SR 83 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7876 (mtm) REVERT: SR 255 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7549 (mtt) REVERT: SR 523 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7061 (tp30) REVERT: SR 575 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7642 (ptp-170) REVERT: SV 111 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7490 (mtp180) REVERT: SV 118 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8437 (mp) outliers start: 237 outliers final: 155 residues processed: 1167 average time/residue: 2.2232 time to fit residues: 3789.8958 Evaluate side-chains 1188 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1009 time to evaluate : 12.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 34 THR Chi-restraints excluded: chain L5 residue 47 THR Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 74 VAL Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 148 THR Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L7 residue 152 VAL Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 27 CYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 115 ARG Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LB residue 187 LYS Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 161 ARG Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 99 MET Chi-restraints excluded: chain LD residue 149 LYS Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 117 LYS Chi-restraints excluded: chain LE residue 118 GLU Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 35 SER Chi-restraints excluded: chain LI residue 53 ASP Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 132 GLN Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LM residue 117 ARG Chi-restraints excluded: chain LN residue 148 LYS Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 101 ASP Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 3 LYS Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 44 LEU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 80 LYS Chi-restraints excluded: chain NL residue 118 VAL Chi-restraints excluded: chain NL residue 334 THR Chi-restraints excluded: chain NL residue 371 LEU Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 7 THR Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 93 SER Chi-restraints excluded: chain NP residue 95 GLU Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 69 THR Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 273 SER Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 95 GLN Chi-restraints excluded: chain SF residue 208 GLU 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 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SH residue 125 LYS Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SK residue 63 CYS Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SK residue 223 LYS Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SL residue 31 LEU Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 239 GLU Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 275 LYS Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 265 LEU Chi-restraints excluded: chain SR residue 285 ILE Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SV residue 111 ARG Chi-restraints excluded: chain SV residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 1098 optimal weight: 9.9990 chunk 1156 optimal weight: 2.9990 chunk 1055 optimal weight: 4.9990 chunk 1125 optimal weight: 0.9990 chunk 677 optimal weight: 0.9980 chunk 490 optimal weight: 6.9990 chunk 883 optimal weight: 0.8980 chunk 345 optimal weight: 4.9990 chunk 1016 optimal weight: 0.9980 chunk 1064 optimal weight: 3.9990 chunk 1121 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 125 ASN LA 21 ASN LA 93 HIS LB 21 GLN LC 125 GLN LF 41 GLN LH 107 HIS ** LK 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 83 ASN LL 100 ASN LM 11 ASN LN 175 GLN LN 328 ASN LP 18 ASN LQ 52 GLN LS 101 ASN LU 92 ASN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 56 GLN NR 122 GLN SD 151 ASN ** SE 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 149 ASN SK 93 GLN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 164058 Z= 0.169 Angle : 0.667 19.875 239541 Z= 0.364 Chirality : 0.033 0.335 29306 Planarity : 0.006 0.128 16365 Dihedral : 22.897 179.826 69865 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.31 % Allowed : 17.23 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % 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: 1.27 (0.09), residues: 8861 helix: 2.06 (0.09), residues: 3567 sheet: 0.34 (0.15), residues: 1114 loop : -0.03 (0.09), residues: 4180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLN 196 HIS 0.007 0.001 HISSK 118 PHE 0.030 0.001 PHELF 42 TYR 0.021 0.001 TYRNP 111 ARG 0.013 0.000 ARGLT 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1055 time to evaluate : 8.