Starting phenix.real_space_refine on Mon Mar 25 16:47:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unu_26633/03_2024/7unu_26633_updated.pdb" } resolution = 2.9 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= 0.000 sd= 1.012 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4605 5.49 5 Mg 607 5.21 5 S 165 5.16 5 C 75141 2.51 5 N 27652 2.21 5 O 41087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 183": "OD1" <-> "OD2" Residue "c TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "d TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d GLU 95": "OE1" <-> "OE2" Residue "d TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 113": "OE1" <-> "OE2" Residue "d TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 102": "OE1" <-> "OE2" Residue "e PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "f ASP 76": "OD1" <-> "OD2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 107": "OD1" <-> "OD2" Residue "k TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 112": "OD1" <-> "OD2" Residue "l ASP 20": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 18": "OD1" <-> "OD2" Residue "q ASP 80": "OD1" <-> "OD2" Residue "u PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "x ASP 702": "OD1" <-> "OD2" Residue "x GLU 832": "OE1" <-> "OE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "P GLU 32": "OE1" <-> "OE2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "Q ASP 107": "OD1" <-> "OD2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R ASP 25": "OD1" <-> "OD2" Residue "S TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "T GLU 31": "OE1" <-> "OE2" Residue "T ASP 34": "OD1" <-> "OD2" Residue "T GLU 62": "OE1" <-> "OE2" Residue "U ASP 22": "OD1" <-> "OD2" Residue "U ASP 94": "OD1" <-> "OD2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "V ASP 36": "OD1" <-> "OD2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V ASP 78": "OD1" <-> "OD2" Residue "V PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X ASP 100": "OD1" <-> "OD2" Residue "X GLU 115": "OE1" <-> "OE2" Residue "X GLU 135": "OE1" <-> "OE2" Residue "X ASP 142": "OD1" <-> "OD2" Residue "Z GLU 65": "OE1" <-> "OE2" Residue "Z PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 16": "OE1" <-> "OE2" Residue "4 ASP 14": "OD1" <-> "OD2" Residue "7 ASP 53": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149259 Number of models: 1 Model: "" Number of chains: 86 Chain: "a" Number of atoms: 32675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1522, 32675 Classifications: {'RNA': 1522} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 123, 'rna2p_pyr': 86, 'rna3p': 8, 'rna3p_pur': 742, 'rna3p_pyr': 562} Link IDs: {'rna2p': 210, 'rna3p': 1311} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1751 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1617 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1134 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 857 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 104} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "g" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1187 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "h" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 793 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "k" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 879 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 891 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "n" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 800 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "q" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 480 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "s" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 671 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 506 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "v" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 65} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3235 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 17, 'TRANS': 454} Chain breaks: 3 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 18, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 229 Chain: "A" Number of atoms: 61891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2884, 61891 Classifications: {'RNA': 2884} Modifications used: {'5*END': 1, 'rna2p': 5, 'rna2p_pur': 276, 'rna2p_pyr': 168, 'rna3p': 8, 'rna3p_pur': 1368, 'rna3p_pyr': 1059} Link IDs: {'rna2p': 449, 'rna3p': 2434} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2495 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 103} Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2072 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "D" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1588 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain: "E" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1521 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1407 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 168} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1307 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 164} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 964 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 144} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "I" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 718 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 99 Chain: "J" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 911 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 9, 'TRANS': 125} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1130 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 132} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1066 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "O" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1085 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 956 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "T" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "V" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "W" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1445 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "Y" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "Z" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "3" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 356 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "8" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Unusual residues: {' MG': 120} Classifications: {'undetermined': 120} Link IDs: {None: 119} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 456 Unusual residues: {' MG': 456} Classifications: {'undetermined': 456} Link IDs: {None: 455} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" 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: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "8" 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: "a" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Classifications: {'water': 169} Link IDs: {None: 168} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0ZLM SG CYS 3 16 122.884 234.140 108.191 1.00 73.05 S ATOM A0ZLY SG CYS 3 18 120.180 236.685 107.400 1.00 71.91 S ATOM A0ZPU SG CYS 3 37 119.725 234.455 110.334 1.00 71.62 S ATOM A0ZQF SG CYS 3 40 119.530 232.985 106.810 1.00 73.38 S ATOM A116L SG CYS 8 11 56.297 145.382 133.531 1.00 35.15 S ATOM A117A SG CYS 8 14 57.294 144.459 137.097 1.00 31.40 S ATOM A11A8 SG CYS 8 27 55.146 142.095 134.936 1.00 32.44 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU e 152 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU e 152 " occ=0.00 residue: pdb=" N VAL e 154 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL e 154 " occ=0.00 residue: pdb=" N ALA e 155 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA e 155 " occ=0.00 residue: pdb=" N ALA e 156 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA e 156 " occ=0.00 residue: pdb=" N LYS e 157 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS e 157 " occ=0.00 residue: pdb=" N ARG e 158 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG e 158 " occ=0.00 residue: pdb=" N GLY e 159 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY e 159 " occ=0.00 residue: pdb=" N FME v 103 " occ=0.80 ... (8 atoms not shown) pdb=" O1 FME v 103 " occ=0.80 Time building chain proxies: 61.04, per 1000 atoms: 0.41 Number of scatterers: 149259 At special positions: 0 Unit cell: (244.8, 255.85, 273.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 165 16.00 P 4605 15.00 Mg 607 11.99 O 41087 8.00 N 27652 7.00 C 75141 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.26 Conformation dependent library (CDL) restraints added in 9.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 18 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 37 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 40 " pdb=" ZN 8 102 " pdb="ZN ZN 8 102 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 102 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 102 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 102 " - pdb=" SG CYS 8 14 " Number of angles added : 9 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11844 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: 189 helices and 79 sheets defined 37.7% alpha, 19.8% beta 1536 base pairs and 2508 stacking pairs defined. Time for finding SS restraints: 78.90 Creating SS restraints... Processing helix chain 'b' and resid 6 through 13 removed outlier: 4.217A pdb=" N LEU b 10 " --> pdb=" O MET b 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS b 11 " --> pdb=" O ARG b 7 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 6 through 13' Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.052A pdb=" N GLY b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE b 32 " --> pdb=" O GLY b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.536A pdb=" N THR b 46 " --> pdb=" O ASN b 42 " (cutoff:3.500A) Proline residue: b 48 - end of helix removed outlier: 4.932A pdb=" N GLY b 63 " --> pdb=" O ARG b 59 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 88 removed outlier: 4.631A pdb=" N ILE b 79 " --> pdb=" O SER b 75 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG b 86 " --> pdb=" O GLU b 82 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS b 87 " --> pdb=" O GLU b 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY b 88 " --> pdb=" O ALA b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 125 removed outlier: 3.610A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR b 125 " --> pdb=" O SER b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 4.786A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.862A pdb=" N GLU b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 removed outlier: 3.543A pdb=" N GLY b 227 " --> pdb=" O ARG b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.990A pdb=" N LYS c 48 " --> pdb=" O GLN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.706A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 Processing helix chain 'c' and resid 129 through 145 removed outlier: 4.254A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.514A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 removed outlier: 4.942A pdb=" N LYS d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS d 32 " --> pdb=" O LEU d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.107A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 4.013A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 removed outlier: 3.602A pdb=" N GLY d 106 " --> pdb=" O VAL d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.883A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.759A pdb=" N ALA d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY d 166 " --> pdb=" O CYS d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.865A pdb=" N LEU d 191 " --> pdb=" O ALA d 187 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 4.450A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 4.604A pdb=" N ASN e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.747A pdb=" N MET e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 156 removed outlier: 3.576A pdb=" N VAL e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA e 155 " --> pdb=" O PRO e 151 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA e 156 " --> pdb=" O GLU e 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 150 through 156' Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.750A pdb=" N GLU e 163 " --> pdb=" O GLY e 159 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 159 through 164' Processing helix chain 'f' and resid 17 through 33 removed outlier: 4.466A pdb=" N ASP f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.982A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.507A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.131A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG g 111 " --> pdb=" O PHE g 107 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 4.415A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.664A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 40 removed outlier: 3.976A pdb=" N GLY i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 56 removed outlier: 4.657A pdb=" N MET i 46 " --> pdb=" O GLU i 42 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.525A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.679A pdb=" N ALA i 101 " --> pdb=" O SER i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.854A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 88 removed outlier: 4.619A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.789A pdb=" N GLY k 51 " --> pdb=" O SER k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 4.185A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 76 removed outlier: 4.412A pdb=" N GLU k 76 " --> pdb=" O GLN k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.657A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.531A pdb=" N TYR l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.160A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.395A pdb=" N GLY m 38 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.813A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.613A pdb=" N GLN m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS m 62 " --> pdb=" O ASN m 58 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.725A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.711A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 3.884A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.827A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 52 removed outlier: 3.512A pdb=" N GLN n 51 " --> pdb=" O ALA n 47 " (cutoff:3.500A) Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.682A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.753A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N HIS o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.857A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.721A pdb=" N GLY p 64 " --> pdb=" O TRP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 81 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.849A pdb=" N ALA r 31 " --> pdb=" O ASN r 27 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.677A pdb=" N LEU r 65 " --> pdb=" O ARG r 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA r 66 " --> pdb=" O ALA r 62 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.830A pdb=" N VAL s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.248A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA s 76 " --> pdb=" O GLY s 72 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 removed outlier: 3.798A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 88 removed outlier: 3.642A pdb=" N THR t 88 " --> pdb=" O LYS t 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 4.036A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU u 16 " --> pdb=" O PHE u 12 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG u 17 " --> pdb=" O ASP u 13 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 4.759A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 63 removed outlier: 3.712A pdb=" N ARG u 62 " --> pdb=" O LYS u 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) Processing helix chain 'x' and resid 354 through 366 removed outlier: 3.598A pdb=" N LYS x 366 " --> pdb=" O ILE x 362 " (cutoff:3.500A) Processing helix chain 'x' and resid 398 through 409 removed outlier: 3.686A pdb=" N ALA x 404 " --> pdb=" O ALA x 400 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET x 405 " --> pdb=" O ALA x 401 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG x 406 " --> pdb=" O PHE x 402 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG x 408 " --> pdb=" O ALA x 404 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY x 409 " --> pdb=" O MET x 405 " (cutoff:3.500A) Processing helix chain 'x' and resid 427 through 441 removed outlier: 3.687A pdb=" N ALA x 440 " --> pdb=" O HIS x 436 " (cutoff:3.500A) Processing helix chain 'x' and resid 458 through 469 removed outlier: 4.778A pdb=" N LYS x 462 " --> pdb=" O PRO x 458 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN x 463 " --> pdb=" O ASP x 459 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA x 467 " --> pdb=" O ASN x 463 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU x 468 " --> pdb=" O GLY x 464 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP x 469 " --> pdb=" O LEU x 465 " (cutoff:3.500A) Processing helix chain 'x' and resid 491 through 504 removed outlier: 4.013A pdb=" N LEU x 500 " --> pdb=" O LEU x 496 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA x 503 " --> pdb=" O VAL x 499 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU x 504 " --> pdb=" O LEU x 500 " (cutoff:3.500A) Processing helix chain 'x' and resid 597 through 623 removed outlier: 3.834A pdb=" N LEU x 617 " --> pdb=" O ARG x 613 " (cutoff:3.500A) Processing helix chain 'x' and resid 648 through 662 removed outlier: 4.013A pdb=" N LEU x 655 " --> pdb=" O SER x 651 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY x 661 " --> pdb=" O GLY x 657 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU x 662 " --> pdb=" O SER x 658 " (cutoff:3.500A) Processing helix chain 'x' and resid 680 through 691 Processing helix chain 'x' and resid 702 through 712 Processing helix chain 'x' and resid 721 through 735 removed outlier: 3.782A pdb=" N ILE x 725 " --> pdb=" O VAL x 721 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE x 726 " --> pdb=" O ILE x 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.672A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N PHE C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 16' Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.040A pdb=" N LEU C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.808A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.983A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.240A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 261 through 269 removed outlier: 6.606A pdb=" N ASP C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 269' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.003A pdb=" N SER C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.626A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 removed outlier: 4.191A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 14 through 19 removed outlier: 3.616A pdb=" N PHE E 18 " --> pdb=" O SER E 14 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 14 through 19' Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.750A pdb=" N ARG E 39 " --> pdb=" O MET E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.331A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 removed outlier: 3.757A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.711A pdb=" N THR E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.630A pdb=" N ALA E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.598A pdb=" N LEU E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 200 removed outlier: 3.584A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 removed outlier: 3.581A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 11 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 removed outlier: 3.563A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 6.446A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.835A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.567A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.546A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.628A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.787A pdb=" N ASN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.937A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.348A pdb=" N PHE G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'H' and resid 22 through 29 removed outlier: 4.010A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 51 Processing helix chain 'H' and resid 52 through 72 removed outlier: 3.968A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.872A pdb=" N ALA H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 22 removed outlier: 3.525A pdb=" N VAL I 12 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 49 removed outlier: 3.939A pdb=" N GLY I 40 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.890A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 104 removed outlier: 6.040A pdb=" N ARG I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.764A pdb=" N ASN I 73 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP I 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 removed outlier: 5.760A pdb=" N LEU J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY J 29 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY J 32 " --> pdb=" O LEU J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.675A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR J 46 " --> pdb=" O PHE J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 85 removed outlier: 3.751A pdb=" N LEU J 79 " --> pdb=" O PRO J 75 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 114 removed outlier: 3.676A pdb=" N GLU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 3.785A pdb=" N ALA J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG J 127 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET J 136 " --> pdb=" O SER J 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 4.054A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 removed outlier: 3.690A pdb=" N ALA L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.235A pdb=" N ILE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.531A pdb=" N ASP L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS L 121 " --> pdb=" O ASP L 117 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 4.848A pdb=" N ARG M 107 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 108' Processing helix chain 'M' and resid 111 through 118 removed outlier: 3.508A pdb=" N VAL M 115 " --> pdb=" O PHE M 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 Processing helix chain 'N' and resid 68 through 75 removed outlier: 4.467A pdb=" N MET N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 68 through 75' Processing helix chain 'N' and resid 78 through 83 removed outlier: 3.696A pdb=" N LEU N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA N 83 " --> pdb=" O THR N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 83' Processing helix chain 'N' and resid 91 through 99 removed outlier: 3.660A pdb=" N ALA N 98 " --> pdb=" O THR N 94 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 139 removed outlier: 3.570A pdb=" N ALA N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY N 139 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 6.063A pdb=" N ILE O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.765A pdb=" N ARG O 115 " --> pdb=" O GLU O 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU O 116 " --> pdb=" O GLU O 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA O 123 " --> pdb=" O ALA O 119 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 13 through 32 removed outlier: 3.579A pdb=" N GLN P 22 " --> pdb=" O LYS P 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU P 30 " --> pdb=" O VAL P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 57 removed outlier: 3.728A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) Proline residue: P 50 - end of helix removed outlier: 3.786A pdb=" N LYS P 56 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 removed outlier: 3.596A pdb=" N ARG P 71 " --> pdb=" O PHE P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 88 removed outlier: 4.403A pdb=" N PHE P 80 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN P 81 " --> pdb=" O GLY P 77 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS P 85 " --> pdb=" O ASN P 81 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P 88 " --> pdb=" O GLY P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 23 removed outlier: 3.941A pdb=" N ARG Q 13 