Starting phenix.real_space_refine on Sat Mar 2 14:54:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wf0_8826/03_2024/5wf0_8826_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.008 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 K 5 8.98 5 P 4805 5.49 5 Mg 1480 5.21 5 S 171 5.16 5 C 76930 2.51 5 N 28326 2.21 5 O 42883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P GLU 8": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U ARG 21": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "4 ARG 36": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "b GLU 51": "OE1" <-> "OE2" Residue "b ARG 94": "NH1" <-> "NH2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "b PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ASP 35": "OD1" <-> "OD2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "c GLU 205": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 80": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f ARG 44": "NH1" <-> "NH2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "g ARG 2": "NH1" <-> "NH2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "h ARG 87": "NH1" <-> "NH2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ASP 112": "OD1" <-> "OD2" Residue "h ARG 113": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i ARG 84": "NH1" <-> "NH2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "k ARG 36": "NH1" <-> "NH2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k GLU 82": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "l ARG 35": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 61": "OE1" <-> "OE2" Residue "l GLU 69": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 70": "NH1" <-> "NH2" Residue "m ARG 89": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 90": "NH1" <-> "NH2" Residue "o ASP 20": "OD1" <-> "OD2" Residue "o GLU 82": "OE1" <-> "OE2" Residue "o ARG 83": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 25": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p GLU 77": "OE1" <-> "OE2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q GLU 51": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 72": "OE1" <-> "OE2" Residue "u GLU 7": "OE1" <-> "OE2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u GLU 38": "OE1" <-> "OE2" Residue "u GLU 62": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z ARG 123": "NH1" <-> "NH2" Residue "z GLU 147": "OE1" <-> "OE2" Residue "z GLU 152": "OE1" <-> "OE2" Residue "z ARG 154": "NH1" <-> "NH2" Residue "z ARG 171": "NH1" <-> "NH2" Residue "z GLU 179": "OE1" <-> "OE2" Residue "z GLU 183": "OE1" <-> "OE2" Residue "z ARG 223": "NH1" <-> "NH2" Residue "z ARG 233": "NH1" <-> "NH2" Residue "z GLU 240": "OE1" <-> "OE2" Residue "z GLU 249": "OE1" <-> "OE2" Residue "z GLU 267": "OE1" <-> "OE2" Residue "z ARG 269": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z GLU 285": "OE1" <-> "OE2" Residue "z ARG 288": "NH1" <-> "NH2" Residue "z GLU 307": "OE1" <-> "OE2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z GLU 342": "OE1" <-> "OE2" Residue "z GLU 345": "OE1" <-> "OE2" Residue "z ARG 373": "NH1" <-> "NH2" Residue "z ARG 377": "NH1" <-> "NH2" Residue "z ARG 381": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154600 Number of models: 1 Model: "" Number of chains: 110 Chain: "A" Number of atoms: 62277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62277 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 250, 'rna2p_pyr': 120, 'rna3p': 17, 'rna3p_pur': 1417, 'rna3p_pyr': 1088} Link IDs: {'rna2p': 377, 'rna3p': 2522} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 59, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1557 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1544 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1120 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "S" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 739 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "W" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 33050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 2, 'rna2p_pur': 113, 'rna2p_pyr': 68, 'rna3p': 9, 'rna3p_pur': 756, 'rna3p_pyr': 592} Link IDs: {'rna2p': 183, 'rna3p': 1356} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 810 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "v" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 6, 'rna3p': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 3, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "y" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1632 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 4 Chain: "z" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3031 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain: "A" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 1015 Unusual residues: {' K': 4, ' MG': 1001} Classifications: {'peptide': 1, 'undetermined': 1005} Link IDs: {None: 1005} 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: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Unusual residues: {' MG': 34} Classifications: {'undetermined': 34} Link IDs: {None: 33} Chain: "D" 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: "E" 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: "L" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" 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: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" 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: "X" 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: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 403 Unusual residues: {' K': 1, ' MG': 402} Classifications: {'undetermined': 403} Link IDs: {None: 402} Chain: "d" 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: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" 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: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "o" 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: "t" 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: "v" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'GTP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 463 Classifications: {'water': 463} Link IDs: {None: 462} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" 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: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" 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: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 61.17, per 1000 atoms: 0.40 Number of scatterers: 154600 At special positions: 0 Unit cell: (277.34, 270.48, 240.1, 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) K 5 19.00 S 171 16.00 P 4805 15.00 Mg 1480 11.99 O 42883 8.00 N 28326 7.00 C 76930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.53 Conformation dependent library (CDL) restraints added in 8.3 seconds 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11604 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: 191 helices and 75 sheets defined 38.2% alpha, 18.8% beta 1363 base pairs and 2382 stacking pairs defined. Time for finding SS restraints: 82.80 Creating SS restraints... Processing helix chain 'C' and resid 9 through 16 removed outlier: 7.636A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.628A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.004A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.673A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.293A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.856A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.065A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 105' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.617A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.503A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.314A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.977A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.753A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 5.024A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.661A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 4.666A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.700A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 61 removed outlier: 4.690A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.728A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 4.048A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.192A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 4.382A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.851A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.655A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.639A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 29 through 34' Processing helix chain 'H' and resid 40 through 50 removed outlier: 5.329A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 4.912A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.740A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.968A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.781A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.547A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.928A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.826A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.837A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.447A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.942A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.564A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 109 through 120 removed outlier: 5.278A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.628A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.021A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.820A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 5.672A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.562A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.270A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.120A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 5.144A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.447A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.677A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.066A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.903A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.706A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.699A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.509A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.604A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.636A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.882A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.528A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.102A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 3.548A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 115 removed outlier: 4.077A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA Q 114 " --> pdb=" O GLU Q 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.761A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.648A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.900A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 11 removed outlier: 4.518A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 5 through 11' Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.864A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.860A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA 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 13 through 24 removed outlier: 3.631A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.988A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.582A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.649A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 8 removed outlier: 4.079A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.641A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 4.386A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 5.210A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.157A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.619A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.756A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.722A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 3.515A pdb=" N ALA 5 10 " --> pdb=" O GLN 5 6 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY 5 21 " --> pdb=" O GLU 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.996A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU 5 41 " --> pdb=" O LYS 5 37 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY 5 45 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 70 removed outlier: 4.162A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 59 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 73 through 79 removed outlier: 4.197A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY 5 78 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) Proline residue: 5 79 - end of helix No H-bonds generated for 'chain '5' and resid 73 through 79' Processing helix chain '5' and resid 94 through 106 removed outlier: 3.737A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.580A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 53 removed outlier: 4.354A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 5.213A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 3.610A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.118A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.544A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.522A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.930A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.529A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 153 removed outlier: 3.621A pdb=" N LYS b 151 " --> pdb=" O GLY b 148 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 4.060A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU c 11 " --> pdb=" O ASN c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.694A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.909A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.644A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.684A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.878A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.013A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.622A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 5.501A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.526A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 removed outlier: 4.076A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 3.591A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.900A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.304A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.744A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.373A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.520A pdb=" N VAL e 136 " --> pdb=" O PRO e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 157 removed outlier: 3.528A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 16 through 33 removed outlier: 4.745A pdb=" N GLY f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.515A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 6.047A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 Processing helix chain 'g' and resid 56 through 69 removed outlier: 3.729A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.992A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.569A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.844A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.751A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.598A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 removed outlier: 3.506A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 53 removed outlier: 4.603A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.668A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.206A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 98 removed outlier: 3.932A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER i 95 " --> pdb=" O GLU i 91 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.662A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.846A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.002A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.192A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 74 removed outlier: 4.597A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.654A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.024A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.714A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.604A pdb=" N LYS m 30 " --> pdb=" O LYS m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.513A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.676A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 23 removed outlier: 3.565A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.858A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.040A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.657A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 25 through 31 removed outlier: 4.140A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.017A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 3.612A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.563A pdb=" N ARG o 52 " --> pdb=" O ASP o 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 62 removed outlier: 3.505A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 80 removed outlier: 3.617A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS p 80 " --> pdb=" O LYS p 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.537A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.383A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 39 removed outlier: 4.987A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 64 Proline residue: t 55 - end of helix removed outlier: 3.787A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 85 removed outlier: 4.317A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.808A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 5.356A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 61 Proline residue: u 40 - end of helix removed outlier: 3.606A pdb=" N LYS u 45 " --> pdb=" O THR u 41 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'z' and resid 24 through 39 removed outlier: 3.845A pdb=" N THR z 28 " --> pdb=" O LYS z 24 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR z 33 " --> pdb=" O ALA z 29 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR z 38 " --> pdb=" O VAL z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 45 through 51 removed outlier: 4.151A pdb=" N ILE z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP z 50 " --> pdb=" O PHE z 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN z 51 " --> pdb=" O ASN z 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 45 through 51' Processing helix chain 'z' and resid 52 through 59 removed outlier: 4.030A pdb=" N LYS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG z 58 " --> pdb=" O GLU z 54 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY z 59 " --> pdb=" O GLU z 55 " (cutoff:3.500A) Processing helix chain 'z' and resid 88 through 99 removed outlier: 4.042A pdb=" N THR z 93 " --> pdb=" O LYS z 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP z 99 " --> pdb=" O ALA z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 112 through 126 removed outlier: 3.602A pdb=" N ARG z 116 " --> pdb=" O MET z 112 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN z 124 " --> pdb=" O LEU z 120 " (cutoff:3.500A) Processing helix chain 'z' and resid 142 through 161 removed outlier: 4.001A pdb=" N LEU z 146 " --> pdb=" O ASP z 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU z 147 " --> pdb=" O GLU z 143 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL z 149 " --> pdb=" O LEU z 145 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU z 150 " --> pdb=" O LEU z 146 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU z 152 " --> pdb=" O LEU z 148 " (cutoff:3.500A) Processing helix chain 'z' and resid 173 through 180 removed outlier: 