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 184 MET cc_start: 0.7781 (mtp) cc_final: 0.7472 (mtp) REVERT: L7 144 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: LB 168 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7764 (ptp90) REVERT: LD 149 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8260 (mptt) REVERT: LE 69 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: LE 117 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7634 (mtpt) REVERT: LE 118 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: LE 136 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: LG 73 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7290 (mtm-85) REVERT: LI 43 ASN cc_start: 0.8169 (t0) cc_final: 0.7656 (t0) REVERT: LL 28 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6992 (pp20) REVERT: LN 148 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6447 (ttmm) REVERT: LQ 117 GLN cc_start: 0.7965 (mt0) cc_final: 0.7670 (mt0) REVERT: LS 3 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6794 (ttmm) REVERT: LX 48 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7638 (mtpm) REVERT: NP 95 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: NR 72 LYS cc_start: 0.7483 (ttpp) cc_final: 0.7132 (ttmm) REVERT: NR 83 ASN cc_start: 0.7113 (t0) cc_final: 0.6900 (t0) REVERT: NR 146 TRP cc_start: 0.7932 (t60) cc_final: 0.7676 (t60) REVERT: SA 35 ASP cc_start: 0.8142 (p0) cc_final: 0.7658 (p0) REVERT: SB 15 ARG cc_start: 0.8027 (ptp90) cc_final: 0.7675 (ptt-90) REVERT: SC 135 GLN cc_start: 0.8409 (mt0) cc_final: 0.8179 (mt0) REVERT: SD 220 MET cc_start: 0.7566 (mtm) cc_final: 0.7265 (mtp) REVERT: SF 95 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: SF 245 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8160 (mtp85) REVERT: SG 86 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6760 (mt) REVERT: SH 42 LEU cc_start: 0.7951 (mp) cc_final: 0.7672 (mp) REVERT: SH 151 ARG cc_start: 0.6802 (ptm160) cc_final: 0.6185 (pmt170) REVERT: SL 221 MET cc_start: 0.6856 (mtp) cc_final: 0.6222 (mtm) REVERT: SM 273 MET cc_start: 0.7665 (mmm) cc_final: 0.7453 (mmp) REVERT: SQ 3 LYS cc_start: 0.6860 (mttt) cc_final: 0.6447 (mppt) REVERT: SQ 5 LYS cc_start: 0.5958 (mmmt) cc_final: 0.5429 (pttm) REVERT: SR 4 TYR cc_start: 0.5442 (OUTLIER) cc_final: 0.5127 (m-80) REVERT: SR 83 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7912 (mtm) REVERT: SR 255 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7421 (mtp) REVERT: SR 523 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7040 (tp30) REVERT: SR 575 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7634 (ptp-170) REVERT: SR 599 LYS cc_start: 0.7529 (mttt) cc_final: 0.7294 (mptt) outliers start: 176 outliers final: 120 residues processed: 1157 average time/residue: 2.1748 time to fit residues: 3675.8265 Evaluate side-chains 1153 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1015 time to evaluate : 8.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 34 THR Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 47 THR Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 74 VAL Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 132 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 148 THR Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 149 LYS Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 117 LYS Chi-restraints excluded: chain LE residue 118 GLU Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LN residue 148 LYS Chi-restraints excluded: chain LN residue 328 ASN Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 101 ASP Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LS residue 3 LYS Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 21 VAL Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LZ residue 8 ARG Chi-restraints excluded: chain NL residue 118 VAL Chi-restraints excluded: chain NL residue 334 THR Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 95 GLU Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 95 GLN Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SH residue 125 LYS Chi-restraints excluded: chain SI residue 137 LEU 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 109 THR Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 31 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SL residue 239 GLU Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 285 ILE Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 590 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 739 optimal weight: 7.9990 chunk 1190 optimal weight: 8.9990 chunk 726 optimal weight: 0.8980 chunk 564 optimal weight: 1.9990 chunk 827 optimal weight: 7.9990 chunk 1248 optimal weight: 0.4980 chunk 1148 optimal weight: 0.3980 chunk 994 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 767 optimal weight: 4.9990 chunk 609 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 70 GLN LA 21 ASN LA 93 HIS LC 