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG Q 20 " --> pdb=" O ARG Q 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 85 removed outlier: 3.745A pdb=" N LYS Q 72 " --> pdb=" O ASP Q 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA Q 78 " --> pdb=" O GLY Q 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU Q 79 " --> pdb=" O GLN Q 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA Q 83 " --> pdb=" O GLU Q 79 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 113 removed outlier: 3.581A pdb=" N GLU Q 111 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 removed outlier: 4.182A pdb=" N GLN R 7 " --> pdb=" O ASN R 3 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN R 8 " --> pdb=" O LYS R 4 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN R 13 " --> pdb=" O ILE R 9 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET R 14 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 105 removed outlier: 4.807A pdb=" N ARG R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 105' Processing helix chain 'S' and resid 6 through 22 removed outlier: 3.518A pdb=" N ARG S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG S 12 " --> pdb=" O VAL S 8 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 3.833A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.741A pdb=" N GLN S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 4.223A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN S 72 " --> pdb=" O GLY S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 removed outlier: 3.775A pdb=" N ALA S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 101 removed outlier: 3.614A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 117 removed outlier: 3.554A pdb=" N ALA S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 25 removed outlier: 3.846A pdb=" N LEU U 19 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.991A pdb=" N ASN U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER U 39 " --> pdb=" O LEU U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.927A pdb=" N GLU U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS U 49 " --> pdb=" O GLU U 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL U 50 " --> pdb=" O ILE U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.767A pdb=" N LEU U 69 " --> pdb=" O ASP U 65 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LYS U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 2 through 9 removed outlier: 4.004A pdb=" N VAL V 6 " --> pdb=" O ASN V 2 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE V 7 " --> pdb=" O GLN V 3 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS V 8 " --> pdb=" O GLU V 4 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL V 9 " --> pdb=" O ARG V 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 2 through 9' Processing helix chain 'V' and resid 16 through 26 removed outlier: 3.504A pdb=" N ASP V 24 " --> pdb=" O THR V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 50 Processing helix chain 'X' and resid 15 through 25 Processing helix chain 'X' and resid 46 through 55 removed outlier: 3.523A pdb=" N LYS X 52 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 122 Processing helix chain 'X' and resid 173 through 179 removed outlier: 5.140A pdb=" N ALA X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY X 179 " --> pdb=" O GLN X 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 63 removed outlier: 3.581A pdb=" N ARG Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 75 Processing helix chain '1' and resid 2 through 10 removed outlier: 3.691A pdb=" N LEU 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER 1 10 " --> pdb=" O LEU 1 6 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 2 through 10' Processing helix chain '1' and resid 11 through 35 removed outlier: 3.592A pdb=" N ASN 1 15 " --> pdb=" O VAL 1 11 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN 1 17 " --> pdb=" O GLN 1 13 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU 1 18 " --> pdb=" O LEU 1 14 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU 1 19 " --> pdb=" O ASN 1 15 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 61 removed outlier: 3.557A pdb=" N LYS 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN 1 60 " --> pdb=" O VAL 1 56 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.728A pdb=" N LEU 2 26 " --> pdb=" O CYS 2 22 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY 2 27 " --> pdb=" O VAL 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.617A pdb=" N MET 2 46 " --> pdb=" O GLU 2 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA 2 50 " --> pdb=" O MET 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 46 removed outlier: 3.557A pdb=" N THR 3 45 " --> pdb=" O HIS 3 41 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 3.537A pdb=" N ARG 4 17 " --> pdb=" O ARG 4 13 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 4 18 " --> pdb=" O ASP 4 14 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS 4 19 " --> pdb=" O MET 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 removed outlier: 3.512A pdb=" N VAL 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 25 removed outlier: 3.671A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 removed outlier: 3.527A pdb=" N VAL 6 30 " --> pdb=" O ASN 6 26 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 3.601A pdb=" N LYS 7 12 " --> pdb=" O SER 7 8 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 36 removed outlier: 4.760A pdb=" N MET 7 35 " --> pdb=" O ILE 7 31 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N THR 7 36 " --> pdb=" O LEU 7 32 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 31 through 36' Processing helix chain '7' and resid 37 through 45 removed outlier: 3.509A pdb=" N LEU 7 43 " --> pdb=" O ARG 7 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG 7 44 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY 7 45 " --> pdb=" O ARG 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 50 through 62 removed outlier: 5.148A pdb=" N ALA 7 55 " --> pdb=" O LYS 7 51 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG 7 56 " --> pdb=" O SER 7 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 7 60 " --> pdb=" O ARG 7 56 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.730A pdb=" N GLY b 185 " --> pdb=" O TYR b 198 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.862A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR c 70 " --> pdb=" O GLU c 104 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.959A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 140 through 144 Processing sheet with id= 5, first strand: chain 'e' and resid 18 through 25 Processing sheet with id= 6, first strand: chain 'e' and resid 85 through 89 removed outlier: 3.895A pdb=" N GLN e 98 " --> pdb=" O LEU e 125 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU e 125 " --> pdb=" O GLN e 98 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.773A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.981A pdb=" N LEU g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.691A pdb=" N THR h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN h 58 " --> pdb=" O SER h 52 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP h 48 " --> pdb=" O GLU h 62 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.799A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE h 103 " --> pdb=" O LEU h 126 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'i' and resid 5 through 11 removed outlier: 4.618A pdb=" N LYS i 60 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS i 27 " --> pdb=" O PHE i 61 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE i 63 " --> pdb=" O LYS i 27 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.367A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 14, first strand: chain 'k' and resid 29 through 36 removed outlier: 4.038A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL k 84 " --> pdb=" O ALA k 108 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.249A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.669A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'p' and resid 4 through 10 removed outlier: 6.623A pdb=" N TYR p 17 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE p 38 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU p 19 " --> pdb=" O ILE p 36 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'q' and resid 10 through 14 Processing sheet with id= 19, first strand: chain 'q' and resid 22 through 34 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 's' and resid 30 through 34 removed outlier: 4.042A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'x' and resid 380 through 386 removed outlier: 7.533A pdb=" N GLY x 380 " --> pdb=" O ASP x 395 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR x 386 " --> pdb=" O GLY x 389 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR x 392 " --> pdb=" O PRO x 343 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL x 347 " --> pdb=" O LEU x 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE x 415 " --> pdb=" O VAL x 344 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'x' and resid 576 through 580 removed outlier: 6.671A pdb=" N THR x 534 " --> pdb=" O VAL x 521 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL x 519 " --> pdb=" O LEU x 536 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY x 516 " --> pdb=" O VAL x 594 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL x 594 " --> pdb=" O GLY x 516 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP x 590 " --> pdb=" O VAL x 520 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'x' and resid 667 through 672 removed outlier: 6.512A pdb=" N GLN x 668 " --> pdb=" O LYS x 638 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE x 642 " --> pdb=" O ARG x 670 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU x 644 " --> pdb=" O VAL x 672 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY x 673 " --> pdb=" O ILE x 642 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU x 644 " --> pdb=" O GLY x 673 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'x' and resid 715 through 718 removed outlier: 4.430A pdb=" N ARG x 717 " --> pdb=" O LEU x 694 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'x' and resid 747 through 751 removed outlier: 3.590A pdb=" N GLY x 747 " --> pdb=" O VAL x 830 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL x 751 " --> pdb=" O ASP x 826 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP x 826 " --> pdb=" O VAL x 751 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE x 789 " --> pdb=" O VAL x 781 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'x' and resid 763 through 767 Processing sheet with id= 27, first strand: chain 'x' and resid 641 through 645 Processing sheet with id= 28, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 29, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.778A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.150A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.344A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.986A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY D 199 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP D 200 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.780A pdb=" N GLU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR D 46 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP D 94 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 179 through 182 Processing sheet with id= 35, first strand: chain 'D' and resid 25 through 30 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'D' and resid 48 through 52 Processing sheet with id= 37, first strand: chain 'D' and resid 105 through 108 removed outlier: 5.384A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.335A pdb=" N MET E 1 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 3 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 5 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLN E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 41 through 46 removed outlier: 7.496A pdb=" N GLY E 41 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N SER E 90 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA E 86 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.886A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.353A pdb=" N ILE F 85 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL F 89 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.510A