3.552A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU z 179 " --> pdb=" O LEU z 175 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY z 180 " --> pdb=" O LYS z 176 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 198 removed outlier: 3.565A pdb=" N ILE z 188 " --> pdb=" O TRP z 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU z 191 " --> pdb=" O LYS z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 282 through 287 removed outlier: 4.014A pdb=" N ILE z 286 " --> pdb=" O LYS z 282 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU z 287 " --> pdb=" O ARG z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain 'C' and resid 72 through 77 removed outlier: 4.298A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.657A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.808A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.474A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.910A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.753A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.926A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.569A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.602A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 11, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 12, first strand: chain 'G' and resid 93 through 97 Processing sheet with id= 13, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.908A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 88 " --> pdb=" O THR G 128 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 16 through 20 removed outlier: 5.534A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.447A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 54 through 57 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.271A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.028A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.795A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.768A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.413A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.424A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= 26, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.596A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.744A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.673A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.625A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL R 63 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.584A pdb=" N ASP R 95 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.218A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.592A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.518A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.019A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 29 through 33 removed outlier: 3.775A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.665A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.893A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 25 through 28 removed outlier: 4.594A pdb=" N GLU W 25 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE W 78 " --> pdb=" O GLY W 44 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'W' and resid 47 through 50 removed outlier: 3.621A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.525A pdb=" N GLY X 14 " --> pdb=" O ARG X 26 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 42, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.198A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '0' and resid 27 through 30 removed outlier: 6.400A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '1' and resid 19 through 23 removed outlier: 7.700A pdb=" N ILE 1 47 " --> pdb=" O SER 1 13 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '3' and resid 21 through 24 removed outlier: 5.716A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '4' and resid 13 through 19 removed outlier: 8.552A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '5' and resid 24 through 28 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain '6' and resid 21 through 25 Processing sheet with id= 49, first strand: chain 'b' and resid 15 through 18 removed outlier: 4.390A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.797A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.550A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.782A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.624A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N TRP d 169 " --> pdb=" O LYS d 182 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 10 through 15 removed outlier: 4.204A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.624A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 31 through 40 removed outlier: 4.636A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.610A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.539A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 60, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.145A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.731A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.608A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.530A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'k' and resid 29 through 35 Processing sheet with id= 65, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.010A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.867A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 4 through 10 removed outlier: 6.008A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 6 through 10 removed outlier: 7.217A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 46 through 51 removed outlier: 4.834A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 64 through 70 removed outlier: 3.815A pdb=" N SER z 65 " --> pdb=" O ASP z 80 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR z 69 " --> pdb=" O TYR z 76 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'z' and resid 75 through 81 current: chain 'z' and resid 11 through 18 removed outlier: 3.932A pdb=" N GLY z 15 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL z 105 " --> pdb=" O PHE z 133 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN z 135 " --> pdb=" O VAL z 105 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'z' and resid 210 through 213 removed outlier: 6.710A pdb=" N PHE z 210 " --> pdb=" O LYS z 294 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 216 through 219 removed outlier: 3.913A pdb=" N ASP z 216 " --> pdb=" O THR z 228 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR z 225 " --> pdb=" O LEU z 278 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'z' and resid 234 through 237 removed outlier: 7.318A pdb=" N GLY z 234 " --> pdb=" O ALA z 270 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'z' and resid 336 through 341 removed outlier: 3.743A pdb=" N GLY z 339 " --> pdb=" O PRO z 328 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TYR z 326 " --> pdb=" O ILE z 341 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU z 372 " --> pdb=" O VAL z 388 " (cutoff:3.500A) 1775 hydrogen bonds defined for protein. 5244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3397 hydrogen bonds 5532 hydrogen bond angles 0 basepair planarities 1363 basepair parallelities 2382 stacking parallelities Total time for adding SS restraints: 344.23 Time building geometry restraints manager: 70.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14140 1.31 - 1.43: 68583 1.43 - 1.56: 72801 1.56 - 1.69: 9647 1.69 - 1.81: 299 Bond restraints: 165470 Sorted by residual: bond pdb=" O4' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.412 1.664 -0.252 1.50e-02 4.44e+03 2.82e+02 bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.486 0.316 2.00e-02 2.50e+03 2.50e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.487 0.315 2.00e-02 2.50e+03 2.48e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.487 0.315 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C4 5MU w 54 " pdb=" C5 5MU w 54 " ideal model delta sigma weight residual 1.802 1.488 0.314 2.00e-02 2.50e+03 2.47e+02 ... (remaining 165465 not shown) Histogram of bond angle deviations from ideal: 72.37 - 91.25: 2 91.25 - 110.13: 74639 110.13 - 129.01: 168216 129.01 - 147.88: 4338 147.88 - 166.76: 1 Bond angle restraints: 247196 Sorted by residual: angle pdb=" C3' 6MZ A1618 " pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " ideal model delta sigma weight residual 120.20 166.76 -46.56 1.50e+00 4.44e-01 9.63e+02 angle pdb=" O3' C w 17 " pdb=" P U w 117 " pdb=" O5' U w 117 " ideal model delta sigma weight residual 104.00 128.46 -24.46 1.50e+00 4.44e-01 2.66e+02 angle pdb=" C3' 6MZ A2030 " pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " ideal model delta sigma weight residual 120.20 142.00 -21.80 1.50e+00 4.44e-01 2.11e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP1 A A2031 " ideal model delta sigma weight residual 108.00 72.37 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C3' U w 117 " pdb=" O3' U w 117 " pdb=" P G w 18 " ideal model delta sigma weight residual 120.20 136.76 -16.56 1.50e+00 4.44e-01 1.22e+02 ... (remaining 247191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 92381 35.87 - 71.74: 11826 71.74 - 107.61: 1483 107.61 - 143.48: 49 143.48 - 179.36: 46 Dihedral angle restraints: 105785 sinusoidal: 87788 harmonic: 17997 Sorted by residual: dihedral pdb=" C5' U w 27 " pdb=" C4' U w 27 " pdb=" C3' U w 27 " pdb=" O3' U w 27 " ideal model delta sinusoidal sigma weight residual 147.00 73.21 73.79 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' G a1305 " pdb=" C4' G a1305 " pdb=" C3' G a1305 " pdb=" O3' G a1305 " ideal model delta sinusoidal sigma weight residual 147.00 73.77 73.23 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C4' U w 27 " pdb=" C3' U w 27 " pdb=" C2' U w 27 " pdb=" C1' U w 27 " ideal model delta sinusoidal sigma weight residual -35.00 32.52 -67.52 1 8.00e+00 1.56e-02 9.26e+01 ... (remaining 105782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 26336 0.154 - 0.309: 5039 0.309 - 0.463: 23 0.463 - 0.617: 9 0.617 - 0.772: 10 Chirality restraints: 31417 Sorted by residual: chirality pdb=" C3' G A1022 " pdb=" C4' G A1022 " pdb=" O3' G A1022 " pdb=" C2' G A1022 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C3' G a1305 " pdb=" C4' G a1305 " pdb=" O3' G a1305 " pdb=" C2' G a1305 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C3' A a1201 " pdb=" C4' A a1201 " pdb=" O3' A a1201 " pdb=" C2' A a1201 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 31414 not shown) Planarity restraints: 13501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2069 " 0.027 2.00e-02 2.50e+03 6.33e-01 9.02e+03 pdb=" C4' 7MG A2069 " 0.472 2.00e-02 2.50e+03 pdb=" O4' 7MG A2069 " 0.779 2.00e-02 2.50e+03 pdb=" C3' 7MG A2069 " -0.606 2.00e-02 2.50e+03 pdb=" O3' 7MG A2069 " -0.654 2.00e-02 2.50e+03 pdb=" C2' 7MG A2069 " -0.180 2.00e-02 2.50e+03 pdb=" O2' 7MG A2069 " 0.952 2.00e-02 2.50e+03 pdb=" C1' 7MG A2069 " 0.209 2.00e-02 2.50e+03 pdb=" N9 7MG A2069 " -1.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " -0.038 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' 2MG a1516 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.680 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.654 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.154 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -0.967 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.234 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.963 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.023 2.00e-02 2.50e+03 6.07e-01 8.29e+03 pdb=" C4' 5MC a1407 " -0.443 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.674 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.637 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.163 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.973 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.223 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.939 2.00e-02 2.50e+03 ... (remaining 13498 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.66: 7 1.66 - 2.53: 852 2.53 - 3.40: 188924 3.40 - 4.27: 593538 4.27 - 5.14: 870691 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1654012 Sorted by model distance: nonbonded pdb=" O4 U a 512 " pdb=" N3 G a 540 " model vdw 0.789 3.120 nonbonded pdb=" O2 C a 392 " pdb=" N7 A a 393 " model vdw 1.274 3.120 nonbonded pdb=" O4 U a 512 " pdb=" C2 G a 540 " model vdw 1.397 3.260 nonbonded pdb=" O LYS o 46 " pdb=" N ASP o 48 " model vdw 1.459 2.520 nonbonded pdb=" O4 U a 543 " pdb=" N2 G a 544 " model vdw 1.462 2.520 ... (remaining 1654007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'v' and (resid 0 through 76 or resid 101)) selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.710 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: 0.150 Extract box with map and model: 17.290 Check model and map are aligned: 1.710 Set scattering table: 1.080 Process input model: 666.360 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 696.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.316 165470 Z= 0.485 Angle : 1.115 46.560 247196 Z= 0.735 Chirality : 0.097 0.772 31417 Planarity : 0.023 0.633 13501 Dihedral : 24.252 179.356 94181 Min Nonbonded Distance : 0.789 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.73 % Favored : 87.83 % Rotamer: Outliers : 4.47 % Allowed : 7.36 % Favored : 88.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.08), residues: 6218 helix: -2.51 (0.09), residues: 1794 sheet: -3.09 (0.13), residues: 1008 loop : -2.88 (0.09), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 212 HIS 0.009 0.001 HIS z 66 PHE 0.018 0.002 PHE u 36 TYR 0.017 0.002 TYR Q 31 ARG 0.024 0.001 ARG q 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2017 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1786 time to evaluate : 6.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 4 LYS cc_start: 0.7990 (pttt) cc_final: 0.7702 (pttp) REVERT: C 12 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7601 (tpt170) REVERT: C 17 LYS cc_start: 0.7008 (mtpt) cc_final: 0.6784 (mtmt) REVERT: C 21 PRO cc_start: 0.7569 (Cg_endo) cc_final: 0.7219 (Cg_exo) REVERT: C 27 LYS cc_start: 0.8044 (mttt) cc_final: 0.7504 (tptt) REVERT: C 44 ASN cc_start: 0.7667 (m-40) cc_final: 0.7403 (m110) REVERT: C 139 THR cc_start: 0.8753 (m) cc_final: 0.8336 (p) REVERT: C 159 THR cc_start: 0.8653 (m) cc_final: 0.8318 (p) REVERT: C 166 ARG cc_start: 0.7173 (ptt180) cc_final: 0.6930 (ptt180) REVERT: C 170 TYR cc_start: 0.7446 (m-80) cc_final: 0.6604 (m-80) REVERT: C 183 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.6832 (t) REVERT: C 196 ASN cc_start: 0.7859 (t0) cc_final: 0.7389 (t0) REVERT: C 213 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7380 (mtt-85) REVERT: C 268 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7665 (tmm-80) REVERT: D 11 MET cc_start: 0.7668 (mtp) cc_final: 0.7354 (mtp) REVERT: D 30 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7035 (mt-10) REVERT: D 42 ASN cc_start: 0.7836 (m110) cc_final: 0.7307 (t0) REVERT: D 61 THR cc_start: 0.8368 (p) cc_final: 0.7962 (t) REVERT: D 100 LEU cc_start: 0.7475 (mp) cc_final: 0.7268 (mp) REVERT: D 169 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7753 (ttt-90) REVERT: D 199 SER cc_start: 0.8162 (p) cc_final: 0.7914 (p) REVERT: D 204 LYS cc_start: 0.7639 (ptpt) cc_final: 0.7353 (pttp) REVERT: E 15 SER cc_start: 0.8224 (t) cc_final: 0.7857 (p) REVERT: E 24 ASN cc_start: 0.8156 (t0) cc_final: 0.7840 (t0) REVERT: E 46 GLN cc_start: 0.8358 (mp10) cc_final: 0.7944 (mp10) REVERT: E 47 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7367 (mttt) REVERT: E 51 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7244 (mt-10) REVERT: E 102 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7309 (mtt180) REVERT: E 108 ILE cc_start: 0.8470 (pt) cc_final: 0.8120 (mt) REVERT: E 117 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6600 (mtm110) REVERT: E 139 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6894 (mptt) REVERT: E 166 LYS cc_start: 0.7561 (mttt) cc_final: 0.7042 (mmtt) REVERT: F 6 TYR cc_start: 0.7515 (t80) cc_final: 0.7258 (t80) REVERT: F 31 GLU cc_start: 0.8264 (tt0) cc_final: 0.7878 (tt0) REVERT: F 68 LYS cc_start: 0.7988 (mptt) cc_final: 0.7488 (mmtt) REVERT: F 72 SER cc_start: 0.4736 (t) cc_final: 0.3865 (t) REVERT: F 93 GLU cc_start: 0.7724 (tp30) cc_final: 0.6831 (tm-30) REVERT: F 97 GLU cc_start: 0.7625 (tp30) cc_final: 0.7189 (tp30) REVERT: F 100 GLU cc_start: 0.7953 (tt0) cc_final: 0.7736 (tt0) REVERT: F 112 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6371 (m-30) REVERT: F 116 LEU cc_start: 0.6295 (tp) cc_final: 0.5908 (tp) REVERT: F 162 ASP cc_start: 0.5873 (p0) cc_final: 0.5615 (m-30) REVERT: F 169 LEU cc_start: 0.7362 (mt) cc_final: 0.7162 (mt) REVERT: G 25 ILE cc_start: 0.6306 (mt) cc_final: 0.6055 (mt) REVERT: G 93 TYR cc_start: 0.6210 (m-10) cc_final: 0.5458 (m-10) REVERT: G 115 GLN cc_start: 0.7222 (tp-100) cc_final: 0.6889 (mp10) REVERT: G 130 ILE cc_start: 0.7933 (mt) cc_final: 0.7608 (mt) REVERT: G 150 TYR cc_start: 0.7837 (m-80) cc_final: 0.7626 (m-80) REVERT: G 159 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7058 (mtmm) REVERT: H 18 GLN cc_start: 0.5724 (OUTLIER) cc_final: 0.4553 (tm-30) REVERT: J 45 THR cc_start: 0.8610 (m) cc_final: 0.8311 (p) REVERT: J 67 ASN cc_start: 0.8013 (m-40) cc_final: 0.7363 (m-40) REVERT: J 85 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7274 (mmpt) REVERT: J 88 THR cc_start: 0.8048 (p) cc_final: 0.7845 (t) REVERT: J 91 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7402 (tp30) REVERT: J 99 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7255 (mmp80) REVERT: K 53 LYS cc_start: 0.8267 (pttp) cc_final: 0.7967 (pptt) REVERT: K 70 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7904 (mmm-85) REVERT: K 71 ARG cc_start: 0.6816 (mmm160) cc_final: 0.6151 (mmt180) REVERT: L 12 SER cc_start: 0.8895 (t) cc_final: 0.8666 (m) REVERT: L 27 LEU cc_start: 0.8049 (pp) cc_final: 0.7602 (pp) REVERT: L 110 VAL cc_start: 0.8579 (t) cc_final: 0.8250 (m) REVERT: L 129 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7771 (ttpt) REVERT: M 44 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7321 (mtm180) REVERT: M 51 ARG cc_start: 0.7332 (mmt90) cc_final: 0.6780 (mmt90) REVERT: M 54 THR cc_start: 0.8735 (m) cc_final: 0.8451 (p) REVERT: M 59 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7953 (mmt90) REVERT: M 65 ILE cc_start: 0.8549 (mt) cc_final: 0.8313 (mt) REVERT: M 136 MET cc_start: 0.6790 (ttp) cc_final: 0.6229 (tmm) REVERT: N 52 ILE cc_start: 0.8148 (mt) cc_final: 0.7942 (mm) REVERT: N 86 ARG cc_start: 0.7234 (ttp-170) cc_final: 0.6718 (ttm-80) REVERT: N 94 TYR cc_start: 0.8763 (m-80) cc_final: 0.8458 (m-80) REVERT: O 12 THR cc_start: 0.8111 (m) cc_final: 0.7760 (p) REVERT: O 19 GLN cc_start: 0.7294 (pt0) cc_final: 0.7065 (pt0) REVERT: O 30 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7420 (ttp-170) REVERT: O 34 HIS cc_start: 0.7384 (m-70) cc_final: 0.6933 (m-70) REVERT: O 94 ARG cc_start: 0.7776 (ptt90) cc_final: 0.7573 (ptt-90) REVERT: P 7 LEU cc_start: 0.8016 (mt) cc_final: 0.7775 (mp) REVERT: P 36 LYS cc_start: 0.6832 (mmmt) cc_final: 0.6146 (mppt) REVERT: P 37 LYS cc_start: 0.7867 (tttp) cc_final: 0.7622 (tttp) REVERT: P 50 ARG cc_start: 0.8538 (ttt90) cc_final: 0.8194 (ttt90) REVERT: P 59 THR cc_start: 0.7447 (p) cc_final: 0.7098 (p) REVERT: P 97 TYR cc_start: 0.8881 (m-80) cc_final: 0.8646 (m-10) REVERT: P 110 LYS cc_start: 0.7651 (tptm) cc_final: 0.7274 (ttmm) REVERT: P 113 LEU cc_start: 0.7335 (tp) cc_final: 0.7133 (tp) REVERT: Q 83 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7736 (mtpp) REVERT: R 1 MET cc_start: 0.6895 (tpt) cc_final: 0.6513 (tpt) REVERT: R 19 THR cc_start: 0.7766 (m) cc_final: 0.7249 (m) REVERT: R 21 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7573 (ttm110) REVERT: R 58 VAL cc_start: 0.7646 (t) cc_final: 0.7110 (p) REVERT: S 1 MET cc_start: 0.6038 (ppp) cc_final: 0.5567 (ppp) REVERT: S 3 THR cc_start: 