125 GLN LF 41 GLN LF 95 ASN LK 93 ASN LL 83 ASN LL 100 ASN LN 175 GLN ** LN 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LQ 52 GLN LS 101 ASN LS 107 GLN LU 20 ASN LU 92 ASN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 56 GLN NR 122 GLN SD 63 GLN SD 151 ASN SE 149 ASN SK 93 GLN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SR 486 GLN SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 164058 Z= 0.181 Angle : 0.665 19.731 239541 Z= 0.362 Chirality : 0.033 0.376 29306 Planarity : 0.007 0.130 16365 Dihedral : 22.862 179.660 69865 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.18 % Allowed : 17.65 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 8861 helix: 2.09 (0.09), residues: 3568 sheet: 0.36 (0.15), residues: 1119 loop : -0.01 (0.09), residues: 4174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLN 196 HIS 0.007 0.001 HISSK 118 PHE 0.033 0.001 PHELP 52 TYR 0.023 0.001 TYRNP 111 ARG 0.015 0.000 ARGLT 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17722 Ramachandran restraints generated. 8861 Oldfield, 0 Emsley, 8861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1032 time to evaluate : 8.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 184 MET cc_start: 0.7791 (mtp) cc_final: 0.7513 (mtp) REVERT: L7 144 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: LB 168 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7731 (ptp90) REVERT: LD 149 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8261 (mptt) REVERT: LE 69 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7726 (mp-120) REVERT: LE 117 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7636 (mtpt) REVERT: LE 118 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: LE 136 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7606 (mtp180) REVERT: LG 73 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7285 (mtm-85) REVERT: LI 43 ASN cc_start: 0.8170 (t0) cc_final: 0.7668 (t0) REVERT: LL 28 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7007 (pp20) REVERT: LN 148 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6459 (ttmm) REVERT: LQ 117 GLN cc_start: 0.7988 (mt0) cc_final: 0.7696 (mt0) REVERT: LS 3 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6797 (ttmm) REVERT: LS 107 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: LX 48 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7609 (mtpm) REVERT: NP 95 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: NR 72 LYS cc_start: 0.7477 (ttpp) cc_final: 0.7125 (ttmm) REVERT: NR 146 TRP cc_start: 0.7991 (t60) cc_final: 0.7725 (t60) REVERT: SA 35 ASP cc_start: 0.8144 (p0) cc_final: 0.7738 (p0) REVERT: SB 15 ARG cc_start: 0.8029 (ptp90) cc_final: 0.7684 (ptt-90) REVERT: SC 135 GLN cc_start: 0.8392 (mt0) cc_final: 0.8149 (mt0) REVERT: SD 220 MET cc_start: 0.7527 (mtm) cc_final: 0.7223 (mtp) REVERT: SF 95 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: SG 86 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6771 (mt) REVERT: SH 42 LEU cc_start: 0.7935 (mp) cc_final: 0.7667 (mp) REVERT: SH 151 ARG cc_start: 0.6810 (ptm160) cc_final: 0.6188 (pmt170) REVERT: SK 237 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6817 (ttp-170) REVERT: SL 221 MET cc_start: 0.6874 (mtp) cc_final: 0.6260 (mtm) REVERT: SM 273 MET cc_start: 0.7625 (mmm) cc_final: 0.7404 (mmp) REVERT: SQ 3 LYS cc_start: 0.6862 (mttt) cc_final: 0.6453 (mppt) REVERT: SQ 5 LYS cc_start: 0.5827 (mmmt) cc_final: 0.5361 (pttm) REVERT: SR 4 TYR cc_start: 0.5409 (OUTLIER) cc_final: 0.5091 (m-80) REVERT: SR 83 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: SR 255 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7367 (mtp) REVERT: SR 523 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7044 (tp30) REVERT: SR 575 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7618 (ptp-170) outliers start: 166 outliers final: 116 residues processed: 1124 average time/residue: 2.1742 time to fit residues: 3575.1816 Evaluate side-chains 1147 residues out of total 7833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1011 time to evaluate : 8.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 51 SER Chi-restraints excluded: chain L5 residue 59 SER Chi-restraints excluded: chain L5 residue 74 VAL Chi-restraints excluded: chain L5 residue 114 ASP Chi-restraints excluded: chain L5 residue 132 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 148 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 144 GLU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 87 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 95 VAL Chi-restraints excluded: chain LB residue 168 ARG Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 149 LYS Chi-restraints excluded: chain LE residue 69 GLN Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 117 LYS Chi-restraints excluded: chain LE residue 118 