pdb=" N LYS G 18 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU G 34 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY G 28 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'G' and resid 42 through 46 removed outlier: 3.517A pdb=" N ARG G 51 " --> pdb=" O GLN G 45 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 82 through 89 removed outlier: 3.517A pdb=" N PHE G 83 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 46, first strand: chain 'H' and resid 16 through 21 removed outlier: 4.632A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU H 5 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 19 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET H 1 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'H' and resid 76 through 81 removed outlier: 3.767A pdb=" N VAL H 77 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 81 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR H 139 " --> pdb=" O VAL H 131 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.806A pdb=" N SER I 24 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 8 through 14 removed outlier: 4.017A pdb=" N LEU J 11 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.944A pdb=" N ASP L 19 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.538A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.318A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN M 82 " --> pdb=" O MET M 7 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY M 81 " --> pdb=" O LYS M 66 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS M 66 " --> pdb=" O GLY M 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG M 64 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= 54, first strand: chain 'M' and resid 68 through 71 removed outlier: 4.098A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'O' and resid 38 through 41 removed outlier: 3.531A pdb=" N TYR O 92 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.784A pdb=" N TYR O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU O 34 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 31 through 37 removed outlier: 7.787A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA O 128 " --> pdb=" O THR O 37 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'P' and resid 33 through 36 removed outlier: 6.539A pdb=" N MET P 110 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Q' and resid 50 through 53 removed outlier: 3.923A pdb=" N ALA Q 50 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'R' and resid 39 through 46 removed outlier: 6.598A pdb=" N THR R 26 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER R 84 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'R' and resid 50 through 53 removed outlier: 3.699A pdb=" N ALA R 50 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER R 58 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.843A pdb=" N LEU T 40 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU T 39 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 41 " --> pdb=" O LYS T 48 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'T' and resid 17 through 21 removed outlier: 4.058A pdb=" N GLU T 18 " --> pdb=" O ILE T 98 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU T 95 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR T 60 " --> pdb=" O THR T 99 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU T 31 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'T' and resid 65 through 76 removed outlier: 3.581A pdb=" N SER T 65 " --> pdb=" O GLU T 95 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN T 91 " --> pdb=" O HIS T 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS T 71 " --> pdb=" O HIS T 89 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS T 89 " --> pdb=" O LYS T 71 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG T 73 " --> pdb=" O GLN T 87 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN T 87 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE T 75 " --> pdb=" O LYS T 85 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS T 85 " --> pdb=" O ILE T 75 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 2 through 8 removed outlier: 5.080A pdb=" N SER U 100 " --> pdb=" O GLY U 79 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 28 through 33 removed outlier: 4.179A pdb=" N LYS V 80 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP V 78 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS V 63 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL V 57 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 10 through 13 removed outlier: 4.762A pdb=" N ASN W 68 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 31 through 34 removed outlier: 8.842A pdb=" N ASP W 31 " --> pdb=" O VAL W 66 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG W 43 " --> pdb=" O VAL W 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS W 60 " --> pdb=" O ILE W 41 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN W 39 " --> pdb=" O ALA W 62 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 81 through 84 removed outlier: 7.318A pdb=" N ARG W 81 " --> pdb=" O LYS W 96 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG W 93 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS W 100 " --> pdb=" O PHE W 95 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 72 through 75 removed outlier: 3.643A pdb=" N LEU X 6 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER X 42 " --> pdb=" O ARG X 11 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA X 92 " --> pdb=" O PRO X 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP X 93 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA X 79 " --> pdb=" O ASP X 93 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 125 through 130 removed outlier: 4.213A pdb=" N GLN X 158 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 132 through 138 removed outlier: 6.602A pdb=" N SER X 132 " --> pdb=" O LEU X 109 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA X 105 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Y' and resid 37 through 40 removed outlier: 3.854A pdb=" N GLN Y 40 " --> pdb=" O HIS Y 57 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N HIS Y 57 " --> pdb=" O GLN Y 40 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Y' and resid 45 through 48 removed outlier: 6.177A pdb=" N ILE Y 82 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER Y 81 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 12 through 19 removed outlier: 4.767A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG Z 45 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '2' and resid 32 through 38 removed outlier: 4.282A pdb=" N HIS 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS 2 5 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU 2 53 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '5' and resid 16 through 22 removed outlier: 7.178A pdb=" N ILE 5 44 " --> pdb=" O SER 5 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '7' and resid 21 through 24 removed outlier: 6.426A pdb=" N LEU 7 21 " --> pdb=" O LEU 7 49 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '8' and resid 24 through 27 removed outlier: 5.231A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) 1939 hydrogen bonds defined for protein. 5742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3881 hydrogen bonds 6058 hydrogen bond angles 0 basepair planarities 1536 basepair parallelities 2508 stacking parallelities Total time for adding SS restraints: 366.85 Time building geometry restraints manager: 66.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 21364 1.33 - 1.45: 67945 1.45 - 1.57: 62163 1.57 - 1.70: 9193 1.70 - 1.82: 289 Bond restraints: 160954 Sorted by residual: bond pdb=" C4 5MU A1926 " pdb=" C5 5MU A1926 " ideal model delta sigma weight residual 1.802 1.474 0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.58e+02 bond pdb=" N1 5MU A1926 " pdb=" C6 5MU A1926 " ideal model delta sigma weight residual 1.635 1.330 0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.635 1.334 0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C5 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.155 1.382 -0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 160949 not shown) Histogram of bond angle deviations from ideal: 80.57 - 92.27: 2 92.27 - 103.98: 15172 103.98 - 115.69: 121431 115.69 - 127.39: 93762 127.39 - 139.10: 9824 Bond angle restraints: 240191 Sorted by residual: angle pdb=" O4' A v 76 " pdb=" C1' A v 76 " pdb=" N9 A v 76 " ideal model delta sigma weight residual 108.20 122.02 -13.82 1.50e+00 4.44e-01 8.49e+01 angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP1 U A1095 " ideal model delta sigma weight residual 108.00 80.57 27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP2 U A1095 " ideal model delta sigma weight residual 108.00 83.93 24.07 3.00e+00 1.11e-01 6.44e+01 angle pdb=" C1' 2MA A2490 " pdb=" N9 2MA A2490 " pdb=" C8 2MA A2490 " ideal model delta sigma weight residual 106.32 126.67 -20.35 3.00e+00 1.11e-01 4.60e+01 angle pdb=" O3' U A1016 " pdb=" C3' U A1016 " pdb=" C2' U A1016 " ideal model delta sigma weight residual 113.70 123.42 -9.72 1.50e+00 4.44e-01 4.20e+01 ... (remaining 240186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 91400 35.87 - 71.75: 10063 71.75 - 107.62: 1156 107.62 - 143.50: 32 143.50 - 179.37: 37 Dihedral angle restraints: 102688 sinusoidal: 84275 harmonic: 18413 Sorted by residual: dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual -180.00 -100.61 -79.39 0 5.00e+00 4.00e-02 2.52e+02 dihedral pdb=" CA LEU T 51 " pdb=" C LEU T 51 " pdb=" N PRO T 52 " pdb=" CA PRO T 52 " ideal model delta harmonic sigma weight residual -180.00 -133.88 -46.12 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" O4' U A1913 " pdb=" C1' U A1913 " pdb=" N1 U A1913 " pdb=" C2 U A1913 " ideal model delta sinusoidal sigma weight residual 200.00 30.80 169.20 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 102685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 30594 0.390 - 0.781: 2 0.781 - 1.171: 0 1.171 - 1.561: 0 1.561 - 1.951: 1 Chirality restraints: 30597 Sorted by residual: chirality pdb=" P U A1095 " pdb=" OP1 U A1095 " pdb=" OP2 U A1095 " pdb=" O5' U A1095 " both_signs ideal model delta sigma weight residual True 2.41 0.46 1.95 2.00e-01 2.50e+01 9.52e+01 chirality pdb=" C3' U A1016 " pdb=" C4' U A1016 " pdb=" O3' U A1016 " pdb=" C2' U A1016 " both_signs ideal model delta sigma weight residual False -2.48 -1.85 -0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" C1' A v 76 " pdb=" O4' A v 76 " pdb=" C2' A v 76 " pdb=" N9 A v 76 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 30594 not shown) Planarity restraints: 13381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 521 " -0.073 2.00e-02 2.50e+03 6.18e-01 8.58e+03 pdb=" C4' 7MG a 521 " -0.443 2.00e-02 2.50e+03 pdb=" O4' 7MG a 521 " -0.613 2.00e-02 2.50e+03 pdb=" C3' 7MG a 521 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 7MG a 521 " 0.692 2.00e-02 2.50e+03 pdb=" C2' 7MG a 521 " 0.151 2.00e-02 2.50e+03 pdb=" O2' 7MG a 521 " -1.035 2.00e-02 2.50e+03 pdb=" C1' 7MG a 521 " -0.213 2.00e-02 2.50e+03 pdb=" N9 7MG a 521 " 0.939 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1510 " 0.064 2.00e-02 2.50e+03 5.95e-01 7.97e+03 pdb=" C4' 2MG a1510 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG a1510 " 0.585 2.00e-02 2.50e+03 pdb=" C3' 2MG a1510 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG a1510 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 2MG a1510 " -0.160 2.00e-02 2.50e+03 pdb=" O2' 2MG a1510 " 0.992 2.00e-02 2.50e+03 pdb=" C1' 2MG a1510 " 0.235 2.00e-02 2.50e+03 pdb=" N9 2MG a1510 " -0.907 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2056 " 0.082 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' 7MG A2056 " 0.425 2.00e-02 2.50e+03 pdb=" O4' 7MG A2056 " 0.541 2.00e-02 2.50e+03 pdb=" C3' 7MG A2056 " -0.600 2.00e-02 2.50e+03 pdb=" O3' 7MG A2056 " -0.662 2.00e-02 2.50e+03 pdb=" C2' 7MG A2056 " -0.153 2.00e-02 2.50e+03 pdb=" O2' 7MG A2056 " 1.019 2.00e-02 2.50e+03 pdb=" C1' 7MG A2056 " 0.230 2.00e-02 2.50e+03 pdb=" N9 7MG A2056 " -0.883 2.00e-02 2.50e+03 ... (remaining 13378 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 1078 2.50 - 3.10: 95334 3.10 - 3.70: 259769 3.70 - 4.30: 412672 4.30 - 4.90: 563788 Nonbonded interactions: 1332641 Sorted by model distance: nonbonded pdb=" N1 A A2601 " pdb="MG MG A3393 " model vdw 1.895 2.250 nonbonded pdb=" N1 A A2808 " pdb="MG MG A3421 " model vdw 1.895 2.250 nonbonded pdb=" N7 A A2564 " pdb="MG MG A3394 " model vdw 1.895 2.250 nonbonded pdb=" N7 G a 245 " pdb="MG MG a3113 " model vdw 1.896 2.250 nonbonded pdb=" OP2 C A2598 " pdb="MG MG A3100 " model vdw 1.932 2.170 ... (remaining 1332636 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.090 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: 0.160 Extract box with map and model: 32.110 Check model and map are aligned: 1.790 Set scattering table: 1.130 Process input model: 702.140 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 763.