0.7878 (p) cc_final: 0.7376 (p) REVERT: S 53 SER cc_start: 0.8638 (t) cc_final: 0.8374 (p) REVERT: S 59 GLU cc_start: 0.7535 (pt0) cc_final: 0.7261 (pt0) REVERT: S 70 LYS cc_start: 0.7931 (mttt) cc_final: 0.7723 (mtmp) REVERT: S 73 LYS cc_start: 0.7645 (mttt) cc_final: 0.7434 (mmtt) REVERT: T 28 ASN cc_start: 0.7618 (t0) cc_final: 0.6815 (t0) REVERT: T 33 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7470 (mtpp) REVERT: T 43 ILE cc_start: 0.8278 (mt) cc_final: 0.8064 (mm) REVERT: T 93 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.3885 (tp) REVERT: U 13 LEU cc_start: 0.8572 (mt) cc_final: 0.8333 (mp) REVERT: U 23 LYS cc_start: 0.7528 (mttm) cc_final: 0.7043 (mtpp) REVERT: U 36 GLU cc_start: 0.7548 (pt0) cc_final: 0.7161 (pm20) REVERT: U 40 LEU cc_start: 0.8036 (mt) cc_final: 0.7427 (mm) REVERT: V 30 ILE cc_start: 0.8392 (mt) cc_final: 0.7729 (tt) REVERT: V 31 TYR cc_start: 0.7030 (p90) cc_final: 0.6641 (p90) REVERT: V 43 ASP cc_start: 0.8160 (t70) cc_final: 0.7656 (t0) REVERT: V 46 LYS cc_start: 0.7116 (mmtm) cc_final: 0.6830 (mmmt) REVERT: W 34 VAL cc_start: 0.8982 (t) cc_final: 0.8689 (p) REVERT: W 64 LYS cc_start: 0.8103 (tptm) cc_final: 0.7660 (tptp) REVERT: W 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7516 (pttp) REVERT: Y 6 LEU cc_start: 0.5965 (mt) cc_final: 0.5547 (mt) REVERT: Y 39 GLN cc_start: 0.8272 (mt0) cc_final: 0.7946 (mm110) REVERT: Y 55 THR cc_start: 0.8200 (m) cc_final: 0.7923 (p) REVERT: 0 8 THR cc_start: 0.8793 (p) cc_final: 0.8557 (p) REVERT: 0 11 LYS cc_start: 0.7557 (mmmt) cc_final: 0.7325 (mmtp) REVERT: 0 47 TYR cc_start: 0.7998 (m-80) cc_final: 0.7704 (m-80) REVERT: 1 6 GLU cc_start: 0.7550 (pt0) cc_final: 0.7274 (pp20) REVERT: 1 7 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7493 (mtmm) REVERT: 1 22 THR cc_start: 0.8372 (p) cc_final: 0.8108 (p) REVERT: 1 50 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6673 (tm-30) REVERT: 2 25 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7447 (ptpt) REVERT: 2 41 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7290 (tpt90) REVERT: 3 14 LYS cc_start: 0.8384 (tttt) cc_final: 0.7820 (mmtp) REVERT: 3 38 LYS cc_start: 0.7453 (ttmt) cc_final: 0.7112 (tttp) REVERT: 3 60 CYS cc_start: 0.8690 (m) cc_final: 0.8352 (m) REVERT: 4 9 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7523 (ttpp) REVERT: 4 15 LYS cc_start: 0.7532 (ttmm) cc_final: 0.6795 (mtmm) REVERT: 5 1 MET cc_start: 0.0298 (tpt) cc_final: -0.0133 (mmm) REVERT: 6 1 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6096 (mtt) REVERT: 6 10 GLU cc_start: 0.7601 (tp30) cc_final: 0.6668 (pt0) REVERT: 6 37 CYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6997 (p) REVERT: 6 56 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.5360 (tpp80) REVERT: b 23 ASN cc_start: 0.8620 (t0) cc_final: 0.7869 (t0) REVERT: b 26 MET cc_start: 0.7751 (mtp) cc_final: 0.7381 (mtp) REVERT: b 30 ILE cc_start: 0.6811 (mt) cc_final: 0.6520 (mt) REVERT: b 47 PRO cc_start: 0.7878 (Cg_exo) cc_final: 0.7618 (Cg_endo) REVERT: b 62 ARG cc_start: 0.6845 (mtp85) cc_final: 0.6319 (mtm110) REVERT: b 65 LYS cc_start: 0.6724 (mtmm) cc_final: 0.6431 (mtpt) REVERT: b 92 ASN cc_start: 0.7573 (p0) cc_final: 0.6858 (p0) REVERT: b 132 GLU cc_start: 0.5781 (mm-30) cc_final: 0.5327 (tp30) REVERT: b 140 LEU cc_start: 0.7106 (tt) cc_final: 0.6646 (tp) REVERT: b 152 ASP cc_start: 0.7923 (m-30) cc_final: 0.7684 (m-30) REVERT: b 169 HIS cc_start: 0.7298 (p90) cc_final: 0.7087 (p90) REVERT: b 186 VAL cc_start: 0.7504 (t) cc_final: 0.7141 (t) REVERT: b 188 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6250 (t) REVERT: b 193 ASP cc_start: 0.6992 (t0) cc_final: 0.6567 (t0) REVERT: c 17 TRP cc_start: 0.7720 (m-90) cc_final: 0.7102 (m-90) REVERT: c 37 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7215 (mttm) REVERT: c 39 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6596 (mtt180) REVERT: c 46 LEU cc_start: 0.7023 (mt) cc_final: 0.6783 (mp) REVERT: c 56 ILE cc_start: 0.7389 (mt) cc_final: 0.7145 (tp) REVERT: c 81 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6736 (tp30) REVERT: c 82 ASP cc_start: 0.7883 (m-30) cc_final: 0.7582 (m-30) REVERT: c 88 LYS cc_start: 0.7334 (mmmt) cc_final: 0.7118 (mmmt) REVERT: c 105 VAL cc_start: 0.7353 (t) cc_final: 0.7028 (p) REVERT: c 131 ARG cc_start: 0.6755 (mmm160) cc_final: 0.6530 (tpt-90) REVERT: c 195 ILE cc_start: 0.8432 (mt) cc_final: 0.8123 (mm) REVERT: d 2 ARG cc_start: 0.5500 (mtp-110) cc_final: 0.4948 (mtp-110) REVERT: d 10 LEU cc_start: 0.8197 (mt) cc_final: 0.7606 (mt) REVERT: d 52 VAL cc_start: 0.8668 (m) cc_final: 0.8442 (p) REVERT: d 57 LYS cc_start: 0.7266 (ttpt) cc_final: 0.6686 (tttm) REVERT: d 70 GLN cc_start: 0.8535 (tt0) cc_final: 0.8142 (mt0) REVERT: d 87 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7312 (tt0) REVERT: d 131 ILE cc_start: 0.7354 (mp) cc_final: 0.6835 (mm) REVERT: d 153 ARG cc_start: 0.6094 (ptm160) cc_final: 0.5571 (ttp80) REVERT: d 183 ARG cc_start: 0.6352 (ptt-90) cc_final: 0.5954 (mtm110) REVERT: d 184 LYS cc_start: 0.7163 (pttt) cc_final: 0.6833 (tmtt) REVERT: e 19 ARG cc_start: 0.7793 (ptt90) cc_final: 0.7351 (ttp80) REVERT: e 25 LYS cc_start: 0.7988 (tttt) cc_final: 0.7756 (tptp) REVERT: e 65 LYS cc_start: 0.7690 (mttm) cc_final: 0.7364 (mttp) REVERT: e 111 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6841 (ttp-170) REVERT: f 2 ARG cc_start: 0.7117 (mmt180) cc_final: 0.6444 (mtt180) REVERT: f 8 PHE cc_start: 0.7391 (p90) cc_final: 0.6950 (p90) REVERT: f 9 MET cc_start: 0.7552 (mtp) cc_final: 0.7306 (mpp) REVERT: f 29 ILE cc_start: 0.7127 (mt) cc_final: 0.6825 (mt) REVERT: f 42 TRP cc_start: 0.7053 (m-10) cc_final: 0.6727 (m-10) REVERT: f 96 VAL cc_start: 0.6514 (m) cc_final: 0.6029 (m) REVERT: g 24 LYS cc_start: 0.6759 (tptm) cc_final: 0.6256 (tptt) REVERT: g 55 LYS cc_start: 0.4510 (OUTLIER) cc_final: 0.4108 (mttp) REVERT: g 90 VAL cc_start: 0.6388 (p) cc_final: 0.6106 (t) REVERT: g 125 ASP cc_start: 0.7347 (m-30) cc_final: 0.7012 (m-30) REVERT: g 136 LYS cc_start: 0.6920 (tttp) cc_final: 0.6688 (tptm) REVERT: g 145 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7038 (mt-10) REVERT: h 20 ASN cc_start: 0.8521 (t0) cc_final: 0.8132 (t0) REVERT: h 49 LYS cc_start: 0.7930 (mttp) cc_final: 0.7358 (mptt) REVERT: h 79 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7822 (ppt90) REVERT: h 93 LYS cc_start: 0.8060 (ptpt) cc_final: 0.7662 (pttt) REVERT: i 37 TYR cc_start: 0.7566 (t80) cc_final: 0.7354 (t80) REVERT: i 42 THR cc_start: 0.5210 (OUTLIER) cc_final: 0.4371 (m) REVERT: j 7 ARG cc_start: 0.4515 (mtt180) cc_final: 0.4264 (ttm-80) REVERT: j 16 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7254 (mtp180) REVERT: j 67 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7152 (pt) REVERT: k 12 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4274 (mmm160) REVERT: k 29 THR cc_start: 0.8148 (p) cc_final: 0.7916 (t) REVERT: k 58 THR cc_start: 0.7073 (OUTLIER) cc_final: 0.6850 (p) REVERT: k 64 VAL cc_start: 0.8350 (p) cc_final: 0.8030 (m) REVERT: k 80 ASN cc_start: 0.7206 (p0) cc_final: 0.6848 (p0) REVERT: l 39 THR cc_start: 0.7276 (m) cc_final: 0.6799 (m) REVERT: l 53 ARG cc_start: 0.6613 (mmm160) cc_final: 0.6369 (tpp80) REVERT: l 71 HIS cc_start: 0.6799 (p90) cc_final: 0.6255 (p90) REVERT: l 85 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7065 (ttt180) REVERT: m 26 LYS cc_start: 0.7843 (tttp) cc_final: 0.7346 (tppt) REVERT: m 52 ILE cc_start: 0.7017 (mt) cc_final: 0.6657 (mp) REVERT: m 65 GLU cc_start: 0.7197 (tp30) cc_final: 0.6851 (pm20) REVERT: n 18 LYS cc_start: 0.6826 (tttt) cc_final: 0.6582 (tttp) REVERT: n 42 TRP cc_start: 0.6957 (t-100) cc_final: 0.6303 (t60) REVERT: n 53 ARG cc_start: 0.6777 (tpp80) cc_final: 0.6195 (tpp80) REVERT: o 30 LEU cc_start: 0.8616 (mp) cc_final: 0.8356 (mp) REVERT: o 37 HIS cc_start: 0.7591 (t70) cc_final: 0.7389 (t70) REVERT: o 44 GLU cc_start: 0.7560 (pm20) cc_final: 0.7238 (pt0) REVERT: o 61 GLN cc_start: 0.7955 (tp40) cc_final: 0.7591 (tt0) REVERT: o 73 ASP cc_start: 0.6183 (t0) cc_final: 0.5861 (m-30) REVERT: p 1 MET cc_start: 0.5374 (ttp) cc_final: 0.4853 (ttp) REVERT: p 13 LYS cc_start: 0.7505 (mmmt) cc_final: 0.7214 (mmmt) REVERT: p 17 TYR cc_start: 0.8161 (m-80) cc_final: 0.7953 (m-10) REVERT: p 19 VAL cc_start: 0.8368 (p) cc_final: 0.8126 (p) REVERT: p 24 SER cc_start: 0.7362 (t) cc_final: 0.6798 (m) REVERT: q 4 ILE cc_start: 0.5157 (OUTLIER) cc_final: 0.4909 (pt) REVERT: q 16 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4552 (ttm) REVERT: q 18 LYS cc_start: 0.7937 (tttt) cc_final: 0.7663 (mtpp) REVERT: q 61 ARG cc_start: 0.7184 (ppp80) cc_final: 0.6916 (ttp-170) REVERT: q 66 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7740 (pp) REVERT: r 29 LYS cc_start: 0.7536 (ttpp) cc_final: 0.7301 (mttm) REVERT: r 47 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7350 (mmt-90) REVERT: r 63 TYR cc_start: 0.8229 (t80) cc_final: 0.7826 (t80) REVERT: r 67 LEU cc_start: 0.8569 (mt) cc_final: 0.8261 (mt) REVERT: s 5 LYS cc_start: 0.4928 (OUTLIER) cc_final: 0.4619 (tppt) REVERT: s 36 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6729 (ptm-80) REVERT: s 43 MET cc_start: 0.7915 (mtp) cc_final: 0.6637 (tpt) REVERT: s 60 PHE cc_start: 0.6702 (t80) cc_final: 0.6450 (t80) REVERT: s 62 THR cc_start: 0.6807 (p) cc_final: 0.6147 (p) REVERT: s 69 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6005 (mttt) REVERT: t 4 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7349 (mmtm) REVERT: t 20 ASN cc_start: 0.8382 (t0) cc_final: 0.8149 (t0) REVERT: t 25 SER cc_start: 0.8891 (t) cc_final: 0.8600 (p) REVERT: t 27 MET cc_start: 0.8087 (ttp) cc_final: 0.7727 (tmm) REVERT: t 28 ARG cc_start: 0.6918 (ptp90) cc_final: 0.5821 (ptm160) REVERT: t 30 PHE cc_start: 0.8202 (m-80) cc_final: 0.7930 (m-10) REVERT: t 31 ILE cc_start: 0.8441 (mt) cc_final: 0.7836 (pt) REVERT: t 50 PHE cc_start: 0.6189 (t80) cc_final: 0.5864 (t80) REVERT: t 68 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7274 (mttm) REVERT: t 73 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: u 34 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6326 (tpt90) REVERT: u 36 PHE cc_start: 0.8215 (t80) cc_final: 0.7233 (t80) REVERT: z 351 MET cc_start: -0.0331 (mmt) cc_final: -0.0570 (mmt) outliers start: 231 outliers final: 44 residues processed: 1931 average time/residue: 1.4756 time to fit residues: 4746.5114 Evaluate side-chains 1330 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1248 time to evaluate : 6.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 80 ARG Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 3 LYS Chi-restraints excluded: chain U residue 18 LYS Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain t residue 4 LYS Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain t residue 63 LYS Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain u residue 34 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 917 optimal weight: 6.9990 chunk 823 optimal weight: 4.9990 chunk 457 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 555 optimal weight: 4.9990 chunk 440 optimal weight: 1.9990 chunk 851 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 518 optimal weight: 0.7980 chunk 634 optimal weight: 7.9990 chunk 987 optimal weight: 0.0270 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 196 ASN C 259 ASN D 58 ASN D 126 ASN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 62 GLN E 195 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 5 GLN K 29 HIS L 99 ASN N 62 ASN N 73 ASN O 104 GLN P 11 GLN Q 43 GLN Q 65 ASN R 18 GLN S 7 HIS U 68 ASN W 72 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Z 8 GLN 0 5 ASN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN c 7 ASN d 88 ASN d 119 HIS d 163 GLN e 121 ASN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN i 109 GLN j 64 GLN k 39 ASN m 51 GLN n 71 HIS o 19 ASN o 27 GLN o 36 ASN ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS r 51 GLN t 67 HIS z 97 GLN z 135 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 165470 Z= 0.206 Angle : 0.771 15.646 247196 Z= 0.415 Chirality : 0.041 0.515 31417 Planarity : 0.007 0.128 13501 Dihedral : 24.320 179.787 82054 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.37 % Favored : 91.80 % Rotamer: Outliers : 4.14 % Allowed : 14.97 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.69 (0.09), residues: 6218 helix: -0.36 (0.11), residues: 1920 sheet: -2.34 (0.13), residues: 1118 loop : -2.52 (0.09), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 200 HIS 0.011 0.001 HIS z 118 PHE 0.021 0.002 PHE s 40 TYR 0.020 0.002 TYR o 77 ARG 0.011 0.001 ARG o 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1346 time to evaluate : 6.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7664 (tpt170) REVERT: C 27 LYS cc_start: 0.8005 (mttt) cc_final: 0.7487 (tptt) REVERT: C 29 PHE cc_start: 0.7696 (t80) cc_final: 0.7393 (t80) REVERT: C 44 ASN cc_start: 0.7737 (m-40) cc_final: 0.7468 (m110) REVERT: C 99 GLU cc_start: 0.7396 (tt0) cc_final: 0.7170 (tp30) REVERT: C 139 THR cc_start: 0.8733 (m) cc_final: 0.8385 (p) REVERT: C 159 THR cc_start: 0.8834 (m) cc_final: 0.8563 (p) REVERT: C 213 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7125 (mtt-85) REVERT: C 268 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7443 (tmm-80) REVERT: D 42 ASN cc_start: 0.7891 (m110) cc_final: 0.7300 (t0) REVERT: D 199 SER cc_start: 0.8236 (p) cc_final: 0.7984 (p) REVERT: D 204 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7654 (mtmm) REVERT: E 24 ASN cc_start: 0.8082 (t0) cc_final: 0.7822 (t0) REVERT: E 51 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7305 (mt-10) REVERT: E 117 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6465 (mtm110) REVERT: E 166 LYS cc_start: 0.7399 (mttt) cc_final: 0.7018 (mmtt) REVERT: E 170 ARG cc_start: 0.7345 (ttm170) cc_final: 0.7100 (ttm110) REVERT: E 173 THR cc_start: 0.7847 (p) cc_final: 0.7625 (p) REVERT: F 25 MET cc_start: 0.6005 (mmp) cc_final: 0.5793 (mmp) REVERT: F 31 GLU cc_start: 0.7672 (tt0) cc_final: 0.7410 (tt0) REVERT: F 33 ILE cc_start: 0.8760 (mt) cc_final: 0.8521 (mp) REVERT: F 37 MET cc_start: 0.8003 (ttm) cc_final: 0.7634 (ttm) REVERT: F 68 LYS cc_start: 0.7850 (mptt) cc_final: 0.7486 (mmtt) REVERT: F 93 GLU cc_start: 0.7597 (tp30) cc_final: 0.7298 (tm-30) REVERT: F 97 GLU cc_start: 0.7559 (tp30) cc_final: 0.7042 (tp30) REVERT: F 112 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6247 (m-30) REVERT: G 36 LEU cc_start: 0.7161 (tp) cc_final: 0.6629 (mp) REVERT: G 86 LEU cc_start: 0.7045 (mp) cc_final: 0.6648 (mt) REVERT: G 115 GLN cc_start: 0.7297 (tp-100) cc_final: 0.6869 (mp10) REVERT: G 129 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7304 (tp30) REVERT: G 159 LYS cc_start: 0.7592 (mtpp) cc_final: 0.7265 (mtmm) REVERT: J 37 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7758 (ttt-90) REVERT: J 45 THR cc_start: 0.8617 (m) cc_final: 0.8215 (p) REVERT: J 53 TYR cc_start: 0.7793 (m-80) cc_final: 0.6914 (m-80) REVERT: J 57 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7545 (mp) REVERT: J 86 GLN cc_start: 0.8870 (pt0) cc_final: 0.8597 (pt0) REVERT: K 7 MET cc_start: 0.7988 (mmt) cc_final: 0.7662 (mmt) REVERT: K 71 ARG cc_start: 0.6666 (mmm160) cc_final: 0.6016 (mmt180) REVERT: K 93 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: L 14 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7092 (tptt) REVERT: L 106 GLU cc_start: 0.8249 (pt0) cc_final: 0.8010 (pm20) REVERT: L 123 ARG cc_start: 0.6507 (mtm-85) cc_final: 0.6004 (mtt90) REVERT: M 44 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.7261 (mtm180) REVERT: M 54 THR cc_start: 0.8384 (m) cc_final: 0.8135 (p) REVERT: M 59 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8017 (mmt-90) REVERT: M 60 GLN cc_start: 0.7834 (mt0) cc_final: 0.7230 (mp10) REVERT: M 136 MET cc_start: 0.7010 (ttp) cc_final: 0.6753 (tmm) REVERT: N 46 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7132 (mtt-85) REVERT: N 74 GLU cc_start: 0.6989 (tt0) cc_final: 0.6620 (tt0) REVERT: N 94 TYR cc_start: 0.8730 (m-80) cc_final: 0.8349 (m-80) REVERT: O 34 HIS cc_start: 0.7376 (m-70) cc_final: 0.6716 (m-70) REVERT: O 36 TYR cc_start: 0.7696 (m-80) cc_final: 0.7409 (m-80) REVERT: P 36 LYS cc_start: 0.6507 (mmmt) cc_final: 0.5805 (mppt) REVERT: P 37 LYS cc_start: 0.7925 (tttp) cc_final: 0.7662 (tttp) REVERT: Q 83 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7853 (mtpp) REVERT: Q 110 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7617 (mt-10) REVERT: R 21 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7676 (ttm110) REVERT: R 60 LYS cc_start: 0.7205 (mtmm) cc_final: 0.6963 (mttp) REVERT: R 97 LYS cc_start: 0.7917 (tttt) cc_final: 0.7579 (ttmm) REVERT: S 73 LYS cc_start: 0.7836 (mttt) cc_final: 0.7489 (mttt) REVERT: S 85 ILE cc_start: 0.8844 (mm) cc_final: 0.8627 (tp) REVERT: S 107 VAL cc_start: 0.8114 (t) cc_final: 0.7822 (m) REVERT: T 28 ASN cc_start: 0.7550 (t0) cc_final: 0.7108 (t0) REVERT: U 6 ARG cc_start: 0.7183 (ttt90) cc_final: 0.6917 (ttm-80) REVERT: U 23 LYS cc_start: 0.7399 (mttm) cc_final: 0.6710 (mtpp) REVERT: U 36 GLU cc_start: 0.7299 (pt0) cc_final: 0.7019 (pm20) REVERT: U 46 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7801 (mtpp) REVERT: V 7 GLU cc_start: 0.6518 (mp0) cc_final: 0.6240 (mm-30) REVERT: V 11 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: V 30 ILE cc_start: 0.8331 (mt) cc_final: 0.7777 (tt) REVERT: V 46 LYS cc_start: 0.7052 (mmtm) cc_final: 0.6833 (mmmt) REVERT: W 64 LYS cc_start: 0.8183 (tptm) cc_final: 0.7629 (tptp) REVERT: W 68 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7511 (pttp) REVERT: X 15 ASN cc_start: 0.8841 (m110) cc_final: 0.8622 (m-40) REVERT: X 36 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7312 (mtm110) REVERT: X 57 VAL cc_start: 0.7896 (t) cc_final: 0.7564 (m) REVERT: Y 6 LEU cc_start: 0.6068 (mt) cc_final: 0.5615 (mt) REVERT: Y 39 GLN cc_start: 0.8254 (mt0) cc_final: 0.7852 (mm110) REVERT: Y 55 THR cc_start: 0.8291 (m) cc_final: 0.8062 (p) REVERT: Z 44 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7193 (mmm160) REVERT: 0 8 THR cc_start: 0.8516 (p) cc_final: 0.8273 (p) REVERT: 0 11 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7340 (mmtp) REVERT: 0 35 GLU cc_start: 0.7839 (tt0) cc_final: 0.7337 (tt0) REVERT: 0 49 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7805 (mtm-85) REVERT: 2 25 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7619 (ptpt) REVERT: 2 41 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7828 (ttm110) REVERT: 3 14 LYS cc_start: 0.8408 (tttt) cc_final: 0.7880 (mmtp) REVERT: 3 38 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7104 (tttm) REVERT: 3 60 CYS cc_start: 0.8293 (m) cc_final: 0.8068 (m) REVERT: 4 8 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7375 (mtpt) REVERT: 4 9 LYS cc_start: 0.7597 (ttmt) cc_final: 0.7325 (ttpp) REVERT: 4 15 LYS cc_start: 0.7505 (ttmm) cc_final: 0.6682 (mttm) REVERT: 5 1 MET cc_start: 0.0402 (tpt) cc_final: 0.0036 (mmm) REVERT: 6 37 CYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5937 (p) REVERT: 6 56 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5018 (tpp80) REVERT: 6 61 ASN cc_start: 0.5976 (m110) cc_final: 0.5751 (p0) REVERT: b 23 ASN cc_start: 0.8683 (t0) cc_final: 0.8008 (t0) REVERT: b 26 MET cc_start: 0.7550 (mtp) cc_final: 0.7283 (mtp) REVERT: b 38 HIS cc_start: 0.7220 (m-70) cc_final: 0.7008 (m-70) REVERT: b 49 PHE cc_start: 0.7422 (p90) cc_final: 0.7172 (t80) REVERT: b 55 GLU cc_start: 0.7133 (tp30) cc_final: 0.6893 (pt0) REVERT: b 62 ARG cc_start: 0.6461 (mtp85) cc_final: 0.6126 (mtm110) REVERT: b 65 LYS cc_start: 0.6378 (mtmm) cc_final: 0.6062 (mtpt) REVERT: b 136 ARG cc_start: 0.5803 (mmm-85) cc_final: 0.5493 (tmm160) REVERT: b 152 ASP cc_start: 0.7917 (m-30) cc_final: 0.7675 (m-30) REVERT: b 176 ASN cc_start: 0.7638 (t0) cc_final: 0.7398 (t0) REVERT: b 211 LEU cc_start: 0.6174 (tp) cc_final: 0.5738 (mt) REVERT: c 17 TRP cc_start: 0.7806 (m-90) cc_final: 0.7214 (m-90) REVERT: c 39 ARG cc_start: 0.6554 (ttm-80) cc_final: 0.6334 (mtt-85) REVERT: c 45 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7341 (tm-30) REVERT: c 46 LEU cc_start: 0.6817 (mt) cc_final: 0.6585 (mp) REVERT: c 71 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6562 (ptp-110) REVERT: c 76 ILE cc_start: 0.6314 (OUTLIER) cc_final: 0.5607 (pt) REVERT: c 81 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6486 (tp30) REVERT: c 82 ASP cc_start: 0.8039 (m-30) cc_final: 0.7692 (m-30) REVERT: c 88 LYS cc_start: 0.7497 (mmmt) cc_final: 0.7296 (mmmt) REVERT: c 105 VAL cc_start: 0.7406 (t) cc_final: 0.7163 (p) REVERT: c 169 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7462 (mt-10) REVERT: c 171 ARG cc_start: 0.6728 (ttp-170) cc_final: 0.6414 (ttm-80) REVERT: c 187 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7828 (mt-10) REVERT: c 192 TYR cc_start: 0.7753 (m-80) cc_final: 0.7549 (m-80) REVERT: c 195 ILE cc_start: 0.8280 (mt) cc_final: 0.7951 (mm) REVERT: d 2 ARG cc_start: 0.5667 (mtp-110) cc_final: 0.4955 (mtp-110) REVERT: d 57 LYS cc_start: 0.6933 (ttpt) cc_final: 0.6714 (tttm) REVERT: d 70 GLN cc_start: 0.8441 (tt0) cc_final: 0.7891 (mt0) REVERT: d 84 ASN cc_start: 0.8044 (t0) cc_final: 0.7566 (t0) REVERT: d 131 ILE cc_start: 0.7563 (mp) cc_final: 0.7113 (mm) REVERT: d 139 ASN cc_start: 0.7283 (t0) cc_final: 0.6839 (m-40) REVERT: d 183 ARG cc_start: 0.6082 (ptt-90) cc_final: 0.5308 (ptp-110) REVERT: d 193 ASP cc_start: 0.7251 (p0) cc_final: 0.6275 (t70) REVERT: e 45 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7610 (p) REVERT: e 72 ASN cc_start: 0.7498 (m-40) cc_final: 0.7233 (t0) REVERT: e 105 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7983 (mt) REVERT: e 121 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6587 (p0) REVERT: f 2 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6670 (mtt180) REVERT: f 9 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6711 (ptp) REVERT: f 44 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7499 (ttt180) REVERT: f 69 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7918 (pt0) REVERT: g 24 LYS cc_start: 0.6367 (tptm) cc_final: 0.5958 (tptt) REVERT: g 61 PHE cc_start: 0.6756 (t80) cc_final: 0.6403 (t80) REVERT: g 125 ASP cc_start: 0.7436 (m-30) cc_final: 0.7180 (m-30) REVERT: h 79 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8083 (ptt90) REVERT: h 110 MET cc_start: 0.7963 (ptp) cc_final: 0.7089 (pmm) REVERT: i 99 LYS cc_start: 0.7566 (ttpt) cc_final: 0.6858 (tptp) REVERT: k 80 ASN cc_start: 0.6326 (p0) cc_final: 0.5965 (p0) REVERT: l 71 HIS cc_start: 0.6596 (p90) cc_final: 0.6258 (p90) REVERT: l 85 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6723 (ttt180) REVERT: l 88 ASP cc_start: 0.7470 (t0) cc_final: 0.7206 (t0) REVERT: m 2 ARG cc_start: 0.6704 (ttm170) cc_final: 0.6222 (tmt-80) REVERT: m 49 GLU cc_start: 0.7675 (tp30) cc_final: 0.7457 (tp30) REVERT: m 51 GLN cc_start: 0.6552 (tt0) cc_final: 0.5927 (mp10) REVERT: m 65 GLU cc_start: 0.7348 (tp30) cc_final: 0.6342 (mm-30) REVERT: n 42 TRP cc_start: 0.6849 (t-100) cc_final: 0.6404 (t60) REVERT: o 44 GLU cc_start: 0.7582 (pm20) cc_final: 0.7351 (pt0) REVERT: o 58 MET cc_start: 0.7084 (mtm) cc_final: 0.6814 (mtt) REVERT: o 61 GLN cc_start: 0.8104 (tp40) cc_final: 0.7661 (tt0) REVERT: o 73 ASP cc_start: 0.6653 (t0) cc_final: 0.6395 (m-30) REVERT: p 1 MET cc_start: 0.5441 (ttp) cc_final: 0.5067 (ttp) REVERT: p 9 HIS cc_start: 0.7854 (m170) cc_final: 0.7592 (m90) REVERT: p 24 SER cc_start: 0.7089 (t) cc_final: 0.6452 (m) REVERT: q 16 MET cc_start: 0.5807 (mtp) cc_final: 0.5398 (ttm) REVERT: q 61 ARG cc_start: 0.6832 (ppp80) cc_final: 0.6557 (ttp-170) REVERT: r 37 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5527 (mtmp) REVERT: r 41 SER cc_start: 0.6871 (p) cc_final: 0.6466 (t) REVERT: s 43 MET cc_start: 0.7932 (mtp) cc_final: 0.7266 (mmm) REVERT: t 27 MET cc_start: 0.8131 (ttp) cc_final: 0.7786 (tmm) REVERT: t 28 ARG cc_start: 0.6472 (ptp90) cc_final: 0.6071 (ptm160) REVERT: t 31 ILE cc_start: 0.8104 (mt) cc_final: 0.7747 (mt) REVERT: t 32 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7197 (mmmt) REVERT: t 42 ASP cc_start: 0.4378 (OUTLIER) cc_final: 0.4163 (t70) REVERT: t 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7101 (mttt) REVERT: t 73 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7433 (mtm-85) REVERT: u 17 ARG cc_start: 0.6140 (ppt-90) cc_final: 0.4535 (mmp80) REVERT: u 34 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6456 (tpt90) REVERT: u 35 GLU cc_start: 0.8021 (tt0) cc_final: 0.7668 (tt0) REVERT: u 36 PHE cc_start: 0.7645 (t80) cc_final: 0.7291 (t80) REVERT: u 39 LYS cc_start: 0.7047 (mttt) cc_final: 0.6839 (mttt) outliers start: 214 outliers final: 94 residues processed: 1466 average time/residue: 1.4522 time to fit residues: 3685.2657 Evaluate side-chains 1311 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1191 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain N residue 46 ARG Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain z residue 135 ASN Chi-restraints excluded: chain z residue 223 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 548 optimal weight: 8.9990 chunk 306 optimal weight: 6.9990 chunk 821 optimal weight: 4.9990 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 988 optimal weight: 9.9990 chunk 1068 optimal weight: 3.9990 chunk 880 optimal weight: 7.9990 chunk 980 optimal weight: 4.9990 chunk 337 optimal weight: 0.9990 chunk 793 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS C 59 GLN C 85 ASN C 231 HIS C 259 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 37 ASN G 142 GLN H 43 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS N 62 ASN O 104 GLN R 18 GLN V 75 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 HIS 4 37 GLN b 18 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 HIS ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN h 15 ASN i 36 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 HIS ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 56 HIS s 68 HIS t 81 GLN z 135 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 165470 Z= 0.322 Angle : 0.782 14.882 247196 Z= 0.420 Chirality : 0.043 0.464 31417 Planarity : 0.008 0.137 13501 Dihedral : 24.219 178.346 81924 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.93 % Favored : 90.32 % Rotamer: Outliers : 5.83 % Allowed : 17.89 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.24 (0.10), residues: 6218 helix: -0.01 (0.11), residues: 1925 sheet: -1.96 (0.14), residues: 1115 loop : -2.29 (0.10), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 22 HIS 0.013 0.002 HIS E 165 PHE 0.028 0.002 PHE s 40 TYR 0.031 0.002 TYR F 6 ARG 0.033 0.001 ARG g 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1574 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1273 time to evaluate : 6.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8067 (mttt) cc_final: 0.7496 (mmmt) REVERT: C 29 PHE cc_start: 0.7648 (t80) cc_final: 0.7162 (t80) REVERT: C 67 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (mmtp) REVERT: C 68 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.5686 (mmm160) REVERT: C 116 GLN cc_start: 0.6234 (tp40) cc_final: 0.5929 (tp40) REVERT: C 139 THR cc_start: 0.8726 (m) cc_final: 0.8460 (p) REVERT: C 145 MET cc_start: 0.7934 (mmm) cc_final: 0.7673 (mmm) REVERT: C 159 THR cc_start: 0.8882 (m) cc_final: 0.8625 (p) REVERT: C 213 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7439 (mtt-85) REVERT: C 268 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7327 (tmm-80) REVERT: C 269 ARG cc_start: 0.7708 (mmm160) cc_final: 0.6920 (mmm-85) REVERT: D 30 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 32 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7589 (m110) REVERT: D 42 ASN cc_start: 0.7881 (m110) cc_final: 0.7207 (t0) REVERT: D 199 SER cc_start: 0.8202 (p) cc_final: 0.7927 (p) REVERT: D 204 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7652 (mtmm) REVERT: E 24 ASN cc_start: 0.8206 (t0) cc_final: 0.7822 (t0) REVERT: E 46 GLN cc_start: 0.8496 (mp10) cc_final: 0.8049 (mp10) REVERT: E 166 LYS cc_start: 0.7022 (mttt) cc_final: 0.6798 (mmtm) REVERT: E 170 ARG cc_start: 0.7768 (ttm170) cc_final: 0.6825 (ttm110) REVERT: F 31 GLU cc_start: 0.7483 (tt0) cc_final: 0.7222 (tt0) REVERT: F 68 LYS cc_start: 0.7775 (mptt) cc_final: 0.7544 (mmtt) REVERT: F 95 MET cc_start: 0.7428 (ttt) cc_final: 0.7128 (ttt) REVERT: F 97 GLU cc_start: 0.7693 (tp30) cc_final: 0.7125 (tp30) REVERT: F 114 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6317 (ttp-170) REVERT: F 128 SER cc_start: 0.7779 (t) cc_final: 0.7522 (p) REVERT: G 115 GLN cc_start: 0.7235 (tp-100) cc_final: 0.6879 (mp10) REVERT: G 159 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7233 (mtmm) REVERT: J 57 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7428 (mp) REVERT: J 67 ASN cc_start: 0.8099 (m-40) cc_final: 0.7866 (m-40) REVERT: J 84 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7489 (tp) REVERT: J 86 GLN cc_start: 0.8814 (pt0) cc_final: 0.8459 (pt0) REVERT: J 91 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7367 (tp30) REVERT: K 93 GLN cc_start: 0.7605 (pt0) cc_final: 0.7060 (pm20) REVERT: L 106 GLU cc_start: 0.8187 (pt0) cc_final: 0.7911 (pm20) REVERT: M 6 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7507 (ptp90) REVERT: M 44 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.7220 (mtm180) REVERT: M 47 GLU cc_start: 0.8018 (tp30) cc_final: 0.7813 (tp30) REVERT: M 59 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8026 (mmt-90) REVERT: M 75 GLU cc_start: 0.7108 (tp30) cc_final: 0.6575 (tm-30) REVERT: M 104 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8042 (mt-10) REVERT: M 136 MET cc_start: 0.6782 (ttp) cc_final: 0.6294 (tmm) REVERT: N 94 TYR cc_start: 0.8742 (m-80) cc_final: 0.8483 (m-80) REVERT: N 99 LYS cc_start: 0.7686 (mttp) cc_final: 0.7316 (mtmm) REVERT: P 36 LYS cc_start: 0.6406 (mmmt) cc_final: 0.5689 (mppt) REVERT: Q 83 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7927 (mtpp) REVERT: Q 110 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7711 (mt-10) REVERT: R 1 MET cc_start: 0.6268 (tpt) cc_final: 0.5807 (tpt) REVERT: R 21 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7703 (ttm110) REVERT: R 27 ILE cc_start: 0.7698 (mm) cc_final: 0.7454 (mm) REVERT: R 31 GLU cc_start: 0.7837 (tt0) cc_final: 0.6849 (tt0) REVERT: R 48 LYS cc_start: 0.7352 (ptmm) cc_final: 0.7069 (ptmm) REVERT: R 60 LYS cc_start: 0.7436 (mtmm) cc_final: 0.7102 (mttp) REVERT: R 97 LYS cc_start: 0.7750 (tttt) cc_final: 0.7526 (ttmm) REVERT: S 73 LYS cc_start: 0.7948 (mttt) cc_final: 0.7575 (mttt) REVERT: S 85 ILE cc_start: 0.8733 (mm) cc_final: 0.8485 (tp) REVERT: T 7 LEU cc_start: 0.8410 (mt) cc_final: 0.8199 (mm) REVERT: T 25 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7201 (pt0) REVERT: T 28 ASN cc_start: 0.7488 (t0) cc_final: 0.7064 (t0) REVERT: T 43 ILE cc_start: 0.8035 (mt) cc_final: 0.7825 (mm) REVERT: U 8 ASP cc_start: 0.7434 (m-30) cc_final: 0.7174 (m-30) REVERT: U 36 GLU cc_start: 0.7478 (pt0) cc_final: 0.6749 (pp20) REVERT: U 40 LEU cc_start: 0.8061 (mm) cc_final: 0.7758 (mm) REVERT: U 46 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7919 (mtpp) REVERT: U 101 THR cc_start: 0.8456 (m) cc_final: 0.8231 (t) REVERT: V 7 GLU cc_start: 0.6610 (mp0) cc_final: 0.6361 (mm-30) REVERT: V 11 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: V 30 ILE cc_start: 0.8235 (mt) cc_final: 0.7548 (tt) REVERT: W 64 LYS cc_start: 0.8032 (tptm) cc_final: 0.7396 (tptp) REVERT: X 15 ASN cc_start: 0.8920 (m110) cc_final: 0.8484 (m110) REVERT: X 36 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7540 (mtm110) REVERT: X 61 LYS cc_start: 0.7489 (mttt) cc_final: 0.7147 (mttm) REVERT: Y 6 LEU cc_start: 0.5985 (mt) cc_final: 0.5643 (mt) REVERT: Y 17 GLU cc_start: 0.8459 (tt0) cc_final: 0.7872 (tm-30) REVERT: Y 39 GLN cc_start: 0.8252 (mt0) cc_final: 0.7653 (mm110) REVERT: 0 11 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7382 (mmtp) REVERT: 0 35 GLU cc_start: 0.7957 (tt0) cc_final: 0.7579 (tt0) REVERT: 0 42 ILE cc_start: 0.8573 (mt) cc_final: 0.8170 (pt) REVERT: 3 14 LYS cc_start: 0.8460 (tttt) cc_final: 0.7770 (mmtp) REVERT: 3 38 LYS cc_start: 0.7325 (ttmt) cc_final: 0.6999 (tttm) REVERT: 3 61 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8436 (pp) REVERT: 4 9 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7323 (ttpp) REVERT: 4 12 ARG cc_start: 0.7552 (ttp-110) cc_final: 0.7337 (ttp-110) REVERT: 4 15 LYS cc_start: 0.7598 (ttmm) cc_final: 0.6834 (mtmm) REVERT: 5 1 MET cc_start: 0.0439 (tpt) cc_final: 0.0063 (mmm) REVERT: 6 16 CYS cc_start: 0.5966 (p) cc_final: 0.5670 (p) REVERT: 6 56 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.5176 (tpp80) REVERT: 6 61 ASN cc_start: 0.6135 (m110) cc_final: 0.5843 (p0) REVERT: b 26 MET cc_start: 0.7322 (mtp) cc_final: 0.7081 (mtp) REVERT: b 63 LYS cc_start: 0.7277 (tptt) cc_final: 0.6389 (mptt) REVERT: b 136 ARG cc_start: 0.5928 (mmm-85) cc_final: 0.5708 (ttp-170) REVERT: b 176 ASN cc_start: 0.7497 (t0) cc_final: 0.7231 (t0) REVERT: c 17 TRP cc_start: 0.8153 (m-90) cc_final: 0.7593 (m-90) REVERT: c 46 LEU cc_start: 0.6864 (mt) cc_final: 0.6602 (mp) REVERT: c 71 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6683 (ptp-110) REVERT: c 82 ASP cc_start: 0.8043 (m-30) cc_final: 0.7383 (m-30) REVERT: c 88 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7319 (mmmt) REVERT: c 105 VAL cc_start: 0.7068 (t) cc_final: 0.6784 (p) REVERT: c 166 TRP cc_start: 0.8288 (p-90) cc_final: 0.7781 (p-90) REVERT: c 171 ARG cc_start: 0.6883 (ttp-170) cc_final: 0.6546 (ttm-80) REVERT: c 187 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7738 (mt-10) REVERT: c 195 ILE cc_start: 0.8097 (mt) cc_final: 0.7885 (mm) REVERT: d 70 GLN cc_start: 0.8731 (tt0) cc_final: 0.8190 (mm-40) REVERT: d 183 ARG cc_start: 0.5672 (ptt-90) cc_final: 0.5170 (ptp-110) REVERT: d 193 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6200 (t70) REVERT: e 40 ASP cc_start: 0.8151 (p0) cc_final: 0.6813 (p0) REVERT: e 85 LYS cc_start: 0.7684 (mptt) cc_final: 0.7265 (mtpp) REVERT: f 1 MET cc_start: 0.6994 (mmm) cc_final: 0.6737 (mmt) REVERT: f 2 ARG cc_start: 0.7404 (mmt180) cc_final: 0.7080 (mtt-85) REVERT: f 9 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6513 (ptp) REVERT: f 62 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6851 (ttm) REVERT: g 20 GLU cc_start: 0.7242 (tt0) cc_final: 0.6926 (mm-30) REVERT: g 24 LYS cc_start: 0.6761 (tptm) cc_final: 0.6359 (tptt) REVERT: g 57 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6665 (mm-30) REVERT: g 69 ARG cc_start: 0.6189 (ttm170) cc_final: 0.5864 (mtm-85) REVERT: g 73 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6657 (tm-30) REVERT: g 142 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6929 (mmm160) REVERT: g 145 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6777 (tm-30) REVERT: h 49 LYS cc_start: 0.7137 (mttp) cc_final: 0.6915 (mmtt) REVERT: h 68 LYS cc_start: 0.7182 (tttp) cc_final: 0.6805 (mmmm) REVERT: h 79 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8130 (ptt90) REVERT: h 86 LYS cc_start: 0.8226 (mttm) cc_final: 0.7858 (mtmm) REVERT: h 87 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.7019 (mtp85) REVERT: h 93 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7358 (pttt) REVERT: i 4 GLN cc_start: 0.4951 (OUTLIER) cc_final: 0.4528 (tt0) REVERT: i 99 LYS cc_start: 0.7580 (ttpt) cc_final: 0.6935 (tptp) REVERT: i 108 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6496 (ptm-80) REVERT: j 14 ASP cc_start: 0.8261 (t0) cc_final: 0.7902 (t0) REVERT: j 27 GLU cc_start: 0.6743 (tt0) cc_final: 0.6246 (pp20) REVERT: j 37 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5945 (mmp80) REVERT: j 53 ILE cc_start: 0.8825 (tt) cc_final: 0.8617 (pt) REVERT: k 80 ASN cc_start: 0.6276 (p0) cc_final: 0.5692 (p0) REVERT: k 125 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7842 (tptm) REVERT: l 71 HIS cc_start: 0.6850 (p90) cc_final: 0.6277 (p90) REVERT: l 85 ARG cc_start: 0.7361 (ptm160) cc_final: 0.7081 (ptm160) REVERT: m 51 GLN cc_start: 0.6684 (tt0) cc_final: 0.5919 (mp10) REVERT: m 65 GLU cc_start: 0.6808 (tp30) cc_final: 0.6100 (mp0) REVERT: m 92 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.6512 (ttp80) REVERT: n 15 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6891 (tt) REVERT: n 20 PHE cc_start: 0.2988 (OUTLIER) cc_final: 0.2233 (t80) REVERT: n 42 TRP cc_start: 0.6881 (t-100) cc_final: 0.6436 (t60) REVERT: o 58 MET cc_start: 0.7156 (mtm) cc_final: 0.6855 (mtt) REVERT: o 61 GLN cc_start: 0.7951 (tp40) cc_final: 0.7583 (tt0) REVERT: p 1 MET cc_start: 0.5689 (ttp) cc_final: 0.5301 (ttp) REVERT: p 24 SER cc_start: 0.7155 (t) cc_final: 0.6600 (m) REVERT: s 11 ASP cc_start: 0.5039 (m-30) cc_final: 0.4578 (m-30) REVERT: s 43 MET cc_start: 0.7885 (mtp) cc_final: 0.7134 (mmm) REVERT: s 55 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: t 17 ARG cc_start: 0.8512 (ptm-80) cc_final: 0.8133 (ptm-80) REVERT: t 27 MET cc_start: 0.8209 (ttp) cc_final: 0.7687 (tmm) REVERT: t 28 ARG cc_start: 0.6892 (ptp90) cc_final: 0.6239 (mtt180) REVERT: t 32 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7259 (mmmt) REVERT: t 68 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.6831 (tppt) REVERT: t 73 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7513 (mtp180) REVERT: u 35 GLU cc_start: 0.8086 (tt0) cc_final: 0.7765 (tt0) outliers start: 301 outliers final: 189 residues processed: 1441 average time/residue: 1.4122 time to fit residues: 3476.0150 Evaluate side-chains 1387 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1174 time to evaluate : 6.