GLU Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 137 GLU Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 109 LYS Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LG residue 115 SER Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LJ residue 34 SER Chi-restraints excluded: chain LJ residue 70 SER Chi-restraints excluded: chain LJ residue 86 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 80 THR Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 89 VAL Chi-restraints excluded: chain LN residue 148 LYS Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 89 SER Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 81 ASN Chi-restraints excluded: chain LQ residue 91 CYS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 65 MET Chi-restraints excluded: chain LR residue 81 SER Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 3 LYS Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 107 GLN Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 92 LEU Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 63 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LZ residue 8 ARG Chi-restraints excluded: chain NL residue 118 VAL Chi-restraints excluded: chain NL residue 334 THR Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 4 SER Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 95 GLU Chi-restraints excluded: chain NR residue 50 LEU Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SA residue 266 THR Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SC residue 45 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SD residue 214 SER Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 95 GLN Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 135 SER Chi-restraints excluded: chain SG residue 166 THR Chi-restraints excluded: chain SG residue 169 ASN Chi-restraints excluded: chain SH residue 63 SER Chi-restraints excluded: chain SH residue 66 SER Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SI residue 137 LEU Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 63 CYS Chi-restraints excluded: chain SK residue 74 ASN Chi-restraints excluded: chain SK residue 93 GLN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 140 GLN Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SL residue 31 LEU Chi-restraints excluded: chain SL residue 169 ILE Chi-restraints excluded: chain SM residue 122 GLU Chi-restraints excluded: chain SM residue 316 GLU Chi-restraints excluded: chain SM residue 391 CYS Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 4 TYR Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 255 MET Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 285 ILE Chi-restraints excluded: chain SR residue 320 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 396 LYS Chi-restraints excluded: chain SR residue 545 ARG Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 590 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1253 random chunks: chunk 789 optimal weight: 7.9990 chunk 1058 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 916 optimal weight: 0.0670 chunk 146 optimal weight: 7.9990 chunk 276 optimal weight: 8.9990 chunk 995 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 1022 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 overall best weight: 2.5922 ------------------------------------------------------------------------------- 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 70 GLN LA 21 ASN LA 93 HIS LC 125 GLN LF 41 GLN LF 44 GLN LF 95 ASN ** LK 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 100 ASN LN 175 GLN ** LN 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LQ 52 GLN LS 101 ASN LU 92 ASN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 56 GLN NR 122 GLN ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SD 151 ASN SE 149 ASN ** SL 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 170 HIS SM 245 HIS SM 418 GLN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SR 486 GLN SV 39 ASN VB 45 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.065139 restraints weight = 340620.517| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.34 r_work: 0.2860 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.242 164058 Z= 0.213 Angle : 0.702 59.196 239541 Z= 0.389 Chirality : 0.035 0.566 29306 Planarity : 0.007 0.130 16365 Dihedral : 22.862 179.676 69865 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 17.82 % Favored : 80.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.09), residues: 8861 helix: 2.09 (0.09), residues: 3568 sheet: 0.36 (0.15), residues: 1119 loop : -0.01 (0.09), residues: 4174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLN 196 HIS 0.007 0.001 HISSK 118 PHE 0.028 0.001 PHESL 113 TYR 0.021 0.001 TYRNP 111 ARG 0.012 0.000 ARGLT 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 58678.41 seconds wall clock time: 1016 minutes 21.95 seconds (60981.95 seconds total)