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 0.328 160954 Z= 0.412 Angle : 0.702 27.434 240191 Z= 0.362 Chirality : 0.044 1.951 30597 Planarity : 0.019 0.618 13381 Dihedral : 22.661 179.371 90844 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.00 % Favored : 91.59 % Rotamer: Outliers : 0.20 % Allowed : 0.24 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: -1.70 (0.10), residues: 6377 helix: -0.48 (0.12), residues: 1972 sheet: -0.47 (0.15), residues: 1218 loop : -1.82 (0.10), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP b 23 HIS 0.013 0.001 HIS P 16 PHE 0.021 0.002 PHE f 8 TYR 0.036 0.002 TYR b 213 ARG 0.008 0.001 ARG P 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1324 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 142 GLU cc_start: 0.7734 (tt0) cc_final: 0.7458 (tt0) REVERT: e 131 SER cc_start: 0.9031 (p) cc_final: 0.8768 (p) REVERT: h 12 THR cc_start: 0.8977 (m) cc_final: 0.8754 (m) REVERT: l 59 ASN cc_start: 0.7921 (m110) cc_final: 0.7705 (m110) REVERT: q 17 SER cc_start: 0.9048 (t) cc_final: 0.8840 (t) REVERT: s 21 VAL cc_start: 0.8254 (t) cc_final: 0.7902 (t) REVERT: t 21 ASN cc_start: 0.8791 (m110) cc_final: 0.8589 (m-40) REVERT: x 609 GLN cc_start: 0.7675 (mm110) cc_final: 0.7337 (mm110) REVERT: G 147 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: U 6 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8367 (ttpt) REVERT: U 70 LYS cc_start: 0.8406 (pttp) cc_final: 0.8163 (pttt) REVERT: X 93 ASP cc_start: 0.7843 (p0) cc_final: 0.7558 (p0) REVERT: Z 3 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8634 (mtt90) outliers start: 10 outliers final: 8 residues processed: 1329 average time/residue: 2.2550 time to fit residues: 4240.4377 Evaluate side-chains 1082 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1072 time to evaluate : 6.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 66 ILE Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain u residue 35 ARG Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain Z residue 3 ARG Chi-restraints excluded: chain 2 residue 5 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 916 optimal weight: 4.9990 chunk 822 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 280 optimal weight: 0.7980 chunk 554 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 850 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 chunk 517 optimal weight: 6.9990 chunk 632 optimal weight: 5.9990 chunk 985 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 ASN b 42 ASN b 215 ASN c 44 GLN ** c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 118 GLN d 89 ASN e 71 ASN e 122 GLN e 136 ASN e 147 ASN e 149 GLN f 77 ASN h 58 GLN h 85 GLN i 75 GLN i 126 GLN j 58 ASN k 81 ASN l 5 ASN l 6 GLN l 29 GLN l 72 HIS l 77 HIS n 45 GLN n 71 HIS o 37 ASN o 40 GLN o 46 ASN o 61 ASN p 18 HIS q 55 GLN s 53 ASN t 68 HIS x 502 GLN x 627 ASN x 691 ASN ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN C 261 ASN D 33 ASN D 50 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 136 ASN D 185 ASN E 172 GLN F 52 ASN F 127 ASN G 22 GLN G 139 GLN G 143 GLN L 23 GLN L 58 ASN N 58 HIS N 99 ASN N 104 HIS N 106 GLN O 96 GLN R 7 GLN R 30 GLN R 76 GLN W 103 GLN X 7 ASN 1 17 GLN 1 39 GLN 1 58 ASN 2 18 ASN 3 6 HIS 6 26 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 160954 Z= 0.201 Angle : 0.640 27.202 240191 Z= 0.347 Chirality : 0.039 1.971 30597 Planarity : 0.006 0.130 13381 Dihedral : 23.084 179.593 78880 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.85 % Favored : 92.74 % Rotamer: Outliers : 2.84 % Allowed : 15.05 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.10), residues: 6377 helix: 0.36 (0.12), residues: 2013 sheet: -0.43 (0.15), residues: 1222 loop : -1.77 (0.10), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 23 HIS 0.007 0.001 HIS P 16 PHE 0.036 0.001 PHE F 114 TYR 0.020 0.001 TYR i 7 ARG 0.008 0.000 ARG c 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1109 time to evaluate : 6.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 142 MET cc_start: 0.7622 (tpt) cc_final: 0.6406 (tpt) REVERT: d 177 LYS cc_start: 0.7369 (ptpp) cc_final: 0.7144 (tptt) REVERT: e 131 SER cc_start: 0.9011 (p) cc_final: 0.8754 (p) REVERT: e 148 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7770 (mmm) REVERT: f 56 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8625 (mptp) REVERT: f 77 ASN cc_start: 0.8196 (m-40) cc_final: 0.7544 (m110) REVERT: g 60 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: g 90 GLU cc_start: 0.7533 (pp20) cc_final: 0.7313 (pp20) REVERT: h 12 THR cc_start: 0.8969 (m) cc_final: 0.8725 (m) REVERT: l 9 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7397 (ttm110) REVERT: l 59 ASN cc_start: 0.7892 (m110) cc_final: 0.7665 (m110) REVERT: q 43 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8455 (mmm160) REVERT: q 63 THR cc_start: 0.8612 (p) cc_final: 0.8354 (t) REVERT: t 17 ARG cc_start: 0.8391 (mtt-85) cc_final: 0.7681 (mtt-85) REVERT: t 21 ASN cc_start: 0.8786 (m110) cc_final: 0.8504 (m-40) REVERT: t 33 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8231 (mmtm) REVERT: x 609 GLN cc_start: 0.7606 (mm110) cc_final: 0.7321 (mm110) REVERT: x 772 MET cc_start: 0.7034 (tmt) cc_final: 0.6697 (tmm) REVERT: E 92 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: L 90 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: M 97 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7798 (mtp180) REVERT: N 132 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7263 (ttp-170) REVERT: R 10 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6984 (pt0) REVERT: U 6 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8227 (ttpt) REVERT: U 70 LYS cc_start: 0.8377 (pttp) cc_final: 0.8141 (pttt) REVERT: X 93 ASP cc_start: 0.7715 (p0) cc_final: 0.7451 (p0) REVERT: Z 3 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7838 (mtt180) outliers start: 143 outliers final: 62 residues processed: 1159 average time/residue: 2.1828 time to fit residues: 3632.1235 Evaluate side-chains 1106 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1035 time to evaluate : 6.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 65 GLU Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 29 GLU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 35 ARG Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain N residue 132 ARG Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain Z residue 3 ARG Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 43 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 547 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 820 optimal weight: 7.9990 chunk 670 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 987 optimal weight: 2.9990 chunk 1066 optimal weight: 0.2980 chunk 879 optimal weight: 0.9990 chunk 978 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 chunk 791 optimal weight: 0.0270 overall best weight: 2.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 44 GLN c 89 GLN d 89 ASN f 37 HIS i 75 GLN l 29 GLN m 76 ASN m 105 ASN q 55 GLN s 53 ASN x 502 GLN x 691 ASN ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 172 GLN F 52 ASN I 103 GLN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN N 106 GLN R 30 GLN S 44 GLN W 99 GLN X 7 ASN 1 36 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 160954 Z= 0.179 Angle : 0.611 27.169 240191 Z= 0.332 Chirality : 0.037 1.970 30597 Planarity : 0.006 0.130 13381 Dihedral : 22.994 179.813 78866 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.81 % Favored : 92.80 % Rotamer: Outliers : 3.77 % Allowed : 18.57 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.10), residues: 6377 helix: 0.84 (0.12), residues: 1996 sheet: -0.39 (0.15), residues: 1210 loop : -1.73 (0.10), residues: 3171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 170 HIS 0.006 0.001 HIS P 16 PHE 0.029 0.001 PHE F 114 TYR 0.022 0.001 TYR i 7 ARG 0.009 0.000 ARG i 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1081 time to evaluate : 6.859 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: e 69 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7994 (mtp180) REVERT: e 131 SER cc_start: 0.9010 (p) cc_final: 0.8769 (p) REVERT: e 148 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7767 (mmm) REVERT: f 56 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8585 (mptp) REVERT: f 77 ASN cc_start: 0.8023 (m-40) cc_final: 0.7670 (m110) REVERT: g 60 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: g 90 GLU cc_start: 0.7596 (pp20) cc_final: 0.7393 (pp20) REVERT: g 139 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7113 (mm-30) REVERT: h 3 MET cc_start: 0.6949 (tpp) cc_final: 0.6687 (tpt) REVERT: h 12 THR cc_start: 0.8937 (m) cc_final: 0.8665 (m) REVERT: h 21 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: l 9 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7366 (ttm110) REVERT: l 59 ASN cc_start: 0.7811 (m110) cc_final: 0.7592 (m110) REVERT: m 105 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7679 (t160) REVERT: q 63 THR cc_start: 0.8576 (p) cc_final: 0.8349 (t) REVERT: s 37 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7885 (ptm160) REVERT: t 21 ASN cc_start: 0.8801 (m110) cc_final: 0.8490 (m-40) REVERT: t 33 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8178 (mmtm) REVERT: x 344 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7577 (p) REVERT: x 772 MET cc_start: 0.7015 (tmt) cc_final: 0.6690 (tmm) REVERT: D 106 MET cc_start: 0.8407 (mmt) cc_final: 0.8034 (mmp) REVERT: E 92 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: F 118 ASN cc_start: 0.7618 (p0) cc_final: 0.7240 (p0) REVERT: L 90 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: O 116 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: R 10 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6952 (pt0) REVERT: U 6 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8243 (ttpt) REVERT: X 38 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7864 (mttp) REVERT: X 153 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8025 (mtpm) outliers start: 190 outliers final: 86 residues processed: 1160 average time/residue: 2.1854 time to fit residues: 3653.1084 Evaluate side-chains 1124 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1024 time to evaluate : 6.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 21 GLU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 92 GLU Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 105 ASN Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 29 GLU Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 35 ARG Chi-restraints excluded: chain x residue 344 VAL Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 38 LYS Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 43 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 975 optimal weight: 5.9990 chunk 742 optimal weight: 0.2980 chunk 512 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 471 optimal weight: 10.0000 chunk 662 optimal weight: 10.0000 chunk 990 optimal weight: 8.9990 chunk 1048 optimal weight: 8.9990 chunk 517 optimal weight: 10.0000 chunk 938 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN d 131 ASN ** d 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN ** i 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN x 399 HIS x 502 GLN x 627 ASN x 691 ASN ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 172 GLN F 52 ASN G 81 GLN I 103 GLN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN R 15 ASN R 30 GLN X 7 ASN 1 36 GLN 1 58 ASN 3 6 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 160954 Z= 0.436 Angle : 0.761 27.580 240191 Z= 0.401 Chirality : 0.046 1.943 30597 Planarity : 0.007 0.143 13381 Dihedral : 23.042 179.777 78858 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.00 % Favored : 91.59 % Rotamer: Outliers : 5.30 % Allowed : 20.60 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.10), residues: 6377 helix: 0.56 (0.12), residues: 2013 sheet: -0.46 (0.15), residues: 1218 loop : -1.89 (0.10), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 23 HIS 0.013 0.001 HIS x 383 PHE 0.027 0.002 PHE F 114 TYR 0.018 0.002 TYR L 53 ARG 0.013 0.001 ARG c 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1063 time to evaluate : 6.