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain d residue 193 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 125 LYS Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 93 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 49 GLN Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 10 CYS Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 42 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 223 ARG Chi-restraints excluded: chain z residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 977 optimal weight: 0.9980 chunk 743 optimal weight: 20.0000 chunk 513 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 471 optimal weight: 0.9990 chunk 664 optimal weight: 20.0000 chunk 992 optimal weight: 6.9990 chunk 1050 optimal weight: 10.0000 chunk 518 optimal weight: 4.9990 chunk 940 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN G 37 ASN G 142 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN O 104 GLN P 114 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN 0 5 ASN 1 44 GLN 4 37 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 GLN d 35 GLN ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 ASN e 42 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN h 15 ASN k 14 GLN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 ASN m 7 ASN ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 165470 Z= 0.226 Angle : 0.699 15.188 247196 Z= 0.380 Chirality : 0.037 0.472 31417 Planarity : 0.007 0.128 13501 Dihedral : 24.116 177.640 81887 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.35 % Favored : 91.94 % Rotamer: Outliers : 5.81 % Allowed : 19.92 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.90 (0.10), residues: 6218 helix: 0.28 (0.12), residues: 1933 sheet: -1.68 (0.14), residues: 1166 loop : -2.12 (0.10), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 200 HIS 0.009 0.001 HIS o 45 PHE 0.025 0.002 PHE F 137 TYR 0.016 0.002 TYR V 31 ARG 0.010 0.001 ARG b 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1222 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8120 (mttt) cc_final: 0.7533 (mmmt) REVERT: C 68 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.5748 (mmm160) REVERT: C 116 GLN cc_start: 0.6564 (tp40) cc_final: 0.6264 (tp40) REVERT: C 139 THR cc_start: 0.8758 (m) cc_final: 0.8433 (p) REVERT: C 145 MET cc_start: 0.7983 (mmm) cc_final: 0.7680 (mmm) REVERT: C 159 THR cc_start: 0.8821 (m) cc_final: 0.8575 (p) REVERT: C 213 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7269 (mtt-85) REVERT: C 265 PHE cc_start: 0.7529 (m-10) cc_final: 0.7317 (m-10) REVERT: C 268 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7409 (tmm-80) REVERT: C 269 ARG cc_start: 0.7662 (mmm160) cc_final: 0.6856 (mmm-85) REVERT: D 30 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7471 (mt-10) REVERT: D 32 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7833 (m110) REVERT: D 42 ASN cc_start: 0.7723 (m110) cc_final: 0.7074 (t0) REVERT: D 81 GLU cc_start: 0.8055 (tt0) cc_final: 0.7795 (tt0) REVERT: D 199 SER cc_start: 0.8213 (p) cc_final: 0.7910 (p) REVERT: D 204 LYS cc_start: 0.7874 (ptpt) cc_final: 0.7636 (mtmm) REVERT: E 24 ASN cc_start: 0.8101 (t0) cc_final: 0.7767 (t0) REVERT: E 108 ILE cc_start: 0.8167 (pt) cc_final: 0.7820 (mt) REVERT: E 111 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: E 166 LYS cc_start: 0.7230 (mttt) cc_final: 0.6923 (mmtm) REVERT: E 168 ASP cc_start: 0.7874 (t0) cc_final: 0.7519 (t0) REVERT: E 170 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7248 (ttm110) REVERT: F 31 GLU cc_start: 0.7526 (tt0) cc_final: 0.7250 (tt0) REVERT: F 68 LYS cc_start: 0.7735 (mptt) cc_final: 0.7530 (mmtt) REVERT: F 97 GLU cc_start: 0.7619 (tp30) cc_final: 0.7055 (tp30) REVERT: F 112 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6172 (m-30) REVERT: F 128 SER cc_start: 0.7884 (t) cc_final: 0.7498 (p) REVERT: G 129 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7508 (mm-30) REVERT: G 154 GLU cc_start: 0.6813 (tt0) cc_final: 0.6471 (mp0) REVERT: G 159 LYS cc_start: 0.7488 (mtpp) cc_final: 0.6808 (mtmm) REVERT: J 57 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7449 (mp) REVERT: J 86 GLN cc_start: 0.8841 (pt0) cc_final: 0.8621 (pt0) REVERT: J 91 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7396 (tp30) REVERT: K 93 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: L 14 LYS cc_start: 0.7623 (ttmm) cc_final: 0.6884 (tptt) REVERT: L 106 GLU cc_start: 0.8265 (pt0) cc_final: 0.7989 (pm20) REVERT: M 6 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7558 (ptp90) REVERT: M 44 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.7172 (mtm180) REVERT: M 47 GLU cc_start: 0.7954 (tp30) cc_final: 0.7743 (tp30) REVERT: M 59 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8062 (mmt-90) REVERT: M 104 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7825 (mt-10) REVERT: N 94 TYR cc_start: 0.8769 (m-80) cc_final: 0.8466 (m-80) REVERT: N 103 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6431 (ttm170) REVERT: O 63 LYS cc_start: 0.5594 (OUTLIER) cc_final: 0.4433 (tptp) REVERT: P 36 LYS cc_start: 0.6466 (mmmt) cc_final: 0.5778 (mppt) REVERT: P 88 ARG cc_start: 0.7053 (ptt-90) cc_final: 0.6394 (ptt90) REVERT: Q 83 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7849 (mtpp) REVERT: R 21 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7696 (ttm110) REVERT: R 27 ILE cc_start: 0.7735 (mm) cc_final: 0.7284 (mt) REVERT: R 31 GLU cc_start: 0.7702 (tt0) cc_final: 0.6857 (tt0) REVERT: S 19 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7649 (mp) REVERT: S 73 LYS cc_start: 0.7925 (mttt) cc_final: 0.7488 (mttt) REVERT: T 25 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7256 (pt0) REVERT: T 28 ASN cc_start: 0.7162 (t0) cc_final: 0.6802 (t0) REVERT: T 56 GLU cc_start: 0.7831 (mm-30) cc_final: 0.6645 (pt0) REVERT: U 8 ASP cc_start: 0.7471 (m-30) cc_final: 0.7034 (m-30) REVERT: U 36 GLU cc_start: 0.7506 (pt0) cc_final: 0.6902 (pm20) REVERT: U 46 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7899 (mtpp) REVERT: U 59 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7007 (mm-30) REVERT: U 101 THR cc_start: 0.8518 (m) cc_final: 0.8315 (t) REVERT: V 11 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: V 30 ILE cc_start: 0.8242 (mt) cc_final: 0.7456 (tt) REVERT: V 46 LYS cc_start: 0.7254 (mmmt) cc_final: 0.7045 (mmmt) REVERT: V 59 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6900 (mp0) REVERT: V 73 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7486 (mmtt) REVERT: W 64 LYS cc_start: 0.7983 (tptm) cc_final: 0.7359 (tptp) REVERT: X 36 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7423 (mtm110) REVERT: X 61 LYS cc_start: 0.7508 (mttt) cc_final: 0.7246 (mttm) REVERT: Y 6 LEU cc_start: 0.6266 (mt) cc_final: 0.5670 (mt) REVERT: Y 17 GLU cc_start: 0.8413 (tt0) cc_final: 0.7879 (tm-30) REVERT: Y 39 GLN cc_start: 0.8248 (mt0) cc_final: 0.7594 (mm-40) REVERT: 0 11 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7322 (mmtp) REVERT: 0 35 GLU cc_start: 0.7961 (tt0) cc_final: 0.7633 (tt0) REVERT: 0 49 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7861 (mtm-85) REVERT: 0 51 ARG cc_start: 0.8260 (ttm170) cc_final: 0.8039 (ttp-170) REVERT: 3 14 LYS cc_start: 0.8366 (tttt) cc_final: 0.7707 (mmtp) REVERT: 3 38 LYS cc_start: 0.7285 (ttmt) cc_final: 0.6990 (tttm) REVERT: 3 61 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8231 (pp) REVERT: 4 9 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7293 (ttpp) REVERT: 4 15 LYS cc_start: 0.7568 (ttmm) cc_final: 0.6788 (mtmm) REVERT: 5 1 MET cc_start: 0.0574 (tpt) cc_final: 0.0235 (mmm) REVERT: 6 16 CYS cc_start: 0.6000 (p) cc_final: 0.5721 (p) REVERT: 6 56 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5011 (tpp80) REVERT: b 8 MET cc_start: 0.6224 (ppp) cc_final: 0.5684 (ppp) REVERT: b 23 ASN cc_start: 0.8741 (t0) cc_final: 0.8433 (t0) REVERT: b 136 ARG cc_start: 0.5767 (mmm-85) cc_final: 0.5527 (tmm160) REVERT: b 176 ASN cc_start: 0.7368 (t0) cc_final: 0.7149 (t0) REVERT: b 197 PHE cc_start: 0.6529 (m-80) cc_final: 0.6123 (m-80) REVERT: b 211 LEU cc_start: 0.5906 (tp) cc_final: 0.5363 (mt) REVERT: c 17 TRP cc_start: 0.8240 (m-90) cc_final: 0.7766 (m-90) REVERT: c 71 ARG cc_start: 0.7222 (mmm-85) cc_final: 0.6701 (mtp85) REVERT: c 76 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6084 (pt) REVERT: c 82 ASP cc_start: 0.7801 (m-30) cc_final: 0.7466 (m-30) REVERT: c 88 LYS cc_start: 0.7496 (mmmt) cc_final: 0.7220 (mmmt) REVERT: c 105 VAL cc_start: 0.6958 (t) cc_final: 0.6675 (p) REVERT: c 166 TRP cc_start: 0.8214 (p-90) cc_final: 0.7644 (p-90) REVERT: c 187 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7830 (mt-10) REVERT: d 57 LYS cc_start: 0.7102 (ttpt) cc_final: 0.6805 (tttm) REVERT: d 183 ARG cc_start: 0.5622 (ptt-90) cc_final: 0.5114 (ptp-110) REVERT: e 85 LYS cc_start: 0.7619 (mptt) cc_final: 0.7293 (mtpp) REVERT: f 1 MET cc_start: 0.7002 (mmm) cc_final: 0.6736 (mmm) REVERT: f 2 ARG cc_start: 0.7500 (mmt180) cc_final: 0.6948 (mtt180) REVERT: f 29 ILE cc_start: 0.6751 (mt) cc_final: 0.6457 (mp) REVERT: f 62 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6742 (ttm) REVERT: f 92 THR cc_start: 0.6540 (OUTLIER) cc_final: 0.6298 (p) REVERT: f 96 VAL cc_start: 0.6464 (m) cc_final: 0.6037 (p) REVERT: g 20 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: g 24 LYS cc_start: 0.6665 (tptm) cc_final: 0.6263 (tptt) REVERT: g 69 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6293 (mtm-85) REVERT: g 142 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6899 (mmm160) REVERT: g 147 ASN cc_start: 0.7437 (m-40) cc_final: 0.7202 (m110) REVERT: h 68 LYS cc_start: 0.7328 (tttp) cc_final: 0.7010 (mmmm) REVERT: h 79 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8074 (ptt90) REVERT: h 86 LYS cc_start: 0.8148 (mttm) cc_final: 0.7855 (mtmm) REVERT: h 87 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6359 (mtt-85) REVERT: h 93 LYS cc_start: 0.8170 (ptpp) cc_final: 0.7423 (pttt) REVERT: i 4 GLN cc_start: 0.4765 (OUTLIER) cc_final: 0.4502 (tp-100) REVERT: i 29 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6104 (mp) REVERT: i 45 MET cc_start: 0.6228 (ptm) cc_final: 0.5998 (ptm) REVERT: i 99 LYS cc_start: 0.7487 (ttpt) cc_final: 0.6988 (tptp) REVERT: i 108 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6141 (ptm-80) REVERT: j 14 ASP cc_start: 0.8221 (t0) cc_final: 0.7894 (t0) REVERT: j 27 GLU cc_start: 0.6853 (tt0) cc_final: 0.6322 (pp20) REVERT: k 14 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6887 (mm-40) REVERT: k 80 ASN cc_start: 0.6199 (p0) cc_final: 0.5992 (p0) REVERT: k 125 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7775 (tptm) REVERT: l 60 PHE cc_start: 0.6877 (m-80) cc_final: 0.6421 (m-10) REVERT: l 69 GLU cc_start: 0.5864 (tt0) cc_final: 0.5642 (mt-10) REVERT: l 71 HIS cc_start: 0.6652 (p90) cc_final: 0.6027 (p90) REVERT: l 72 ASN cc_start: 0.6879 (p0) cc_final: 0.6481 (p0) REVERT: l 85 ARG cc_start: 0.7363 (ptm160) cc_final: 0.6858 (ptp-170) REVERT: m 65 GLU cc_start: 0.6681 (tp30) cc_final: 0.5649 (mp0) REVERT: m 91 ARG cc_start: 0.7221 (ptp90) cc_final: 0.5300 (ptm160) REVERT: m 92 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.6605 (ttp80) REVERT: n 3 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7170 (mt0) REVERT: n 15 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7054 (tt) REVERT: n 20 PHE cc_start: 0.3101 (OUTLIER) cc_final: 0.2498 (t80) REVERT: n 22 LYS cc_start: 0.7909 (tptp) cc_final: 0.7545 (mmtm) REVERT: n 42 TRP cc_start: 0.6813 (t-100) cc_final: 0.6415 (t60) REVERT: o 25 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7124 (mp0) REVERT: o 58 MET cc_start: 0.7168 (mtm) cc_final: 0.6879 (mtt) REVERT: o 61 GLN cc_start: 0.7962 (tp40) cc_final: 0.7543 (tt0) REVERT: p 1 MET cc_start: 0.5560 (ttp) cc_final: 0.5226 (ttp) REVERT: p 24 SER cc_start: 0.7124 (t) cc_final: 0.6586 (m) REVERT: p 52 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7261 (tt) REVERT: q 78 VAL cc_start: 0.4970 (OUTLIER) cc_final: 0.4765 (p) REVERT: s 11 ASP cc_start: 0.4765 (OUTLIER) cc_final: 0.4264 (m-30) REVERT: s 43 MET cc_start: 0.7861 (mtp) cc_final: 0.7140 (mmm) REVERT: s 55 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: s 65 MET cc_start: 0.6069 (ptp) cc_final: 0.5199 (ptp) REVERT: t 14 GLU cc_start: 0.6370 (tp30) cc_final: 0.6097 (tp30) REVERT: t 17 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.8066 (ptm-80) REVERT: t 28 ARG cc_start: 0.6855 (ptp90) cc_final: 0.6558 (mtt180) REVERT: t 32 LYS cc_start: 0.7646 (mmmt) cc_final: 0.7349 (mmmt) REVERT: t 68 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7159 (mttm) REVERT: t 73 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7573 (mtp180) REVERT: u 16 ARG cc_start: 0.5885 (ttp-110) cc_final: 0.5643 (ttp-110) REVERT: u 17 ARG cc_start: 0.6116 (ppt-90) cc_final: 0.4463 (mmp80) REVERT: u 32 ARG cc_start: 0.6961 (tmt90) cc_final: 0.6688 (tmt90) REVERT: u 39 LYS cc_start: 0.7071 (mttt) cc_final: 0.6825 (mttt) outliers start: 300 outliers final: 183 residues processed: 1397 average time/residue: 1.4198 time to fit residues: 3382.4599 Evaluate side-chains 1350 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1136 time to evaluate : 6.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 186 SER Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 112 VAL Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 10 CYS Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain r residue 42 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 223 ARG Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 875 optimal weight: 5.9990 chunk 596 optimal weight: 10.0000 chunk 15 optimal weight: 10.9990 chunk 782 optimal weight: 10.0000 chunk 433 optimal weight: 3.9990 chunk 896 optimal weight: 0.7980 chunk 726 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 536 optimal weight: 5.9990 chunk 943 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 195 GLN G 127 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN O 104 GLN X 15 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 4 37 GLN b 14 HIS ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 197 HIS ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN k 118 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 HIS ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 66 HIS z 118 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 165470 Z= 0.326 Angle : 0.772 15.503 247196 Z= 0.411 Chirality : 0.040 0.405 31417 Planarity : 0.007 0.138 13501 Dihedral : 24.151 179.743 81885 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.94 % Favored : 90.40 % Rotamer: Outliers : 6.56 % Allowed : 20.14 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.10), residues: 6218 helix: 0.11 (0.12), residues: 1936 sheet: -1.61 (0.14), residues: 1124 loop : -2.09 (0.10), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 200 HIS 0.012 0.002 HIS V 44 PHE 0.019 0.002 PHE V 26 TYR 0.021 0.002 TYR Q 75 ARG 0.008 0.001 ARG s 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1176 time to evaluate : 6.648 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: C 27 LYS cc_start: 0.8146 (mttt) cc_final: 0.7555 (mmmt) REVERT: C 68 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.5818 (mmm160) REVERT: C 99 GLU cc_start: 0.7612 (tt0) cc_final: 0.7401 (tt0) REVERT: C 116 GLN cc_start: 0.6642 (tp40) cc_final: 0.6391 (tp40) REVERT: C 139 THR cc_start: 0.8720 (m) cc_final: 0.8454 (p) REVERT: C 145 MET cc_start: 0.8114 (mmm) cc_final: 0.7779 (mmm) REVERT: C 159 THR cc_start: 0.8975 (m) cc_final: 0.8689 (p) REVERT: C 213 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7500 (mtt-85) REVERT: C 265 PHE cc_start: 0.7788 (m-10) cc_final: 0.7587 (m-10) REVERT: C 268 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7400 (tmm-80) REVERT: C 269 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7011 (mmm-85) REVERT: D 42 ASN cc_start: 0.7674 (m110) cc_final: 0.6804 (t0) REVERT: D 199 SER cc_start: 0.8124 (p) cc_final: 0.7813 (p) REVERT: E 24 ASN cc_start: 0.8105 (t0) cc_final: 0.7772 (t0) REVERT: E 108 ILE cc_start: 0.8196 (pt) cc_final: 0.7964 (mt) REVERT: E 111 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: E 166 LYS cc_start: 0.7162 (mttt) cc_final: 0.6891 (mmtm) REVERT: F 31 GLU cc_start: 0.7484 (tt0) cc_final: 0.7227 (tt0) REVERT: F 93 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6822 (tm-30) REVERT: F 95 MET cc_start: 0.7378 (ttp) cc_final: 0.7081 (ttt) REVERT: F 97 GLU cc_start: 0.7584 (tp30) cc_final: 0.6963 (tp30) REVERT: F 114 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6226 (ttp-170) REVERT: F 128 SER cc_start: 0.7899 (t) cc_final: 0.7445 (p) REVERT: G 154 GLU cc_start: 0.6843 (tt0) cc_final: 0.6486 (tt0) REVERT: G 159 LYS cc_start: 0.7429 (mtpp) cc_final: 0.7043 (mtmm) REVERT: J 57 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7348 (mp) REVERT: J 75 TYR cc_start: 0.8433 (m-80) cc_final: 0.8096 (m-80) REVERT: J 84 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7463 (tp) REVERT: K 93 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: L 106 GLU cc_start: 0.8244 (pt0) cc_final: 0.7939 (pm20) REVERT: M 6 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7511 (ptp90) REVERT: M 44 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7133 (mtt180) REVERT: M 59 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8058 (mmt-90) REVERT: M 65 ILE cc_start: 0.8617 (mt) cc_final: 0.8390 (mt) REVERT: M 75 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6977 (tm-30) REVERT: N 96 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7799 (ttm170) REVERT: N 103 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6362 (ttm170) REVERT: N 114 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6174 (pm20) REVERT: O 4 LYS cc_start: 0.8316 (tptp) cc_final: 0.8033 (tptt) REVERT: P 36 LYS cc_start: 0.6332 (mmmt) cc_final: 0.5660 (mppt) REVERT: P 88 ARG cc_start: 0.7002 (ptt-90) cc_final: 0.6347 (ptt90) REVERT: Q 83 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7817 (mtpp) REVERT: R 21 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7655 (ttm110) REVERT: R 31 GLU cc_start: 0.7846 (tt0) cc_final: 0.7024 (tt0) REVERT: S 73 LYS cc_start: 0.7989 (mttt) cc_final: 0.7726 (mtpt) REVERT: T 12 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7858 (tpm170) REVERT: T 25 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7341 (pt0) REVERT: T 28 ASN cc_start: 0.7223 (t0) cc_final: 0.6978 (t0) REVERT: T 56 GLU cc_start: 0.8031 (mm-30) cc_final: 0.6772 (pt0) REVERT: U 4 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8189 (mp) REVERT: U 8 ASP cc_start: 0.7571 (m-30) cc_final: 0.7177 (m-30) REVERT: U 36 GLU cc_start: 0.7657 (pt0) cc_final: 0.7036 (pm20) REVERT: U 46 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7926 (mtpt) REVERT: U 59 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6782 (mm-30) REVERT: V 11 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: V 73 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7495 (mmtt) REVERT: W 64 LYS cc_start: 0.7745 (tptm) cc_final: 0.7155 (tptp) REVERT: X 61 LYS cc_start: 0.7544 (mttt) cc_final: 0.7316 (mttm) REVERT: Y 6 LEU cc_start: 0.6238 (mt) cc_final: 0.5709 (mt) REVERT: Y 17 GLU cc_start: 0.8453 (tt0) cc_final: 0.7911 (tm-30) REVERT: Y 39 GLN cc_start: 0.8251 (mt0) cc_final: 0.7634 (mm-40) REVERT: 0 11 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7321 (mmtp) REVERT: 0 35 GLU cc_start: 0.7909 (tt0) cc_final: 0.7577 (tt0) REVERT: 3 14 LYS cc_start: 0.8508 (tttt) cc_final: 0.7809 (mmtp) REVERT: 3 27 ASN cc_start: 0.8945 (m-40) cc_final: 0.8727 (m-40) REVERT: 3 38 LYS cc_start: 0.7311 (ttmt) cc_final: 0.6964 (tttm) REVERT: 4 9 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7332 (ptmm) REVERT: 4 15 LYS cc_start: 0.7596 (ttmm) cc_final: 0.6823 (mtmm) REVERT: 5 1 MET cc_start: 0.0798 (tpt) cc_final: 0.0512 (mmm) REVERT: 6 16 CYS cc_start: 0.5719 (p) cc_final: 0.5421 (p) REVERT: 6 56 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5116 (tpp80) REVERT: b 8 MET cc_start: 0.6384 (ppp) cc_final: 0.5729 (ppp) REVERT: b 136 ARG cc_start: 0.5707 (mmm-85) cc_final: 0.5420 (ttp-170) REVERT: c 17 TRP cc_start: 0.8346 (m-90) cc_final: 0.7917 (m-90) REVERT: c 71 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6764 (mtp85) REVERT: c 79 LYS cc_start: 0.5752 (tptt) cc_final: 0.5404 (mmtt) REVERT: c 82 ASP cc_start: 0.7809 (m-30) cc_final: 0.7559 (m-30) REVERT: c 88 LYS cc_start: 0.7552 (mmmt) cc_final: 0.7352 (mmmt) REVERT: c 105 VAL cc_start: 0.6856 (t) cc_final: 0.6596 (p) REVERT: c 166 TRP cc_start: 0.8188 (p-90) cc_final: 0.7781 (p-90) REVERT: c 169 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7378 (mt-10) REVERT: c 187 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7736 (mt-10) REVERT: d 57 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6842 (tttp) REVERT: d 70 GLN cc_start: 0.8537 (tt0) cc_final: 0.8070 (mm-40) REVERT: d 183 ARG cc_start: 0.5391 (ptt-90) cc_final: 0.5036 (ptp-110) REVERT: e 85 LYS cc_start: 0.7895 (mptt) cc_final: 0.7438 (mtpp) REVERT: f 2 ARG cc_start: 0.7560 (mmt180) cc_final: 0.6891 (mtt180) REVERT: f 29 ILE cc_start: 0.6933 (mt) cc_final: 0.6703 (mp) REVERT: f 62 MET cc_start: 0.7189 (ttm) cc_final: 0.6795 (ttm) REVERT: f 92 THR cc_start: 0.6355 (OUTLIER) cc_final: 0.5526 (p) REVERT: g 20 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: g 24 LYS cc_start: 0.6629 (tptm) cc_final: 0.6334 (tptp) REVERT: g 69 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6470 (mtm-85) REVERT: g 109 LYS cc_start: 0.7499 (mptt) cc_final: 0.7047 (ptpt) REVERT: g 134 VAL cc_start: 0.7413 (p) cc_final: 0.7186 (m) REVERT: h 49 LYS cc_start: 0.6844 (mptt) cc_final: 0.6616 (mmtt) REVERT: h 57 GLU cc_start: 0.7251 (tm-30) cc_final: 0.7050 (tm-30) REVERT: h 68 LYS cc_start: 0.7395 (tttp) cc_final: 0.7130 (mmtp) REVERT: h 79 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7953 (ptt90) REVERT: h 86 LYS cc_start: 0.8176 (mttm) cc_final: 0.7849 (mtmm) REVERT: i 4 GLN cc_start: 0.4764 (OUTLIER) cc_final: 0.4454 (tp-100) REVERT: i 29 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.5815 (mp) REVERT: i 99 LYS cc_start: 0.7438 (ttpt) cc_final: 0.6912 (tptp) REVERT: i 108 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6316 (ptm-80) REVERT: j 19 ASP cc_start: 0.6766 (m-30) cc_final: 0.6516 (m-30) REVERT: j 20 GLN cc_start: 0.7219 (mp10) cc_final: 0.6697 (mp10) REVERT: j 27 GLU cc_start: 0.6859 (tt0) cc_final: 0.6276 (pp20) REVERT: j 50 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7827 (p) REVERT: j 68 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7602 (mtt180) REVERT: k 79 LYS cc_start: 0.8072 (mppt) cc_final: 0.7721 (mmtt) REVERT: k 80 ASN cc_start: 0.6301 (p0) cc_final: 0.6093 (p0) REVERT: k 115 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8047 (mt) REVERT: k 125 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7741 (tptm) REVERT: l 69 GLU cc_start: 0.6042 (tt0) cc_final: 0.5761 (mt-10) REVERT: l 71 HIS cc_start: 0.6662 (p90) cc_final: 0.5903 (p90) REVERT: l 72 ASN cc_start: 0.6835 (p0) cc_final: 0.6527 (p0) REVERT: l 85 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6833 (ptp-170) REVERT: l 111 GLN cc_start: 0.7570 (mt0) cc_final: 0.7219 (mt0) REVERT: m 91 ARG cc_start: 0.7324 (ptp90) cc_final: 0.5463 (ptm160) REVERT: m 92 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.6670 (ttp80) REVERT: n 22 LYS cc_start: 0.7849 (tptp) cc_final: 0.7492 (mmtt) REVERT: n 42 TRP cc_start: 0.6810 (t-100) cc_final: 0.6372 (t60) REVERT: o 25 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7168 (mp0) REVERT: o 58 MET cc_start: 0.7170 (mtm) cc_final: 0.6881 (mtt) REVERT: o 61 GLN cc_start: 0.8049 (tp40) cc_final: 0.7508 (tt0) REVERT: p 24 SER cc_start: 0.7249 (t) cc_final: 0.6762 (m) REVERT: p 52 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.7013 (tt) REVERT: q 78 VAL cc_start: 0.5012 (OUTLIER) cc_final: 0.4741 (p) REVERT: s 43 MET cc_start: 0.7997 (mtp) cc_final: 0.7523 (mmm) REVERT: s 65 MET cc_start: 0.5985 (ptp) cc_final: 0.5202 (ptp) REVERT: t 14 GLU cc_start: 0.6554 (tp30) cc_final: 0.6308 (tp30) REVERT: t 68 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6989 (tppt) REVERT: u 32 ARG cc_start: 0.7026 (tmt90) cc_final: 0.6715 (tmt90) REVERT: u 35 GLU cc_start: 0.8096 (tt0) cc_final: 0.7805 (tt0) REVERT: u 39 LYS cc_start: 0.6947 (mttt) cc_final: 0.6697 (mttt) REVERT: z 139 MET cc_start: 0.0027 (mmm) cc_final: -0.0180 (mmm) REVERT: z 223 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.4561 (tpt90) outliers start: 339 outliers final: 240 residues processed: 1377 average time/residue: 1.3778 time to fit residues: 3260.9510 Evaluate side-chains 1402 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1135 time to evaluate : 6.