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 144 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6897 (pp) REVERT: e 69 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7978 (mtp180) REVERT: f 56 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8588 (mptp) REVERT: f 101 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: g 60 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: g 90 GLU cc_start: 0.7596 (pp20) cc_final: 0.7393 (pp20) REVERT: g 101 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7418 (mtt) REVERT: h 12 THR cc_start: 0.8951 (m) cc_final: 0.8707 (m) REVERT: l 86 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7144 (tpp-160) REVERT: q 51 ASP cc_start: 0.7318 (t0) cc_final: 0.6834 (p0) REVERT: q 68 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7167 (ptm160) REVERT: s 37 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8018 (ptm160) REVERT: s 81 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7406 (mtt180) REVERT: t 21 ASN cc_start: 0.8843 (m110) cc_final: 0.8596 (m110) REVERT: t 33 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8284 (mmtm) REVERT: u 35 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8215 (mtt-85) REVERT: x 609 GLN cc_start: 0.6853 (mm110) cc_final: 0.6613 (mm110) REVERT: x 736 MET cc_start: 0.7678 (pmm) cc_final: 0.7082 (pmm) REVERT: E 92 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: J 121 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7564 (p0) REVERT: L 31 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: L 90 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: O 116 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: R 10 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7003 (pt0) REVERT: R 85 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8740 (tp) REVERT: S 112 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8105 (tmtt) REVERT: U 6 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8262 (ttpt) REVERT: V 26 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7605 (ptpt) REVERT: W 78 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8268 (ptmm) REVERT: X 41 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: X 153 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8044 (mtpm) REVERT: Y 72 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8124 (ptpt) outliers start: 267 outliers final: 143 residues processed: 1177 average time/residue: 2.1579 time to fit residues: 3668.9759 Evaluate side-chains 1190 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1024 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 76 GLU Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 71 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 29 GLU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain q residue 68 ARG Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 78 ARG Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 35 ARG Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 716 MET Chi-restraints excluded: chain x residue 787 VAL Chi-restraints excluded: chain x residue 793 LEU Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 112 LYS Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 26 LYS Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 38 LYS Chi-restraints excluded: chain X residue 41 GLN Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 873 optimal weight: 0.8980 chunk 595 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 780 optimal weight: 3.9990 chunk 432 optimal weight: 0.8980 chunk 894 optimal weight: 4.9990 chunk 724 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 535 optimal weight: 6.9990 chunk 941 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 118 GLN d 54 GLN d 89 ASN d 196 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN n 43 ASN q 54 ASN s 53 ASN x 627 ASN x 691 ASN ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 136 ASN E 28 HIS E 172 GLN F 52 ASN G 81 GLN I 103 GLN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN R 30 GLN 1 36 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 160954 Z= 0.185 Angle : 0.628 27.194 240191 Z= 0.341 Chirality : 0.038 1.975 30597 Planarity : 0.006 0.129 13381 Dihedral : 22.976 179.663 78858 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.62 % Favored : 92.99 % Rotamer: Outliers : 4.59 % Allowed : 22.94 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.10), residues: 6377 helix: 0.87 (0.12), residues: 2002 sheet: -0.45 (0.15), residues: 1214 loop : -1.78 (0.10), residues: 3161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.006 0.001 HIS D 164 PHE 0.026 0.001 PHE F 114 TYR 0.020 0.001 TYR x 361 ARG 0.014 0.000 ARG x 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1066 time to evaluate : 6.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 144 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6980 (pp) REVERT: e 69 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7809 (mtp180) REVERT: e 148 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7743 (mmm) REVERT: f 56 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8584 (mptp) REVERT: g 60 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: g 139 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7115 (mm-30) REVERT: h 3 MET cc_start: 0.6949 (tpp) cc_final: 0.6561 (tpt) REVERT: h 12 THR cc_start: 0.8932 (m) cc_final: 0.8650 (m) REVERT: i 129 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7398 (ptpt) REVERT: l 9 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7360 (ttm110) REVERT: l 86 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7121 (tpp-160) REVERT: q 63 THR cc_start: 0.8642 (p) cc_final: 0.8359 (t) REVERT: q 68 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7264 (ptm160) REVERT: r 26 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8304 (mp) REVERT: s 37 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7853 (ptm160) REVERT: s 81 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7442 (mtt180) REVERT: t 21 ASN cc_start: 0.8779 (m110) cc_final: 0.8484 (m110) REVERT: t 33 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (mmtm) REVERT: u 35 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8227 (mtt-85) REVERT: x 772 MET cc_start: 0.6931 (tmt) cc_final: 0.6614 (tmm) REVERT: D 1 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.4853 (tpt) REVERT: D 106 MET cc_start: 0.8392 (mmt) cc_final: 0.8099 (mmp) REVERT: F 114 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.5589 (p90) REVERT: J 17 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6423 (pp30) REVERT: J 121 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7345 (p0) REVERT: L 31 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6351 (mm-30) REVERT: O 116 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: O 127 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8800 (pp) REVERT: R 10 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6933 (pt0) REVERT: R 45 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: S 112 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8095 (tmtt) REVERT: U 6 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8202 (ttpt) REVERT: W 78 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8260 (ptmm) REVERT: X 153 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7987 (mtpm) REVERT: Y 72 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7970 (ptpt) REVERT: 2 10 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8161 (mtmm) outliers start: 231 outliers final: 119 residues processed: 1174 average time/residue: 2.1571 time to fit residues: 3668.5064 Evaluate side-chains 1163 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1019 time to evaluate : 6.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 204 TYR Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 89 GLU Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 129 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain q residue 68 ARG Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 35 ARG Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 112 LYS Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 352 optimal weight: 10.0000 chunk 944 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 615 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 1049 optimal weight: 9.9990 chunk 871 optimal weight: 3.9990 chunk 486 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 1.9990 chunk 551 optimal weight: 10.0000 overall best weight: 5.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 118 GLN d 89 ASN d 196 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN ** i 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 54 ASN s 53 ASN x 609 GLN x 691 ASN ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 172 GLN F 52 ASN G 81 GLN I 103 GLN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN R 30 GLN 1 36 GLN 3 33 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 160954 Z= 0.358 Angle : 0.712 27.430 240191 Z= 0.379 Chirality : 0.043 1.952 30597 Planarity : 0.007 0.139 13381 Dihedral : 22.989 178.924 78858 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.75 % Favored : 91.85 % Rotamer: Outliers : 5.54 % Allowed : 23.36 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % 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: -1.11 (0.10), residues: 6377 helix: 0.74 (0.12), residues: 2006 sheet: -0.49 (0.15), residues: 1215 loop : -1.86 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.009 0.001 HIS x 383 PHE 0.025 0.002 PHE F 114 TYR 0.024 0.002 TYR x 361 ARG 0.017 0.001 ARG c 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1313 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1034 time to evaluate : 6.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 THR cc_start: 0.8735 (t) cc_final: 0.8461 (p) REVERT: c 144 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7159 (pp) REVERT: e 69 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7868 (mtp180) REVERT: e 98 GLN cc_start: 0.8893 (pt0) cc_final: 0.8646 (pt0) REVERT: f 2 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8304 (mtt180) REVERT: f 56 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8590 (mptp) REVERT: g 60 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: h 12 THR cc_start: 0.8930 (m) cc_final: 0.8653 (m) REVERT: l 86 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7147 (tpp-160) REVERT: q 68 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7118 (ptm160) REVERT: r 26 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8306 (mp) REVERT: s 37 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7835 (ptm160) REVERT: s 81 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7407 (mtt180) REVERT: t 21 ASN cc_start: 0.8833 (m110) cc_final: 0.8558 (m110) REVERT: t 33 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: D 130 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: F 114 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.5811 (p90) REVERT: J 17 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6361 (pp30) REVERT: J 121 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7408 (p0) REVERT: L 31 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6407 (mm-30) REVERT: L 90 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: O 116 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: O 127 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8797 (pp) REVERT: R 10 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7005 (pt0) REVERT: R 85 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8728 (tp) REVERT: U 6 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8247 (ttpt) REVERT: V 26 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7592 (ptpt) REVERT: W 78 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8272 (ptmm) REVERT: X 86 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7924 (mmpt) REVERT: X 153 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7997 (mtpm) REVERT: 2 10 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8214 (mtmm) REVERT: 2 44 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7253 (mmt180) outliers start: 279 outliers final: 157 residues processed: 1175 average time/residue: 2.1718 time to fit residues: 3705.2156 Evaluate side-chains 1210 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1027 time to evaluate : 7.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 54 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain q residue 68 ARG Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 403 THR Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain x residue 430 THR Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 496 LEU Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 716 MET Chi-restraints excluded: chain x residue 793 LEU Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 5 LYS Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 112 LYS Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 26 LYS Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 141 LYS Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 151 MET Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 2 residue 44 ARG Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 1012 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 598 optimal weight: 8.9990 chunk 766 optimal weight: 0.9990 chunk 593 optimal weight: 10.0000 chunk 883 optimal weight: 4.9990 chunk 586 optimal weight: 10.0000 chunk 1045 optimal weight: 4.9990 chunk 654 optimal weight: 10.0000 chunk 637 optimal weight: 7.9990 chunk 482 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 118 GLN d 89 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN ** i 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 GLN ** q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 53 ASN x 609 GLN x 627 ASN x 691 ASN ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN F 52 ASN G 81 GLN I 103 GLN L 23 GLN R 30 GLN 1 36 GLN 3 6 HIS 3 33 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 160954 Z= 0.337 Angle : 0.705 27.395 240191 Z= 0.376 Chirality : 0.043 1.957 30597 Planarity : 0.007 0.137 13381 Dihedral : 22.993 179.093 78854 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.42 % Favored : 92.14 % Rotamer: Outliers : 5.50 % Allowed : 24.09 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.10), residues: 6377 helix: 0.68 (0.12), residues: 2018 sheet: -0.51 (0.15), residues: 1226 loop : -1.86 (0.10), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 201 HIS 0.009 0.001 HIS x 383 PHE 0.023 0.002 PHE F 114 TYR 0.025 0.002 TYR x 361 ARG 0.011 0.001 ARG f 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1042 time to evaluate : 6.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 THR cc_start: 0.8750 (t) cc_final: 0.8492 (p) REVERT: c 144 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6999 (pp) REVERT: e 69 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: f 56 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8584 (mptp) REVERT: f 101 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: g 60 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: h 3 MET cc_start: 0.7072 (tpp) cc_final: 0.6655 (tpt) REVERT: h 12 THR cc_start: 0.8928 (m) cc_final: 0.8645 (m) REVERT: i 129 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7578 (ptpt) REVERT: l 77 HIS cc_start: 0.8757 (m90) cc_final: 0.8527 (m90) REVERT: l 86 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7203 (tpp-160) REVERT: r 26 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8292 (mp) REVERT: s 37 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7831 (ptm160) REVERT: s 81 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7392 (mtt180) REVERT: t 21 ASN cc_start: 0.8816 (m110) cc_final: 0.8537 (m110) REVERT: t 33 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8210 (mmtm) REVERT: x 736 MET cc_start: 0.8013 (pmm) cc_final: 0.7807 (pmm) REVERT: D 1 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.5303 (tpt) REVERT: D 130 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: F 114 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.5908 (p90) REVERT: J 17 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6405 (pp30) REVERT: J 121 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7394 (p0) REVERT: L 31 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6385 (mm-30) REVERT: L 90 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: O 116 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: O 127 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (pp) REVERT: R 10 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7001 (pt0) REVERT: R 85 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8725 (tp) REVERT: U 6 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8244 (ttpt) REVERT: V 26 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7577 (ptpt) REVERT: W 78 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8268 (ptmm) REVERT: X 46 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6788 (mm-30) REVERT: X 76 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7929 (tt) REVERT: X 86 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7911 (mmpt) REVERT: X 153 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7983 (mtpm) REVERT: 2 10 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8215 (mtmm) REVERT: 2 44 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7201 (mmt180) outliers start: 277 outliers final: 177 residues processed: 1188 average time/residue: 2.1449 time to fit residues: 3706.6935 Evaluate side-chains 1223 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1017 time to evaluate : 6.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 129 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 403 THR Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain x residue 430 THR Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 496 LEU Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 716 MET Chi-restraints excluded: chain x residue 787 VAL Chi-restraints excluded: chain x residue 793 LEU Chi-restraints excluded: chain x residue 797 ARG Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 123 LYS Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 112 LYS Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 26 LYS Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 78 LYS Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 46 GLU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 141 LYS Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 151 MET Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 2 residue 44 ARG Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 5 residue 47 GLU Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 646 optimal weight: 50.0000 chunk 417 optimal weight: 5.9990 chunk 624 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 664 optimal weight: 10.0000 chunk 712 optimal weight: 10.0000 chunk 517 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 822 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 120 GLN c 118 GLN d 89 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN ** i 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN x 609 GLN x 627 ASN ** x 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 172 GLN F 52 ASN G 81 GLN I 103 GLN L 23 GLN R 30 GLN 1 36 GLN 3 33 HIS 3 41 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.149 160954 Z= 0.458 Angle : 0.791 27.531 240191 Z= 0.415 Chirality : 0.048 1.946 30597 Planarity : 0.007 0.145 13381 Dihedral : 23.064 179.901 78854 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.33 % Favored : 91.23 % Rotamer: Outliers : 5.94 % Allowed : 24.33 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.10), residues: 6377 helix: 0.47 (0.12), residues: 2016 sheet: -0.57 (0.15), residues: 1230 loop : -1.96 (0.10), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 23 HIS 0.011 0.001 HIS x 383 PHE 0.024 0.002 PHE f 8 TYR 0.027 0.002 TYR x 361 ARG 0.013 0.001 ARG f 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1047 time to evaluate : 6.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 THR cc_start: 0.8807 (t) cc_final: 0.8544 (p) REVERT: c 144 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.6932 (pp) REVERT: e 69 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7706 (mtp180) REVERT: e 148 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7674 (mmm) REVERT: f 101 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6565 (pp20) REVERT: g 60 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: h 3 MET cc_start: 0.7188 (tpp) cc_final: 0.6824 (tpt) REVERT: h 12 THR cc_start: 0.8926 (m) cc_final: 0.8648 (m) REVERT: i 46 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6450 (tpt) REVERT: i 129 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7657 (ptpt) REVERT: l 76 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7805 (tm-30) REVERT: l 77 HIS cc_start: 0.8834 (m90) cc_final: 0.8622 (m90) REVERT: l 86 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7192 (tpp-160) REVERT: m 91 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8370 (m-70) REVERT: q 51 ASP cc_start: 0.7303 (t0) cc_final: 0.7089 (p0) REVERT: q 65 ARG cc_start: 0.8092 (ptt90) cc_final: 0.7831 (ptt90) REVERT: r 26 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8284 (mp) REVERT: s 37 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7920 (ptm160) REVERT: s 81 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7376 (mtt180) REVERT: t 21 ASN cc_start: 0.8823 (m110) cc_final: 0.8580 (m110) REVERT: t 33 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8278 (mmtm) REVERT: x 736 MET cc_start: 0.8062 (pmm) cc_final: 0.7796 (pmm) REVERT: x 737 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.5670 (tp) REVERT: C 3 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7899 (pp) REVERT: D 1 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.5476 (tpt) REVERT: D 95 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6967 (mm110) REVERT: F 114 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.5986 (p90) REVERT: G 10 LYS cc_start: 0.7466 (mppt) cc_final: 0.7166 (pmtt) REVERT: J 17 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6389 (pp30) REVERT: J 121 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7386 (p0) REVERT: L 31 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: L 90 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: N 141 LYS cc_start: 0.8453 (tppp) cc_final: 0.8165 (tttt) REVERT: O 112 GLU cc_start: 0.7274 (tp30) cc_final: 0.6141 (mm-30) REVERT: O 116 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: O 127 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8808 (pp) REVERT: R 10 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7051 (pt0) REVERT: R 85 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8754 (tp) REVERT: U 6 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8277 (ttpt) REVERT: V 26 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7627 (ptpt) REVERT: X 41 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: X 76 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7940 (tt) REVERT: X 86 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7875 (mmpt) REVERT: X 153 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (mtpm) REVERT: 2 10 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8257 (mttm) REVERT: 2 44 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7288 (mmt180) outliers start: 299 outliers final: 184 residues processed: 1206 average time/residue: 2.1012 time to fit residues: 3682.1438 Evaluate side-chains 1243 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1027 time to evaluate : 6.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 36 ASN Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 101 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 46 MET Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 129 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 109 SER Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 403 THR Chi-restraints excluded: chain x residue 420 VAL Chi-restraints excluded: chain x residue 426 VAL Chi-restraints excluded: chain x residue 430 THR Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 496 LEU Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 642 ILE Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 716 MET Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 787 VAL Chi-restraints excluded: chain x residue 797 ARG Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 31 GLU Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 112 LYS Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 26 LYS Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 41 GLN Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 151 MET Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 2 residue 44 ARG Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 32 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 47 SER Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 951 optimal weight: 0.9990 chunk 1001 optimal weight: 10.0000 chunk 914 optimal weight: 9.9990 chunk 974 optimal weight: 0.9980 chunk 586 optimal weight: 10.0000 chunk 424 optimal weight: 1.9990 chunk 765 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 880 optimal weight: 3.9990 chunk 921 optimal weight: 0.9980 chunk 971 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 118 GLN d 89 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 29 GLN n 43 ASN p 63 GLN q 54 ASN s 53 ASN x 609 GLN x 627 ASN x 691 ASN x 774 HIS C 153 GLN C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN F 52 ASN G 81 GLN L 23 GLN R 30 GLN 1 36 GLN 3 33 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.115 160954 Z= 0.146 Angle : 0.628 26.911 240191 Z= 0.340 Chirality : 0.037 1.993 30597 Planarity : 0.006 0.125 13381 Dihedral : 22.980 179.629 78854 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.24 % Favored : 93.37 % Rotamer: Outliers : 3.57 % Allowed : 26.97 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 6377 helix: 0.91 (0.12), residues: 2002 sheet: -0.41 (0.15), residues: 1224 loop : -1.77 (0.10), residues: 3151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 101 HIS 0.005 0.001 HIS X 101 PHE 0.020 0.001 PHE F 114 TYR 0.022 0.001 TYR x 361 ARG 0.016 0.000 ARG f 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1073 time to evaluate : 6.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 THR cc_start: 0.8667 (t) cc_final: 0.8431 (p) REVERT: c 144 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6982 (pp) REVERT: e 69 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7600 (mtp180) REVERT: g 60 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: g 101 MET cc_start: 0.7786 (mtt) cc_final: 0.7548 (mtm) REVERT: g 139 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7059 (mm-30) REVERT: h 3 MET cc_start: 0.6955 (tpp) cc_final: 0.6677 (tpt) REVERT: h 12 THR cc_start: 0.8885 (m) cc_final: 0.8615 (m) REVERT: i 129 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7382 (ptpt) REVERT: l 14 ARG cc_start: 0.6192 (mtp85) cc_final: 0.5771 (mtt-85) REVERT: l 76 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7684 (tm-30) REVERT: l 77 HIS cc_start: 0.8765 (m90) cc_final: 0.8540 (m90) REVERT: l 86 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7160 (tpp-160) REVERT: q 63 THR cc_start: 0.8642 (p) cc_final: 0.8385 (t) REVERT: t 17 ARG cc_start: 0.8511 (mtt-85) cc_final: 0.7878 (mtt90) REVERT: t 21 ASN cc_start: 0.8763 (m110) cc_final: 0.8423 (m-40) REVERT: x 736 MET cc_start: 0.7975 (pmm) cc_final: 0.7737 (pmm) REVERT: x 737 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.5399 (tp) REVERT: x 772 MET cc_start: 0.6914 (tmt) cc_final: 0.6579 (tmm) REVERT: C 52 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7531 (ptm-80) REVERT: D 106 MET cc_start: 0.8335 (mmt) cc_final: 0.8028 (mmp) REVERT: D 131 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: F 114 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.5963 (p90) REVERT: I 103 GLN cc_start: 0.7583 (tp40) cc_final: 0.7346 (tp40) REVERT: J 17 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6267 (pp30) REVERT: J 121 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7247 (p0) REVERT: N 141 LYS cc_start: 0.8397 (tppp) cc_final: 0.8103 (tttt) REVERT: O 116 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: R 10 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6977 (pt0) REVERT: U 6 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8212 (ttpt) REVERT: X 86 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7798 (mmpt) REVERT: X 153 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7932 (mtpm) REVERT: 2 44 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7085 (mmt180) outliers start: 180 outliers final: 108 residues processed: 1168 average time/residue: 2.1818 time to fit residues: 3699.3315 Evaluate side-chains 1159 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1036 time to evaluate : 6.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 125 GLU Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain d residue 204 TYR Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 129 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 496 LEU Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 691 ASN Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 123 LYS Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 151 MET Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain 2 residue 44 ARG Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 639 optimal weight: 10.0000 chunk 1030 optimal weight: 0.0030 chunk 628 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 716 optimal weight: 10.0000 chunk 1080 optimal weight: 0.7980 chunk 994 optimal weight: 0.9980 chunk 860 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 664 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 overall best weight: 4.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 42 ASN b 190 ASN b 215 ASN d 89 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN l 29 GLN n 49 GLN ** q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN x 502 GLN x 609 GLN ** x 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN F 52 ASN G 81 GLN L 23 GLN R 30 GLN S 14 HIS 1 36 GLN 3 6 HIS 3 33 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 160954 Z= 0.266 Angle : 0.660 59.200 240191 Z= 0.358 Chirality : 0.040 1.983 30597 Planarity : 0.006 0.126 13381 Dihedral : 22.973 179.599 78850 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.40 % Favored : 93.19 % Rotamer: Outliers : 3.22 % Allowed : 27.73 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.10), residues: 6377 helix: 0.88 (0.12), residues: 2008 sheet: -0.40 (0.15), residues: 1229 loop : -1.77 (0.10), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 101 HIS 0.008 0.001 HIS f 3 PHE 0.020 0.001 PHE F 114 TYR 0.022 0.002 TYR x 361 ARG 0.020 0.001 ARG q 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12754 Ramachandran restraints generated. 6377 Oldfield, 0 Emsley, 6377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1034 time to evaluate : 7.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 THR cc_start: 0.8677 (t) cc_final: 0.8438 (p) REVERT: c 144 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6995 (pp) REVERT: d 113 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: d 132 ILE cc_start: 0.8778 (pp) cc_final: 0.8563 (pt) REVERT: d 177 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7596 (tptp) REVERT: e 69 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7606 (mtp180) REVERT: g 60 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: g 101 MET cc_start: 0.7799 (mtt) cc_final: 0.7566 (mtm) REVERT: g 139 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7054 (mm-30) REVERT: h 3 MET cc_start: 0.6969 (tpp) cc_final: 0.6692 (tpt) REVERT: h 12 THR cc_start: 0.8898 (m) cc_final: 0.8629 (m) REVERT: i 60 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7829 (tmmt) REVERT: i 129 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7391 (ptpt) REVERT: l 14 ARG cc_start: 0.6182 (mtp85) cc_final: 0.5785 (mtt-85) REVERT: l 76 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7704 (tm-30) REVERT: l 86 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7166 (tpp-160) REVERT: q 63 THR cc_start: 0.8653 (p) cc_final: 0.8395 (t) REVERT: t 17 ARG cc_start: 0.8518 (mtt-85) cc_final: 0.7885 (mtt90) REVERT: t 21 ASN cc_start: 0.8754 (m110) cc_final: 0.8427 (m-40) REVERT: x 736 MET cc_start: 0.7979 (pmm) cc_final: 0.7752 (pmm) REVERT: x 737 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.5429 (tp) REVERT: x 772 MET cc_start: 0.6931 (tmt) cc_final: 0.6587 (tmm) REVERT: C 52 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7528 (ptm-80) REVERT: F 114 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.5971 (p90) REVERT: I 103 GLN cc_start: 0.7590 (tp40) cc_final: 0.7354 (tp40) REVERT: J 17 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6276 (pp30) REVERT: J 121 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7277 (p0) REVERT: L 31 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6497 (mm-30) REVERT: L 90 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: N 141 LYS cc_start: 0.8398 (tppp) cc_final: 0.8108 (tttt) REVERT: O 116 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: O 127 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8778 (pp) REVERT: R 10 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6984 (pt0) REVERT: U 6 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8223 (ttpt) REVERT: X 86 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7804 (mmpt) REVERT: X 153 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7937 (mtpm) REVERT: 2 10 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: 2 44 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7094 (mmt180) outliers start: 162 outliers final: 125 residues processed: 1124 average time/residue: 2.1913 time to fit residues: 3570.1651 Evaluate side-chains 1164 residues out of total 5258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1020 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 125 GLU Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 ASN Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain d residue 204 TYR Chi-restraints excluded: chain e residue 30 ARG Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 27 MET Chi-restraints excluded: chain g residue 60 GLU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 129 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 75 LEU Chi-restraints excluded: chain k residue 109 SER Chi-restraints excluded: chain l residue 29 GLN Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 348 MET Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 496 LEU Chi-restraints excluded: chain x residue 505 VAL Chi-restraints excluded: chain x residue 615 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 826 ASP Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 123 LYS Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain X residue 141 LYS Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 151 MET Chi-restraints excluded: chain X residue 153 LYS Chi-restraints excluded: chain X residue 163 SER Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 2 residue 44 ARG Chi-restraints excluded: chain 3 residue 12 ILE Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 27 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 6 residue 44 VAL Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 683 optimal weight: 10.0000 chunk 916 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 793 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 862 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 885 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 42 ASN b 190 ASN d 89 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN n 49 GLN ** q 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 53 ASN x 609 GLN C 252 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN F 52 ASN G 81 GLN L 23 GLN R 30 GLN 1 36 GLN 3 33 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099723 restraints weight = 210195.700| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 0.71 r_work: 0.3019 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.418 160954 Z= 0.294 Angle : 0.712 65.899 240191 Z= 0.400 Chirality : 0.040 1.982 30597 Planarity : 0.007 0.280 13381 Dihedral : 22.971 179.611 78850 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.43 % Favored : 93.18 % Rotamer: Outliers : 3.08 % Allowed : 27.81 % Favored : 69.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.10), residues: 6377 helix: 0.88 (0.12), residues: 2008 sheet: -0.40 (0.15), residues: 1226 loop : -1.76 (0.10), residues: 3143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 101 HIS 0.010 0.001 HIS f 11 PHE 0.020 0.001 PHE F 114 TYR 0.021 0.002 TYR x 361 ARG 0.015 0.000 ARG q 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50995.90 seconds wall clock time: 883 minutes 7.81 seconds (52987.81 seconds total)