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 86 CYS Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 193 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 125 LYS Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 63 ASP Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 112 VAL Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 10 CYS Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain r residue 42 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 223 ARG Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 353 optimal weight: 3.9990 chunk 946 optimal weight: 0.0870 chunk 207 optimal weight: 7.9990 chunk 616 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 1051 optimal weight: 7.9990 chunk 873 optimal weight: 9.9990 chunk 486 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 552 optimal weight: 0.9980 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 134 HIS D 136 ASN E 195 GLN H 20 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 62 ASN N 73 ASN O 104 GLN P 40 GLN X 15 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 4 37 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 40 HIS ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 165470 Z= 0.162 Angle : 0.662 15.036 247196 Z= 0.361 Chirality : 0.034 0.473 31417 Planarity : 0.006 0.124 13501 Dihedral : 24.047 179.068 81875 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.20 % Favored : 92.17 % Rotamer: Outliers : 4.67 % Allowed : 22.36 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.64 (0.10), residues: 6218 helix: 0.44 (0.12), residues: 1943 sheet: -1.37 (0.14), residues: 1155 loop : -2.00 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 200 HIS 0.007 0.001 HIS d 40 PHE 0.018 0.001 PHE h 65 TYR 0.018 0.001 TYR D 45 ARG 0.007 0.000 ARG n 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1204 time to evaluate : 6.583 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: C 27 LYS cc_start: 0.8076 (mttt) cc_final: 0.7518 (mmmt) REVERT: C 86 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6594 (ttm-80) REVERT: C 97 ASP cc_start: 0.7295 (p0) cc_final: 0.6701 (p0) REVERT: C 139 THR cc_start: 0.8775 (m) cc_final: 0.8431 (p) REVERT: C 145 MET cc_start: 0.8127 (mmm) cc_final: 0.7802 (mmm) REVERT: C 159 THR cc_start: 0.8813 (m) cc_final: 0.8544 (p) REVERT: C 193 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7032 (mt-10) REVERT: C 213 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7312 (mtt-85) REVERT: C 265 PHE cc_start: 0.7832 (m-10) cc_final: 0.7626 (m-10) REVERT: C 268 ARG cc_start: 0.7590 (ttt90) cc_final: 0.7354 (tmm-80) REVERT: C 269 ARG cc_start: 0.7631 (mmm160) cc_final: 0.6998 (mmm-85) REVERT: D 42 ASN cc_start: 0.7604 (m110) cc_final: 0.6789 (t0) REVERT: D 199 SER cc_start: 0.8118 (p) cc_final: 0.7793 (p) REVERT: E 24 ASN cc_start: 0.8084 (t0) cc_final: 0.7757 (t0) REVERT: E 108 ILE cc_start: 0.8163 (pt) cc_final: 0.7957 (mt) REVERT: E 111 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: E 166 LYS cc_start: 0.7171 (mttt) cc_final: 0.6883 (mmtm) REVERT: E 170 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7213 (ttm110) REVERT: F 31 GLU cc_start: 0.7517 (tt0) cc_final: 0.7228 (tt0) REVERT: F 93 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6829 (tm-30) REVERT: F 95 MET cc_start: 0.7390 (ttp) cc_final: 0.7159 (ttt) REVERT: F 97 GLU cc_start: 0.7542 (tp30) cc_final: 0.6926 (tp30) REVERT: F 114 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6552 (ttp-170) REVERT: F 128 SER cc_start: 0.7963 (t) cc_final: 0.7497 (p) REVERT: G 154 GLU cc_start: 0.6745 (tt0) cc_final: 0.6293 (tt0) REVERT: G 159 LYS cc_start: 0.7393 (mtpp) cc_final: 0.7164 (mtmm) REVERT: J 75 TYR cc_start: 0.8324 (m-80) cc_final: 0.7999 (m-80) REVERT: J 84 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7470 (tp) REVERT: K 93 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: L 7 SER cc_start: 0.8424 (p) cc_final: 0.7820 (t) REVERT: L 106 GLU cc_start: 0.8266 (pt0) cc_final: 0.8045 (pm20) REVERT: M 6 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7587 (ptp90) REVERT: M 75 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6626 (tm-30) REVERT: N 103 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6256 (ttm170) REVERT: O 63 LYS cc_start: 0.5589 (OUTLIER) cc_final: 0.4462 (tptp) REVERT: O 100 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.6729 (p90) REVERT: P 36 LYS cc_start: 0.6444 (mmmt) cc_final: 0.5757 (mppt) REVERT: P 88 ARG cc_start: 0.7117 (ptt-90) cc_final: 0.6467 (ptt90) REVERT: Q 83 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7862 (mtpp) REVERT: R 21 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7582 (ttm110) REVERT: R 27 ILE cc_start: 0.7769 (mm) cc_final: 0.7392 (mt) REVERT: R 31 GLU cc_start: 0.7880 (tt0) cc_final: 0.7170 (tt0) REVERT: R 46 GLU cc_start: 0.7135 (mp0) cc_final: 0.6856 (mp0) REVERT: S 73 LYS cc_start: 0.7848 (mttt) cc_final: 0.7546 (mtpt) REVERT: T 25 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7363 (pt0) REVERT: T 28 ASN cc_start: 0.7199 (t0) cc_final: 0.6851 (t0) REVERT: T 56 GLU cc_start: 0.7961 (mm-30) cc_final: 0.6719 (pt0) REVERT: U 4 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (mp) REVERT: U 8 ASP cc_start: 0.7462 (m-30) cc_final: 0.7211 (m-30) REVERT: U 9 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: U 36 GLU cc_start: 0.7584 (pt0) cc_final: 0.6989 (pp20) REVERT: U 46 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7857 (mtpp) REVERT: V 11 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: W 64 LYS cc_start: 0.7886 (tptm) cc_final: 0.7271 (tptp) REVERT: Y 5 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7419 (mt-10) REVERT: Y 6 LEU cc_start: 0.6205 (mt) cc_final: 0.5649 (mt) REVERT: Y 17 GLU cc_start: 0.8401 (tt0) cc_final: 0.7894 (tm-30) REVERT: Y 39 GLN cc_start: 0.8179 (mt0) cc_final: 0.7514 (mm-40) REVERT: 0 11 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7279 (mmtp) REVERT: 0 35 GLU cc_start: 0.7923 (tt0) cc_final: 0.7578 (tt0) REVERT: 0 49 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7847 (mtm-85) REVERT: 1 7 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7617 (mttp) REVERT: 3 14 LYS cc_start: 0.8348 (tttt) cc_final: 0.7666 (mmtp) REVERT: 3 38 LYS cc_start: 0.7272 (ttmt) cc_final: 0.6947 (tttm) REVERT: 4 9 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7293 (ptmm) REVERT: 4 15 LYS cc_start: 0.7583 (ttmm) cc_final: 0.6808 (mtmm) REVERT: 5 1 MET cc_start: 0.0849 (tpt) cc_final: 0.0404 (mmm) REVERT: 6 16 CYS cc_start: 0.5940 (p) cc_final: 0.5680 (p) REVERT: 6 56 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.4986 (tpp80) REVERT: b 8 MET cc_start: 0.6447 (ppp) cc_final: 0.5811 (ppp) REVERT: b 23 ASN cc_start: 0.8678 (t0) cc_final: 0.8314 (t0) REVERT: b 67 LEU cc_start: 0.7809 (mt) cc_final: 0.7464 (mt) REVERT: b 86 CYS cc_start: 0.5350 (t) cc_final: 0.5143 (t) REVERT: b 107 ARG cc_start: 0.6880 (mtm110) cc_final: 0.5662 (mmm-85) REVERT: b 136 ARG cc_start: 0.5604 (mmm-85) cc_final: 0.5337 (ttp-170) REVERT: b 144 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7414 (pt0) REVERT: b 168 GLU cc_start: 0.7492 (mp0) cc_final: 0.6830 (mp0) REVERT: c 17 TRP cc_start: 0.8248 (m-90) cc_final: 0.7780 (m-90) REVERT: c 71 ARG cc_start: 0.7327 (mmm-85) cc_final: 0.6790 (mtp85) REVERT: c 76 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6141 (pt) REVERT: c 79 LYS cc_start: 0.5748 (tptt) cc_final: 0.5399 (mmtt) REVERT: c 82 ASP cc_start: 0.7861 (m-30) cc_final: 0.7595 (m-30) REVERT: c 105 VAL cc_start: 0.6777 (t) cc_final: 0.6501 (p) REVERT: c 166 TRP cc_start: 0.8166 (p-90) cc_final: 0.7493 (p-90) REVERT: c 169 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7224 (mt-10) REVERT: c 171 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6535 (ttm-80) REVERT: d 98 ASP cc_start: 0.8130 (p0) cc_final: 0.7859 (p0) REVERT: d 183 ARG cc_start: 0.5441 (ptt-90) cc_final: 0.5076 (ptp-110) REVERT: e 13 LYS cc_start: 0.8308 (tttp) cc_final: 0.7979 (tttp) REVERT: e 18 ASN cc_start: 0.7839 (m-40) cc_final: 0.7439 (m-40) REVERT: e 23 THR cc_start: 0.7641 (m) cc_final: 0.7330 (t) REVERT: e 63 MET cc_start: 0.7630 (mmt) cc_final: 0.7341 (mmt) REVERT: e 85 LYS cc_start: 0.7887 (mptt) cc_final: 0.7378 (mtpp) REVERT: e 95 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7957 (mtm) REVERT: e 111 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: f 2 ARG cc_start: 0.7506 (mmt180) cc_final: 0.6855 (mtt180) REVERT: f 62 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7085 (ttm) REVERT: g 20 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: g 24 LYS cc_start: 0.6499 (tptm) cc_final: 0.6203 (tptp) REVERT: g 69 ARG cc_start: 0.6805 (ttm170) cc_final: 0.6407 (mtm-85) REVERT: g 105 GLU cc_start: 0.7540 (tp30) cc_final: 0.7078 (tp30) REVERT: g 109 LYS cc_start: 0.7420 (mptt) cc_final: 0.7009 (ptpt) REVERT: g 134 VAL cc_start: 0.7396 (p) cc_final: 0.7186 (m) REVERT: g 142 ARG cc_start: 0.6892 (mmm160) cc_final: 0.6678 (mmm160) REVERT: h 42 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7236 (mt-10) REVERT: h 68 LYS cc_start: 0.7353 (tttp) cc_final: 0.7014 (mmmm) REVERT: h 86 LYS cc_start: 0.8141 (mttm) cc_final: 0.7873 (mtmm) REVERT: h 87 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6429 (mtt-85) REVERT: i 4 GLN cc_start: 0.4880 (OUTLIER) cc_final: 0.4568 (tp-100) REVERT: i 99 LYS cc_start: 0.7378 (ttpt) cc_final: 0.6803 (tptp) REVERT: i 108 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6019 (ptm-80) REVERT: j 19 ASP cc_start: 0.6859 (m-30) cc_final: 0.6645 (m-30) REVERT: j 27 GLU cc_start: 0.6835 (tt0) cc_final: 0.6198 (pp20) REVERT: j 50 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7766 (p) REVERT: j 68 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7612 (mtt180) REVERT: j 82 LYS cc_start: 0.6735 (mmmt) cc_final: 0.6377 (mmtt) REVERT: j 88 MET cc_start: 0.7198 (mmt) cc_final: 0.6894 (mmm) REVERT: k 79 LYS cc_start: 0.8078 (mppt) cc_final: 0.7672 (mmtt) REVERT: k 80 ASN cc_start: 0.6299 (p0) cc_final: 0.6084 (p0) REVERT: k 125 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7781 (tptm) REVERT: l 69 GLU cc_start: 0.6065 (tt0) cc_final: 0.5772 (mt-10) REVERT: l 71 HIS cc_start: 0.6728 (p90) cc_final: 0.5926 (p90) REVERT: l 72 ASN cc_start: 0.7060 (p0) cc_final: 0.6741 (p0) REVERT: l 85 ARG cc_start: 0.7330 (ptm160) cc_final: 0.6836 (ptp-170) REVERT: l 111 GLN cc_start: 0.7615 (mt0) cc_final: 0.7289 (mt0) REVERT: m 18 LEU cc_start: 0.7413 (mt) cc_final: 0.7104 (mp) REVERT: m 65 GLU cc_start: 0.6672 (tp30) cc_final: 0.5648 (mm-30) REVERT: m 91 ARG cc_start: 0.7286 (ptp90) cc_final: 0.5484 (ptm160) REVERT: m 92 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.6838 (ttp80) REVERT: n 22 LYS cc_start: 0.7757 (tptp) cc_final: 0.7361 (mmtm) REVERT: n 42 TRP cc_start: 0.6756 (t-100) cc_final: 0.6360 (t60) REVERT: n 62 ASN cc_start: 0.8091 (t0) cc_final: 0.7876 (t0) REVERT: o 25 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7317 (mp0) REVERT: o 58 MET cc_start: 0.7166 (mtm) cc_final: 0.6896 (mtt) REVERT: o 61 GLN cc_start: 0.8016 (tp40) cc_final: 0.7439 (tt0) REVERT: p 1 MET cc_start: 0.5620 (ttp) cc_final: 0.5390 (ttt) REVERT: p 24 SER cc_start: 0.7054 (t) cc_final: 0.6554 (m) REVERT: q 78 VAL cc_start: 0.4892 (OUTLIER) cc_final: 0.4625 (p) REVERT: s 43 MET cc_start: 0.7927 (mtp) cc_final: 0.7496 (tpp) REVERT: s 65 MET cc_start: 0.5937 (ptp) cc_final: 0.4963 (ptp) REVERT: t 14 GLU cc_start: 0.6491 (tp30) cc_final: 0.6287 (tp30) REVERT: t 68 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.6976 (tppt) REVERT: u 32 ARG cc_start: 0.6951 (tmt90) cc_final: 0.6646 (tmt90) outliers start: 241 outliers final: 171 residues processed: 1344 average time/residue: 1.4219 time to fit residues: 3272.4804 Evaluate side-chains 1340 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1145 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 114 LEU Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 10 CYS Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 38 ILE Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain z residue 223 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 1013 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 599 optimal weight: 0.8980 chunk 768 optimal weight: 10.0000 chunk 595 optimal weight: 8.9990 chunk 885 optimal weight: 2.9990 chunk 587 optimal weight: 9.9990 chunk 1047 optimal weight: 30.0000 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 20.0000 chunk 483 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 136 ASN E 195 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS N 62 ASN N 73 ASN O 104 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 4 37 GLN b 50 ASN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN h 15 ASN k 118 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 165470 Z= 0.333 Angle : 0.763 15.352 247196 Z= 0.405 Chirality : 0.040 0.401 31417 Planarity : 0.007 0.137 13501 Dihedral : 24.063 179.769 81863 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.88 % Favored : 90.48 % Rotamer: Outliers : 5.92 % Allowed : 21.84 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.77 (0.10), residues: 6218 helix: 0.20 (0.12), residues: 1949 sheet: -1.39 (0.15), residues: 1164 loop : -2.01 (0.10), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 200 HIS 0.009 0.001 HIS C 229 PHE 0.035 0.002 PHE b 49 TYR 0.024 0.002 TYR V 31 ARG 0.021 0.001 ARG T 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1162 time to evaluate : 8.616 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: C 27 LYS cc_start: 0.8114 (mttt) cc_final: 0.7528 (mmmt) REVERT: C 68 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.5765 (mmm160) REVERT: C 86 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6543 (ttm-80) REVERT: C 97 ASP cc_start: 0.7459 (p0) cc_final: 0.6814 (p0) REVERT: C 99 GLU cc_start: 0.7610 (tt0) cc_final: 0.7271 (tt0) REVERT: C 116 GLN cc_start: 0.6901 (tp40) cc_final: 0.6463 (tp40) REVERT: C 131 MET cc_start: 0.8200 (mtt) cc_final: 0.7990 (mtt) REVERT: C 139 THR cc_start: 0.8741 (m) cc_final: 0.8475 (p) REVERT: C 145 MET cc_start: 0.8158 (mmm) cc_final: 0.7806 (mmm) REVERT: C 159 THR cc_start: 0.8979 (m) cc_final: 0.8679 (p) REVERT: C 213 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7524 (mtt-85) REVERT: C 268 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7386 (tmm-80) REVERT: C 269 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7063 (mmm-85) REVERT: D 42 ASN cc_start: 0.7446 (m110) cc_final: 0.6713 (t0) REVERT: D 199 SER cc_start: 0.8086 (p) cc_final: 0.7768 (p) REVERT: E 24 ASN cc_start: 0.8180 (t0) cc_final: 0.7845 (t0) REVERT: E 108 ILE cc_start: 0.8153 (pt) cc_final: 0.7913 (mt) REVERT: E 111 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: E 166 LYS cc_start: 0.7310 (mttt) cc_final: 0.6994 (mmtm) REVERT: F 31 GLU cc_start: 0.7552 (tt0) cc_final: 0.7255 (tt0) REVERT: F 93 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6889 (tm-30) REVERT: F 95 MET cc_start: 0.7619 (ttp) cc_final: 0.7394 (ttp) REVERT: F 97 GLU cc_start: 0.7486 (tp30) cc_final: 0.6924 (tp30) REVERT: F 114 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6240 (ttp-170) REVERT: F 128 SER cc_start: 0.7906 (t) cc_final: 0.7442 (p) REVERT: G 154 GLU cc_start: 0.6837 (tt0) cc_final: 0.6419 (tt0) REVERT: G 159 LYS cc_start: 0.7310 (mtpp) cc_final: 0.6947 (mtmm) REVERT: J 75 TYR cc_start: 0.8429 (m-80) cc_final: 0.8115 (m-80) REVERT: J 84 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7513 (tp) REVERT: K 93 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: L 106 GLU cc_start: 0.8155 (pt0) cc_final: 0.7891 (pm20) REVERT: M 6 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7547 (ptp90) REVERT: M 44 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7450 (mtt180) REVERT: M 75 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6758 (tm-30) REVERT: N 103 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.5673 (ttm-80) REVERT: N 114 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: P 36 LYS cc_start: 0.6438 (mmmt) cc_final: 0.5746 (mppt) REVERT: P 88 ARG cc_start: 0.6971 (ptt-90) cc_final: 0.6470 (ptt90) REVERT: Q 83 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7817 (mtpp) REVERT: R 21 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7625 (ttm110) REVERT: R 31 GLU cc_start: 0.7924 (tt0) cc_final: 0.7158 (tt0) REVERT: S 19 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7766 (mp) REVERT: S 73 LYS cc_start: 0.7954 (mttt) cc_final: 0.7707 (mtpt) REVERT: T 3 ARG cc_start: 0.7589 (ptp90) cc_final: 0.7379 (ptp-170) REVERT: T 7 LEU cc_start: 0.8098 (mm) cc_final: 0.7640 (mt) REVERT: T 25 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7443 (pt0) REVERT: T 28 ASN cc_start: 0.7313 (t0) cc_final: 0.7033 (t0) REVERT: T 42 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7616 (mp0) REVERT: T 56 GLU cc_start: 0.8190 (mm-30) cc_final: 0.6817 (pt0) REVERT: T 76 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7595 (ptm160) REVERT: U 8 ASP cc_start: 0.7687 (m-30) cc_final: 0.7426 (m-30) REVERT: U 9 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: U 40 LEU cc_start: 0.8110 (mm) cc_final: 0.7829 (mm) REVERT: U 46 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7920 (mtpt) REVERT: V 11 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: V 46 LYS cc_start: 0.7285 (mmmt) cc_final: 0.7001 (mmmt) REVERT: W 64 LYS cc_start: 0.7700 (tptm) cc_final: 0.7079 (tptp) REVERT: X 61 LYS cc_start: 0.7605 (mttt) cc_final: 0.7332 (mttm) REVERT: Y 5 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7300 (mt-10) REVERT: Y 6 LEU cc_start: 0.6149 (mt) cc_final: 0.5646 (mt) REVERT: Y 17 GLU cc_start: 0.8426 (tt0) cc_final: 0.7920 (tm-30) REVERT: Y 39 GLN cc_start: 0.8204 (mt0) cc_final: 0.7650 (mm110) REVERT: 0 11 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7062 (mmtp) REVERT: 0 35 GLU cc_start: 0.7847 (tt0) cc_final: 0.7481 (tt0) REVERT: 1 7 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7548 (mttp) REVERT: 3 14 LYS cc_start: 0.8487 (tttt) cc_final: 0.7787 (mmtp) REVERT: 3 38 LYS cc_start: 0.7301 (ttmt) cc_final: 0.7022 (tttm) REVERT: 4 9 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7371 (ptmm) REVERT: 4 15 LYS cc_start: 0.7615 (ttmm) cc_final: 0.6829 (mtmm) REVERT: 5 1 MET cc_start: 0.0950 (tpt) cc_final: 0.0711 (mmm) REVERT: 6 16 CYS cc_start: 0.5497 (p) cc_final: 0.5220 (p) REVERT: 6 56 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5134 (tpp80) REVERT: b 8 MET cc_start: 0.6617 (ppp) cc_final: 0.5758 (ppp) REVERT: b 23 ASN cc_start: 0.8639 (t0) cc_final: 0.8292 (t0) REVERT: b 67 LEU cc_start: 0.7820 (mt) cc_final: 0.7441 (mt) REVERT: b 136 ARG cc_start: 0.5656 (mmm-85) cc_final: 0.5375 (ttp-170) REVERT: b 144 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7447 (pt0) REVERT: b 212 TYR cc_start: 0.7081 (m-80) cc_final: 0.6766 (m-80) REVERT: c 17 TRP cc_start: 0.8446 (m-90) cc_final: 0.8074 (m-90) REVERT: c 61 LYS cc_start: 0.7234 (mtpt) cc_final: 0.7010 (mtpp) REVERT: c 71 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.6954 (mtp85) REVERT: c 76 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6691 (mt) REVERT: c 79 LYS cc_start: 0.5836 (tptt) cc_final: 0.5564 (mmtt) REVERT: c 82 ASP cc_start: 0.7909 (m-30) cc_final: 0.7657 (m-30) REVERT: c 105 VAL cc_start: 0.6655 (t) cc_final: 0.6388 (p) REVERT: c 166 TRP cc_start: 0.8116 (p-90) cc_final: 0.7661 (p-90) REVERT: c 169 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7314 (mt-10) REVERT: c 171 ARG cc_start: 0.6759 (ttp-170) cc_final: 0.6476 (ttm-80) REVERT: c 187 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7795 (mt-10) REVERT: d 57 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6851 (tttp) REVERT: d 98 ASP cc_start: 0.8251 (p0) cc_final: 0.7974 (p0) REVERT: d 183 ARG cc_start: 0.5446 (ptt-90) cc_final: 0.5117 (ptp-110) REVERT: e 18 ASN cc_start: 0.7966 (m-40) cc_final: 0.7542 (m-40) REVERT: e 70 MET cc_start: 0.8196 (tpp) cc_final: 0.7772 (tpp) REVERT: e 85 LYS cc_start: 0.7977 (mptt) cc_final: 0.7578 (mtpp) REVERT: f 2 ARG cc_start: 0.7359 (mmt180) cc_final: 0.6772 (mtt180) REVERT: f 29 ILE cc_start: 0.7133 (mt) cc_final: 0.6787 (mp) REVERT: f 62 MET cc_start: 0.7142 (ttm) cc_final: 0.6600 (ttt) REVERT: f 87 SER cc_start: 0.7954 (p) cc_final: 0.7417 (m) REVERT: f 90 MET cc_start: 0.7942 (mmm) cc_final: 0.7617 (mmt) REVERT: f 92 THR cc_start: 0.6074 (OUTLIER) cc_final: 0.5856 (p) REVERT: g 20 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: g 24 LYS cc_start: 0.6519 (tptm) cc_final: 0.6225 (tptp) REVERT: g 69 ARG cc_start: 0.6812 (ttm170) cc_final: 0.6446 (mtm-85) REVERT: g 109 LYS cc_start: 0.7558 (mptt) cc_final: 0.7100 (ptpt) REVERT: g 134 VAL cc_start: 0.7365 (p) cc_final: 0.7124 (m) REVERT: h 68 LYS cc_start: 0.7448 (tttp) cc_final: 0.7102 (mmtp) REVERT: h 86 LYS cc_start: 0.8220 (mttm) cc_final: 0.7892 (mtmm) REVERT: h 87 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7058 (mtt-85) REVERT: i 4 GLN cc_start: 0.4737 (OUTLIER) cc_final: 0.4457 (tp-100) REVERT: i 29 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.5995 (mp) REVERT: i 99 LYS cc_start: 0.7408 (ttpt) cc_final: 0.6872 (tptp) REVERT: i 108 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6166 (ptm-80) REVERT: j 19 ASP cc_start: 0.7057 (m-30) cc_final: 0.6778 (m-30) REVERT: j 27 GLU cc_start: 0.6894 (tt0) cc_final: 0.6317 (pp20) REVERT: j 50 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7826 (p) REVERT: j 68 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7702 (mtt180) REVERT: j 82 LYS cc_start: 0.6739 (mmmt) cc_final: 0.6390 (mmtt) REVERT: j 88 MET cc_start: 0.7209 (mmt) cc_final: 0.6874 (mmm) REVERT: k 39 ASN cc_start: 0.7484 (m-40) cc_final: 0.7169 (m-40) REVERT: k 79 LYS cc_start: 0.8109 (mppt) cc_final: 0.7657 (mmtt) REVERT: k 80 ASN cc_start: 0.6387 (p0) cc_final: 0.6148 (p0) REVERT: k 115 ILE cc_start: 0.8344 (mt) cc_final: 0.8046 (tp) REVERT: k 125 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7685 (tptm) REVERT: l 69 GLU cc_start: 0.6191 (tt0) cc_final: 0.5936 (mt-10) REVERT: l 85 ARG cc_start: 0.7294 (ptm160) cc_final: 0.6820 (ptp-170) REVERT: l 111 GLN cc_start: 0.7626 (mt0) cc_final: 0.7291 (mt0) REVERT: m 91 ARG cc_start: 0.7450 (ptp90) cc_final: 0.5618 (ptm160) REVERT: m 92 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.6714 (ttp80) REVERT: m 108 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7237 (mmm160) REVERT: n 22 LYS cc_start: 0.7790 (tptp) cc_final: 0.7371 (mmtm) REVERT: n 42 TRP cc_start: 0.6812 (t-100) cc_final: 0.6419 (t60) REVERT: n 62 ASN cc_start: 0.8183 (t0) cc_final: 0.7976 (t0) REVERT: o 25 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7609 (mp0) REVERT: o 58 MET cc_start: 0.7196 (mtm) cc_final: 0.6901 (mtt) REVERT: o 61 GLN cc_start: 0.8155 (tp40) cc_final: 0.7517 (tt0) REVERT: p 24 SER cc_start: 0.7254 (t) cc_final: 0.6784 (m) REVERT: q 78 VAL cc_start: 0.5061 (OUTLIER) cc_final: 0.4744 (p) REVERT: s 43 MET cc_start: 0.7935 (mtp) cc_final: 0.7519 (tpp) REVERT: s 55 GLN cc_start: 0.7678 (pm20) cc_final: 0.7006 (pm20) REVERT: s 61 VAL cc_start: 0.7005 (t) cc_final: 0.6781 (t) REVERT: s 65 MET cc_start: 0.6096 (ptp) cc_final: 0.5274 (ptp) REVERT: t 58 ASP cc_start: 0.8016 (t0) cc_final: 0.7551 (t0) REVERT: t 68 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7017 (tppt) REVERT: z 223 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.4446 (tpt90) outliers start: 306 outliers final: 234 residues processed: 1349 average time/residue: 1.3940 time to fit residues: 3227.1483 Evaluate side-chains 1396 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1136 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 86 LYS Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 53 ILE Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 193 ASP Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 111 ARG Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 108 ARG Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 10 CYS Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 30 GLU Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 223 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 648 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 625 optimal weight: 10.0000 chunk 315 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 666 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 517 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 823 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 134 HIS E 195 GLN F 26 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS N 62 ASN U 73 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 4 37 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 119 GLN c 122 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN h 15 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 ASN p 63 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 165470 Z= 0.424 Angle : 0.848 15.727 247196 Z= 0.445 Chirality : 0.045 0.419 31417 Planarity : 0.008 0.139 13501 Dihedral : 24.223 179.684 81863 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.91 % Favored : 90.45 % Rotamer: Outliers : 6.62 % Allowed : 21.78 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.19 (0.10), residues: 6218 helix: -0.23 (0.11), residues: 1949 sheet: -1.57 (0.15), residues: 1168 loop : -2.23 (0.10), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 22 HIS 0.020 0.002 HIS k 117 PHE 0.039 0.003 PHE u 11 TYR 0.036 0.003 TYR D 45 ARG 0.014 0.001 ARG k 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1173 time to evaluate : 6.705 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: C 27 LYS cc_start: 0.8030 (mttt) cc_final: 0.7456 (mmmt) REVERT: C 68 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.5537 (mmm160) REVERT: C 86 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6507 (ttm-80) REVERT: C 97 ASP cc_start: 0.7367 (p0) cc_final: 0.6980 (p0) REVERT: C 99 GLU cc_start: 0.7591 (tt0) cc_final: 0.7294 (tt0) REVERT: C 116 GLN cc_start: 0.6951 (tp40) cc_final: 0.6526 (tp40) REVERT: C 139 THR cc_start: 0.8720 (m) cc_final: 0.8408 (p) REVERT: C 159 THR cc_start: 0.9027 (m) cc_final: 0.8732 (p) REVERT: C 193 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7151 (mt-10) REVERT: C 200 MET cc_start: 0.8509 (ptt) cc_final: 0.8198 (ptm) REVERT: C 213 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7409 (mtp85) REVERT: C 268 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7305 (tmm-80) REVERT: D 42 ASN cc_start: 0.7238 (m110) cc_final: 0.6611 (t0) REVERT: D 168 GLU cc_start: 0.7785 (tt0) cc_final: 0.7541 (mm-30) REVERT: D 169 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8212 (ttt-90) REVERT: D 199 SER cc_start: 0.8215 (p) cc_final: 0.7897 (p) REVERT: E 24 ASN cc_start: 0.8079 (t0) cc_final: 0.7754 (t0) REVERT: E 111 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: E 166 LYS cc_start: 0.7353 (mttt) cc_final: 0.7008 (mmtm) REVERT: E 168 ASP cc_start: 0.8002 (t0) cc_final: 0.7374 (t0) REVERT: E 170 ARG cc_start: 0.7658 (ttm170) cc_final: 0.6838 (ttm110) REVERT: F 31 GLU cc_start: 0.7546 (tt0) cc_final: 0.7237 (tt0) REVERT: F 97 GLU cc_start: 0.7431 (tp30) cc_final: 0.6928 (tp30) REVERT: F 114 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6434 (ttp-170) REVERT: F 128 SER cc_start: 0.7901 (t) cc_final: 0.7347 (p) REVERT: G 154 GLU cc_start: 0.6784 (tt0) cc_final: 0.6348 (tt0) REVERT: G 159 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6890 (mtmm) REVERT: J 75 TYR cc_start: 0.8499 (m-80) cc_final: 0.8211 (m-80) REVERT: J 84 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7456 (tp) REVERT: K 93 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: L 106 GLU cc_start: 0.8087 (pt0) cc_final: 0.7716 (pm20) REVERT: M 6 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7524 (ptp90) REVERT: M 75 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6790 (tm-30) REVERT: N 112 TYR cc_start: 0.8106 (m-80) cc_final: 0.7624 (m-80) REVERT: N 114 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6754 (pt0) REVERT: P 36 LYS cc_start: 0.6535 (mmmt) cc_final: 0.5954 (mppt) REVERT: P 88 ARG cc_start: 0.7002 (ptt-90) cc_final: 0.6440 (ptt90) REVERT: Q 83 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7661 (mtpp) REVERT: R 21 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7798 (ttm170) REVERT: R 31 GLU cc_start: 0.7673 (tt0) cc_final: 0.7015 (tt0) REVERT: S 73 LYS cc_start: 0.7997 (mttt) cc_final: 0.7652 (mtpt) REVERT: T 3 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7290 (ptp90) REVERT: T 25 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7307 (mm-30) REVERT: T 28 ASN cc_start: 0.7315 (t0) cc_final: 0.7097 (t0) REVERT: T 42 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7611 (mp0) REVERT: T 76 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7602 (ptm160) REVERT: U 8 ASP cc_start: 0.7651 (m-30) cc_final: 0.7328 (m-30) REVERT: U 9 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: U 40 LEU cc_start: 0.7887 (mm) cc_final: 0.7647 (mm) REVERT: U 46 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7869 (mtpt) REVERT: V 11 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: V 46 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6848 (mmmt) REVERT: W 64 LYS cc_start: 0.7604 (tptm) cc_final: 0.6983 (tptp) REVERT: X 61 LYS cc_start: 0.7551 (mttt) cc_final: 0.7253 (mttm) REVERT: Y 6 LEU cc_start: 0.6151 (mt) cc_final: 0.5702 (mt) REVERT: Y 17 GLU cc_start: 0.8447 (tt0) cc_final: 0.7916 (tm-30) REVERT: Y 39 GLN cc_start: 0.8262 (mt0) cc_final: 0.7402 (mm-40) REVERT: 0 11 LYS cc_start: 0.7855 (mmmt) cc_final: 0.7220 (mmtp) REVERT: 0 35 GLU cc_start: 0.7860 (tt0) cc_final: 0.7524 (tt0) REVERT: 3 14 LYS cc_start: 0.8572 (tttt) cc_final: 0.7760 (mmtp) REVERT: 3 38 LYS cc_start: 0.7290 (ttmt) cc_final: 0.7017 (ttmm) REVERT: 4 9 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7471 (ptmm) REVERT: 4 15 LYS cc_start: 0.7645 (ttmm) cc_final: 0.6820 (mtmm) REVERT: 4 30 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6784 (tp30) REVERT: 5 1 MET cc_start: 0.1586 (tpt) cc_final: 0.1247 (mmt) REVERT: 5 52 MET cc_start: -0.1261 (OUTLIER) cc_final: -0.1572 (ttp) REVERT: 5 86 MET cc_start: 0.2242 (mmm) cc_final: 0.1445 (mmm) REVERT: 6 16 CYS cc_start: 0.5352 (p) cc_final: 0.5033 (p) REVERT: 6 56 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.5209 (tpp80) REVERT: b 8 MET cc_start: 0.6872 (ppp) cc_final: 0.6527 (ppp) REVERT: b 67 LEU cc_start: 0.7860 (mt) cc_final: 0.7479 (mt) REVERT: b 136 ARG cc_start: 0.5740 (mmm-85) cc_final: 0.5396 (ttp-170) REVERT: c 17 TRP cc_start: 0.8322 (m-90) cc_final: 0.8090 (m-90) REVERT: c 71 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.6954 (mtp85) REVERT: c 76 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6556 (mt) REVERT: c 79 LYS cc_start: 0.5640 (tptt) cc_final: 0.5220 (mtmm) REVERT: c 82 ASP cc_start: 0.7957 (m-30) cc_final: 0.7688 (m-30) REVERT: c 105 VAL cc_start: 0.6463 (t) cc_final: 0.6163 (p) REVERT: c 107 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7396 (tttp) REVERT: c 111 ASP cc_start: 0.7599 (t0) cc_final: 0.7314 (t0) REVERT: c 166 TRP cc_start: 0.8088 (p-90) cc_final: 0.7738 (p-90) REVERT: c 169 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7317 (mt-10) REVERT: c 202 PHE cc_start: 0.7947 (t80) cc_final: 0.7540 (t80) REVERT: d 57 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6954 (tttp) REVERT: d 98 ASP cc_start: 0.8288 (p0) cc_final: 0.7996 (p0) REVERT: d 137 SER cc_start: 0.7621 (t) cc_final: 0.7364 (p) REVERT: d 183 ARG cc_start: 0.5406 (ptt-90) cc_final: 0.5174 (ptp-110) REVERT: e 18 ASN cc_start: 0.8133 (m-40) cc_final: 0.7742 (m-40) REVERT: e 23 THR cc_start: 0.7708 (m) cc_final: 0.7393 (t) REVERT: e 85 LYS cc_start: 0.7933 (mptt) cc_final: 0.7559 (mtpp) REVERT: f 2 ARG cc_start: 0.7400 (mmt180) cc_final: 0.6826 (mmt180) REVERT: f 29 ILE cc_start: 0.7321 (mt) cc_final: 0.7068 (mp) REVERT: f 62 MET cc_start: 0.7282 (ttm) cc_final: 0.6963 (ttm) REVERT: f 87 SER cc_start: 0.7891 (p) cc_final: 0.7325 (m) REVERT: f 92 THR cc_start: 0.6038 (OUTLIER) cc_final: 0.5834 (p) REVERT: g 20 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: g 105 GLU cc_start: 0.7603 (tp30) cc_final: 0.7396 (tp30) REVERT: g 109 LYS cc_start: 0.7720 (mptt) cc_final: 0.7121 (ptpt) REVERT: h 25 THR cc_start: 0.7818 (p) cc_final: 0.7553 (m) REVERT: h 46 GLU cc_start: 0.7429 (tp30) cc_final: 0.7134 (tt0) REVERT: h 68 LYS cc_start: 0.7599 (tttp) cc_final: 0.7090 (mmtp) REVERT: i 4 GLN cc_start: 0.4703 (OUTLIER) cc_final: 0.4370 (tm-30) REVERT: i 29 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.5825 (mp) REVERT: i 99 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7121 (tptp) REVERT: i 108 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6309 (ptm-80) REVERT: i 129 ARG cc_start: 0.7392 (mmp-170) cc_final: 0.7146 (mmp-170) REVERT: j 27 GLU cc_start: 0.6933 (tt0) cc_final: 0.6429 (pp20) REVERT: j 68 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7750 (mtt180) REVERT: j 72 ARG cc_start: 0.7035 (mmt-90) cc_final: 0.6817 (mmt90) REVERT: j 82 LYS cc_start: 0.6781 (mmmt) cc_final: 0.6385 (mmtt) REVERT: j 88 MET cc_start: 0.7390 (mmt) cc_final: 0.7042 (mmm) REVERT: k 39 ASN cc_start: 0.7566 (m-40) cc_final: 0.7244 (m-40) REVERT: k 79 LYS cc_start: 0.8076 (mppt) cc_final: 0.7703 (mmtt) REVERT: k 80 ASN cc_start: 0.6179 (p0) cc_final: 0.5925 (p0) REVERT: k 84 MET cc_start: 0.6721 (mmm) cc_final: 0.6473 (mmt) REVERT: k 115 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8096 (mt) REVERT: k 125 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7767 (tptm) REVERT: l 69 GLU cc_start: 0.6214 (tt0) cc_final: 0.5927 (mt-10) REVERT: l 110 LYS cc_start: 0.6840 (tttt) cc_final: 0.6368 (mmtm) REVERT: l 111 GLN cc_start: 0.7613 (mt0) cc_final: 0.7363 (mt0) REVERT: m 92 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.6728 (ttp80) REVERT: n 22 LYS cc_start: 0.7797 (tptp) cc_final: 0.7394 (mmtt) REVERT: n 42 TRP cc_start: 0.6664 (t-100) cc_final: 0.6289 (t60) REVERT: o 58 MET cc_start: 0.7324 (mtm) cc_final: 0.7015 (mtt) REVERT: o 61 GLN cc_start: 0.8086 (tp40) cc_final: 0.7487 (tt0) REVERT: p 18 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7223 (mm-40) REVERT: p 24 SER cc_start: 0.7297 (t) cc_final: 0.6824 (m) REVERT: q 12 VAL cc_start: 0.8644 (t) cc_final: 0.8387 (m) REVERT: q 39 ARG cc_start: 0.7180 (mmt90) cc_final: 0.6401 (mmp-170) REVERT: s 20 LYS cc_start: 0.6201 (ttpp) cc_final: 0.5675 (tptp) REVERT: s 43 MET cc_start: 0.8088 (mtp) cc_final: 0.7459 (tpp) REVERT: s 46 LEU cc_start: 0.7284 (mt) cc_final: 0.6581 (mp) REVERT: s 61 VAL cc_start: 0.7042 (t) cc_final: 0.6754 (t) REVERT: s 63 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7106 (t70) REVERT: s 65 MET cc_start: 0.6005 (ptp) cc_final: 0.5211 (ptp) REVERT: t 58 ASP cc_start: 0.7882 (t0) cc_final: 0.7300 (t0) REVERT: t 68 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7008 (tppt) outliers start: 342 outliers final: 258 residues processed: 1381 average time/residue: 1.4557 time to fit residues: 3452.7124 Evaluate side-chains 1407 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1125 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 59 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 53 ILE Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 193 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 99 SER Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 51 GLU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 109 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 116 TYR Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 10 CYS Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 63 ASP Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 30 GLU Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain z residue 26 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 953 optimal weight: 4.9990 chunk 1003 optimal weight: 0.8980 chunk 915 optimal weight: 0.5980 chunk 976 optimal weight: 6.9990 chunk 587 optimal weight: 0.9980 chunk 425 optimal weight: 0.0980 chunk 766 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 882 optimal weight: 10.0000 chunk 923 optimal weight: 4.9990 chunk 972 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 134 HIS E 195 GLN G 37 ASN H 18 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS N 62 ASN V 75 GLN Y 15 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 4 37 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN h 15 ASN i 36 GLN k 118 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN q 46 HIS r 18 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS t 81 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 165470 Z= 0.156 Angle : 0.674 15.057 247196 Z= 0.367 Chirality : 0.035 0.474 31417 Planarity : 0.006 0.123 13501 Dihedral : 24.069 179.119 81863 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.88 % Favored : 91.51 % Rotamer: Outliers : 4.18 % Allowed : 24.43 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.76 (0.10), residues: 6218 helix: 0.26 (0.12), residues: 1949 sheet: -1.43 (0.14), residues: 1181 loop : -2.01 (0.10), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 200 HIS 0.007 0.001 HIS s 13 PHE 0.020 0.001 PHE f 8 TYR 0.020 0.002 TYR D 45 ARG 0.012 0.001 ARG z 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1219 time to evaluate : 6.984 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: C 27 LYS cc_start: 0.8079 (mttt) cc_final: 0.7535 (mmmt) REVERT: C 86 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6527 (ttm-80) REVERT: C 97 ASP cc_start: 0.7093 (p0) cc_final: 0.6634 (p0) REVERT: C 99 GLU cc_start: 0.7551 (tt0) cc_final: 0.7214 (tt0) REVERT: C 116 GLN cc_start: 0.7122 (tp40) cc_final: 0.6900 (tp40) REVERT: C 145 MET cc_start: 0.8009 (mmm) cc_final: 0.7747 (mmm) REVERT: C 159 THR cc_start: 0.8880 (m) cc_final: 0.8589 (p) REVERT: C 200 MET cc_start: 0.8534 (ptt) cc_final: 0.8172 (ptm) REVERT: C 213 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7467 (mtt-85) REVERT: C 268 ARG cc_start: 0.7605 (ttt90) cc_final: 0.7366 (tmm-80) REVERT: C 269 ARG cc_start: 0.7607 (mmm160) cc_final: 0.6704 (mmm-85) REVERT: D 42 ASN cc_start: 0.7223 (m110) cc_final: 0.6647 (t0) REVERT: D 199 SER cc_start: 0.8097 (p) cc_final: 0.7767 (p) REVERT: E 166 LYS cc_start: 0.7298 (mttt) cc_final: 0.6975 (mmtm) REVERT: E 170 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7110 (ttm110) REVERT: F 6 TYR cc_start: 0.7305 (t80) cc_final: 0.6909 (t80) REVERT: F 32 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7450 (pttt) REVERT: F 90 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7414 (pp) REVERT: F 93 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6842 (tm-30) REVERT: F 95 MET cc_start: 0.7166 (ttp) cc_final: 0.6924 (ttt) REVERT: F 97 GLU cc_start: 0.7517 (tp30) cc_final: 0.6888 (tp30) REVERT: F 114 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6513 (ttp-170) REVERT: F 128 SER cc_start: 0.7859 (t) cc_final: 0.7299 (p) REVERT: F 162 ASP cc_start: 0.6091 (p0) cc_final: 0.5498 (m-30) REVERT: G 154 GLU cc_start: 0.6646 (tt0) cc_final: 0.6208 (tt0) REVERT: G 159 LYS cc_start: 0.7224 (mtpp) cc_final: 0.6968 (mtmm) REVERT: G 169 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.6088 (mtm110) REVERT: J 53 TYR cc_start: 0.8091 (m-80) cc_final: 0.7619 (m-80) REVERT: J 75 TYR cc_start: 0.8397 (m-80) cc_final: 0.8062 (m-80) REVERT: K 93 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: K 114 LYS cc_start: 0.6723 (mtmt) cc_final: 0.6046 (ttpt) REVERT: L 7 SER cc_start: 0.8351 (p) cc_final: 0.7833 (t) REVERT: L 69 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6611 (mtm-85) REVERT: L 106 GLU cc_start: 0.8145 (pt0) cc_final: 0.7893 (pm20) REVERT: M 6 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7623 (ptp90) REVERT: M 75 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6564 (tm-30) REVERT: O 3 LYS cc_start: 0.7416 (mttt) cc_final: 0.7195 (mtmt) REVERT: O 4 LYS cc_start: 0.8158 (tptp) cc_final: 0.7880 (tptt) REVERT: O 100 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.6778 (p90) REVERT: P 36 LYS cc_start: 0.6717 (mmmt) cc_final: 0.6109 (mppt) REVERT: P 88 ARG cc_start: 0.7030 (ptt-90) cc_final: 0.6644 (ptt90) REVERT: Q 83 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7780 (mtpp) REVERT: R 6 GLN cc_start: 0.8304 (tt0) cc_final: 0.8055 (tt0) REVERT: R 21 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7610 (ttm110) REVERT: R 31 GLU cc_start: 0.7853 (tt0) cc_final: 0.7301 (tt0) REVERT: S 38 TYR cc_start: 0.8157 (m-80) cc_final: 0.7553 (m-80) REVERT: S 73 LYS cc_start: 0.7885 (mttt) cc_final: 0.7557 (mtpt) REVERT: T 3 ARG cc_start: 0.7582 (ptp90) cc_final: 0.7206 (ptp90) REVERT: T 25 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7411 (pp20) REVERT: T 28 ASN cc_start: 0.7275 (t0) cc_final: 0.7028 (t0) REVERT: T 42 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7626 (mp0) REVERT: T 76 ARG cc_start: 0.8083 (ptm160) cc_final: 0.7604 (ptm160) REVERT: U 8 ASP cc_start: 0.7669 (m-30) cc_final: 0.7215 (m-30) REVERT: U 9 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: U 40 LEU cc_start: 0.8003 (mm) cc_final: 0.7776 (mm) REVERT: U 46 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7851 (mtpt) REVERT: V 11 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: Y 6 LEU cc_start: 0.6031 (mt) cc_final: 0.5495 (mt) REVERT: Y 17 GLU cc_start: 0.8382 (tt0) cc_final: 0.7867 (tm-30) REVERT: Y 39 GLN cc_start: 0.8173 (mt0) cc_final: 0.7357 (mm-40) REVERT: 0 11 LYS cc_start: 0.7599 (mmmt) cc_final: 0.7072 (mmtp) REVERT: 0 35 GLU cc_start: 0.7890 (tt0) cc_final: 0.7547 (tt0) REVERT: 0 49 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7662 (mtm-85) REVERT: 1 7 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7299 (mttt) REVERT: 3 14 LYS cc_start: 0.8336 (tttt) cc_final: 0.7631 (mmtp) REVERT: 3 38 LYS cc_start: 0.7219 (ttmt) cc_final: 0.6966 (ttmm) REVERT: 4 9 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7330 (ptmm) REVERT: 4 15 LYS cc_start: 0.7563 (ttmm) cc_final: 0.6746 (mtmm) REVERT: 5 1 MET cc_start: 0.1549 (tpt) cc_final: 0.1146 (mmm) REVERT: 5 86 MET cc_start: 0.2516 (mmm) cc_final: 0.1612 (mmm) REVERT: 6 10 GLU cc_start: 0.7575 (tp30) cc_final: 0.7006 (tt0) REVERT: 6 16 CYS cc_start: 0.5500 (p) cc_final: 0.5221 (p) REVERT: 6 56 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.5176 (tpp80) REVERT: b 23 ASN cc_start: 0.8602 (t0) cc_final: 0.8267 (t0) REVERT: b 67 LEU cc_start: 0.8014 (mt) cc_final: 0.7623 (mt) REVERT: b 136 ARG cc_start: 0.5691 (mmm-85) cc_final: 0.5415 (ttp-170) REVERT: b 144 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7475 (pt0) REVERT: b 211 LEU cc_start: 0.5959 (tp) cc_final: 0.5237 (mt) REVERT: b 212 TYR cc_start: 0.7080 (m-80) cc_final: 0.6492 (m-80) REVERT: b 224 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5419 (mtp85) REVERT: c 17 TRP cc_start: 0.8262 (m-90) cc_final: 0.7929 (m-90) REVERT: c 45 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7295 (tm-30) REVERT: c 71 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6710 (mtp85) REVERT: c 81 GLU cc_start: 0.6529 (pp20) cc_final: 0.6259 (pp20) REVERT: c 82 ASP cc_start: 0.8000 (m-30) cc_final: 0.7707 (m-30) REVERT: c 105 VAL cc_start: 0.6593 (t) cc_final: 0.6276 (p) REVERT: c 166 TRP cc_start: 0.8054 (p-90) cc_final: 0.7418 (p-90) REVERT: c 171 ARG cc_start: 0.6823 (ttp-170) cc_final: 0.6576 (ttm-80) REVERT: c 182 ASP cc_start: 0.8936 (t0) cc_final: 0.8733 (t0) REVERT: c 187 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7992 (mt-10) REVERT: d 57 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6778 (tttm) REVERT: d 70 GLN cc_start: 0.8319 (tt0) cc_final: 0.7873 (mm-40) REVERT: d 98 ASP cc_start: 0.8257 (p0) cc_final: 0.7979 (p0) REVERT: d 140 ASP cc_start: 0.5492 (m-30) cc_final: 0.4920 (m-30) REVERT: d 183 ARG cc_start: 0.5369 (ptt-90) cc_final: 0.5126 (ptp-110) REVERT: e 18 ASN cc_start: 0.7990 (m-40) cc_final: 0.7548 (m-40) REVERT: e 23 THR cc_start: 0.7617 (m) cc_final: 0.7281 (t) REVERT: e 85 LYS cc_start: 0.7901 (mptt) cc_final: 0.7487 (mtpp) REVERT: f 2 ARG cc_start: 0.7446 (mmt180) cc_final: 0.6754 (mtt180) REVERT: f 24 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7750 (mtt180) REVERT: f 45 ARG cc_start: 0.6997 (ttt90) cc_final: 0.6414 (ptm-80) REVERT: f 62 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7064 (ttm) REVERT: f 92 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.5976 (p) REVERT: g 20 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: g 24 LYS cc_start: 0.6137 (tptm) cc_final: 0.5886 (mmmt) REVERT: g 69 ARG cc_start: 0.6727 (ttm170) cc_final: 0.6249 (mtm-85) REVERT: g 105 GLU cc_start: 0.7557 (tp30) cc_final: 0.7308 (tp30) REVERT: g 109 LYS cc_start: 0.7555 (mptt) cc_final: 0.7120 (ptpt) REVERT: g 125 ASP cc_start: 0.7443 (m-30) cc_final: 0.6932 (m-30) REVERT: g 147 ASN cc_start: 0.7342 (m-40) cc_final: 0.7094 (m110) REVERT: h 46 GLU cc_start: 0.7456 (tp30) cc_final: 0.7203 (tt0) REVERT: h 68 LYS cc_start: 0.7501 (tttp) cc_final: 0.7096 (mmmm) REVERT: h 86 LYS cc_start: 0.8131 (mttm) cc_final: 0.7893 (mtmm) REVERT: h 87 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6492 (mtt-85) REVERT: h 93 LYS cc_start: 0.8173 (ptpp) cc_final: 0.7441 (pttt) REVERT: i 4 GLN cc_start: 0.4701 (OUTLIER) cc_final: 0.4425 (tp-100) REVERT: i 99 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6900 (tptp) REVERT: i 108 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.5922 (ptm-80) REVERT: i 127 SER cc_start: 0.8122 (m) cc_final: 0.7566 (p) REVERT: j 19 ASP cc_start: 0.7026 (m-30) cc_final: 0.6701 (m-30) REVERT: j 27 GLU cc_start: 0.6921 (tt0) cc_final: 0.6355 (pp20) REVERT: j 68 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7695 (mtt180) REVERT: j 82 LYS cc_start: 0.6735 (mmmt) cc_final: 0.6343 (mmtt) REVERT: j 88 MET cc_start: 0.7286 (mmt) cc_final: 0.6946 (mmm) REVERT: k 79 LYS cc_start: 0.8173 (mppt) cc_final: 0.7676 (mmtt) REVERT: k 80 ASN cc_start: 0.6408 (p0) cc_final: 0.6201 (p0) REVERT: k 84 MET cc_start: 0.6756 (mmm) cc_final: 0.6383 (mmt) REVERT: k 115 ILE cc_start: 0.8330 (mt) cc_final: 0.8002 (tp) REVERT: k 125 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7731 (tptm) REVERT: l 69 GLU cc_start: 0.6388 (tt0) cc_final: 0.6051 (mt-10) REVERT: l 85 ARG cc_start: 0.7465 (ptm160) cc_final: 0.7101 (ptp-170) REVERT: m 26 LYS cc_start: 0.7113 (ttmm) cc_final: 0.6857 (tppt) REVERT: m 92 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.6776 (ttp-170) REVERT: n 22 LYS cc_start: 0.7767 (tptp) cc_final: 0.7379 (mmtt) REVERT: n 42 TRP cc_start: 0.6700 (t-100) cc_final: 0.6341 (t60) REVERT: n 62 ASN cc_start: 0.8142 (t0) cc_final: 0.7872 (t0) REVERT: n 80 SER cc_start: 0.8371 (m) cc_final: 0.8129 (m) REVERT: n 92 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7436 (mp0) REVERT: o 25 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7886 (mp0) REVERT: o 58 MET cc_start: 0.7176 (mtm) cc_final: 0.6900 (mtt) REVERT: o 61 GLN cc_start: 0.8040 (tp40) cc_final: 0.7436 (tt0) REVERT: p 24 SER cc_start: 0.6980 (t) cc_final: 0.6614 (m) REVERT: q 39 ARG cc_start: 0.7043 (mmt90) cc_final: 0.6252 (mmp-170) REVERT: s 43 MET cc_start: 0.7855 (mtp) cc_final: 0.7244 (tpp) REVERT: s 46 LEU cc_start: 0.7312 (mt) cc_final: 0.6661 (mp) REVERT: s 55 GLN cc_start: 0.7686 (pm20) cc_final: 0.7017 (pm20) REVERT: s 61 VAL cc_start: 0.6945 (t) cc_final: 0.6633 (t) REVERT: s 63 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7009 (t70) REVERT: s 65 MET cc_start: 0.5947 (ptp) cc_final: 0.5114 (ptp) REVERT: t 58 ASP cc_start: 0.8025 (t0) cc_final: 0.7484 (t0) REVERT: t 68 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7003 (tppt) outliers start: 216 outliers final: 163 residues processed: 1342 average time/residue: 1.3987 time to fit residues: 3214.9730 Evaluate side-chains 1342 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1158 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 169 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 53 ILE Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 18 LYS Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 63 ASP Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain z residue 26 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 641 optimal weight: 4.9990 chunk 1032 optimal weight: 10.0000 chunk 630 optimal weight: 3.9990 chunk 489 optimal weight: 0.0030 chunk 717 optimal weight: 10.0000 chunk 1082 optimal weight: 30.0000 chunk 996 optimal weight: 0.9990 chunk 862 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 666 optimal weight: 10.0000 chunk 528 optimal weight: 3.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN E 195 GLN H 20 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN N 62 ASN N 73 ASN V 75 GLN X 15 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 3 27 ASN 4 37 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN k 118 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 165470 Z= 0.222 Angle : 0.690 15.225 247196 Z= 0.373 Chirality : 0.036 0.446 31417 Planarity : 0.007 0.130 13501 Dihedral : 23.992 179.247 81863 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.25 % Favored : 91.17 % Rotamer: Outliers : 3.99 % Allowed : 24.76 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.69 (0.10), residues: 6218 helix: 0.32 (0.12), residues: 1945 sheet: -1.34 (0.14), residues: 1203 loop : -2.00 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 200 HIS 0.007 0.001 HIS C 229 PHE 0.019 0.002 PHE s 60 TYR 0.032 0.002 TYR D 45 ARG 0.011 0.000 ARG n 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12436 Ramachandran restraints generated. 6218 Oldfield, 0 Emsley, 6218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1151 time to evaluate : 6.747 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: C 27 LYS cc_start: 0.8078 (mttt) cc_final: 0.7536 (mmmt) REVERT: C 86 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6569 (ttm-80) REVERT: C 97 ASP cc_start: 0.7124 (p0) cc_final: 0.6375 (p0) REVERT: C 99 GLU cc_start: 0.7568 (tt0) cc_final: 0.7182 (tt0) REVERT: C 116 GLN cc_start: 0.7071 (tp40) cc_final: 0.6783 (tp40) REVERT: C 145 MET cc_start: 0.7917 (mmm) cc_final: 0.7691 (mmm) REVERT: C 159 THR cc_start: 0.8934 (m) cc_final: 0.8681 (p) REVERT: C 193 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7232 (mt-10) REVERT: C 213 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7488 (mtt-85) REVERT: C 268 ARG cc_start: 0.7565 (ttt90) cc_final: 0.7340 (tmm-80) REVERT: C 269 ARG cc_start: 0.7693 (mmm160) cc_final: 0.6766 (mmm-85) REVERT: D 42 ASN cc_start: 0.7091 (m110) cc_final: 0.6557 (t0) REVERT: D 169 ARG cc_start: 0.8504 (ttt-90) cc_final: 0.7960 (ttt-90) REVERT: D 199 SER cc_start: 0.8124 (p) cc_final: 0.7789 (p) REVERT: E 105 LEU cc_start: 0.8511 (mt) cc_final: 0.8311 (tp) REVERT: E 166 LYS cc_start: 0.7311 (mttt) cc_final: 0.6962 (mmtm) REVERT: E 170 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7040 (ttm110) REVERT: F 6 TYR cc_start: 0.7317 (t80) cc_final: 0.6978 (t80) REVERT: F 93 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6852 (tm-30) REVERT: F 95 MET cc_start: 0.7095 (ttp) cc_final: 0.6861 (ttt) REVERT: F 97 GLU cc_start: 0.7462 (tp30) cc_final: 0.6883 (tp30) REVERT: F 114 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6451 (ttp-170) REVERT: F 128 SER cc_start: 0.7844 (t) cc_final: 0.7289 (p) REVERT: F 162 ASP cc_start: 0.6205 (p0) cc_final: 0.5602 (m-30) REVERT: G 142 GLN cc_start: 0.7247 (tp40) cc_final: 0.7032 (tp-100) REVERT: G 154 GLU cc_start: 0.6671 (tt0) cc_final: 0.6150 (tt0) REVERT: G 159 LYS cc_start: 0.7222 (mtpp) cc_final: 0.6933 (mtmm) REVERT: J 53 TYR cc_start: 0.8097 (m-80) cc_final: 0.7603 (m-80) REVERT: J 75 TYR cc_start: 0.8423 (m-80) cc_final: 0.8101 (m-80) REVERT: J 84 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7497 (tp) REVERT: K 93 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: K 114 LYS cc_start: 0.6797 (mtmt) cc_final: 0.6094 (ttpt) REVERT: L 7 SER cc_start: 0.8358 (p) cc_final: 0.7831 (t) REVERT: L 106 GLU cc_start: 0.8194 (pt0) cc_final: 0.7931 (pm20) REVERT: M 6 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7625 (ptp90) REVERT: M 75 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6604 (tm-30) REVERT: N 112 TYR cc_start: 0.8224 (m-80) cc_final: 0.7884 (m-80) REVERT: O 100 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6661 (p90) REVERT: P 36 LYS cc_start: 0.6738 (mmmt) cc_final: 0.6135 (mppt) REVERT: P 88 ARG cc_start: 0.7028 (ptt-90) cc_final: 0.6589 (ptt90) REVERT: Q 83 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7786 (mtpp) REVERT: R 6 GLN cc_start: 0.8296 (tt0) cc_final: 0.8063 (tp-100) REVERT: R 21 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7569 (ttm110) REVERT: R 31 GLU cc_start: 0.7872 (tt0) cc_final: 0.7309 (tt0) REVERT: S 19 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7629 (mp) REVERT: S 27 LYS cc_start: 0.7336 (mttp) cc_final: 0.6616 (mmmt) REVERT: S 73 LYS cc_start: 0.7908 (mttt) cc_final: 0.7583 (mtpt) REVERT: T 3 ARG cc_start: 0.7573 (ptp90) cc_final: 0.7173 (ptp90) REVERT: T 25 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7333 (pp20) REVERT: T 28 ASN cc_start: 0.7293 (t0) cc_final: 0.7041 (t0) REVERT: T 42 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7615 (mp0) REVERT: T 76 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7595 (ptm160) REVERT: U 8 ASP cc_start: 0.7641 (m-30) cc_final: 0.7215 (m-30) REVERT: U 9 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: U 46 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7881 (mtpt) REVERT: V 11 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: V 75 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: W 64 LYS cc_start: 0.7638 (tptm) cc_final: 0.7008 (tptp) REVERT: Y 6 LEU cc_start: 0.6132 (mt) cc_final: 0.5612 (mt) REVERT: Y 17 GLU cc_start: 0.8388 (tt0) cc_final: 0.7875 (tm-30) REVERT: Y 39 GLN cc_start: 0.8159 (mt0) cc_final: 0.7332 (mm-40) REVERT: 0 11 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7328 (mmtp) REVERT: 0 35 GLU cc_start: 0.7902 (tt0) cc_final: 0.7548 (tt0) REVERT: 0 49 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7675 (mtm-85) REVERT: 1 7 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7344 (mttt) REVERT: 3 14 LYS cc_start: 0.8418 (tttt) cc_final: 0.7728 (mmtp) REVERT: 3 38 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6924 (tttm) REVERT: 4 9 LYS cc_start: 0.7587 (ttmt) cc_final: 0.7335 (ptmm) REVERT: 4 15 LYS cc_start: 0.7637 (ttmm) cc_final: 0.6802 (mtmm) REVERT: 5 1 MET cc_start: 0.1426 (tpt) cc_final: 0.1137 (mmm) REVERT: 5 86 MET cc_start: 0.2518 (mmm) cc_final: 0.1615 (mmm) REVERT: 6 10 GLU cc_start: 0.7564 (tp30) cc_final: 0.7005 (tt0) REVERT: 6 16 CYS cc_start: 0.5430 (p) cc_final: 0.5162 (p) REVERT: 6 56 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5026 (tpp80) REVERT: b 67 LEU cc_start: 0.7913 (mt) cc_final: 0.7441 (mt) REVERT: b 136 ARG cc_start: 0.5703 (mmm-85) cc_final: 0.5392 (ttp-170) REVERT: b 144 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7474 (pt0) REVERT: b 211 LEU cc_start: 0.5921 (tp) cc_final: 0.5196 (mt) REVERT: b 212 TYR cc_start: 0.7040 (m-80) cc_final: 0.6595 (m-80) REVERT: c 17 TRP cc_start: 0.8271 (m-90) cc_final: 0.7907 (m-90) REVERT: c 71 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6701 (mtp85) REVERT: c 82 ASP cc_start: 0.8028 (m-30) cc_final: 0.7726 (m-30) REVERT: c 105 VAL cc_start: 0.6392 (t) cc_final: 0.6059 (p) REVERT: c 166 TRP cc_start: 0.8005 (p-90) cc_final: 0.7472 (p-90) REVERT: c 171 ARG cc_start: 0.6818 (ttp-170) cc_final: 0.6499 (ttm-80) REVERT: c 182 ASP cc_start: 0.8987 (t0) cc_final: 0.8697 (t0) REVERT: c 187 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7973 (mt-10) REVERT: d 57 LYS cc_start: 0.7023 (ttpt) cc_final: 0.6755 (tttm) REVERT: d 70 GLN cc_start: 0.8442 (tt0) cc_final: 0.8006 (mm-40) REVERT: d 98 ASP cc_start: 0.8258 (p0) cc_final: 0.7983 (p0) REVERT: d 140 ASP cc_start: 0.5189 (m-30) cc_final: 0.4945 (m-30) REVERT: d 183 ARG cc_start: 0.5523 (ptt-90) cc_final: 0.5254 (ptp-110) REVERT: e 18 ASN cc_start: 0.8011 (m-40) cc_final: 0.7543 (m-40) REVERT: e 85 LYS cc_start: 0.7929 (mptt) cc_final: 0.7542 (mtpp) REVERT: f 2 ARG cc_start: 0.7385 (mmt180) cc_final: 0.6780 (mtt180) REVERT: f 29 ILE cc_start: 0.6955 (mp) cc_final: 0.6652 (mp) REVERT: f 62 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6841 (ttt) REVERT: f 92 THR cc_start: 0.6301 (OUTLIER) cc_final: 0.6066 (p) REVERT: g 20 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: g 69 ARG cc_start: 0.6827 (ttm170) cc_final: 0.6399 (mtm-85) REVERT: g 105 GLU cc_start: 0.7539 (tp30) cc_final: 0.7337 (tp30) REVERT: g 109 LYS cc_start: 0.7496 (mptt) cc_final: 0.7079 (ptpt) REVERT: g 125 ASP cc_start: 0.7538 (m-30) cc_final: 0.7045 (m-30) REVERT: h 46 GLU cc_start: 0.7450 (tp30) cc_final: 0.7187 (tt0) REVERT: h 68 LYS cc_start: 0.7538 (tttp) cc_final: 0.7172 (mmmm) REVERT: h 86 LYS cc_start: 0.8294 (mttm) cc_final: 0.7951 (mtmm) REVERT: h 87 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6593 (mtt-85) REVERT: i 4 GLN cc_start: 0.4695 (OUTLIER) cc_final: 0.4397 (tm-30) REVERT: i 99 LYS cc_start: 0.7329 (ttpt) cc_final: 0.6965 (tptp) REVERT: i 108 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.5829 (ptm-80) REVERT: i 127 SER cc_start: 0.8150 (m) cc_final: 0.7500 (p) REVERT: j 27 GLU cc_start: 0.6923 (tt0) cc_final: 0.6302 (pp20) REVERT: j 68 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7731 (mtt180) REVERT: j 82 LYS cc_start: 0.6765 (mmmt) cc_final: 0.6397 (mmtt) REVERT: j 88 MET cc_start: 0.7283 (mmt) cc_final: 0.6929 (mmm) REVERT: k 39 ASN cc_start: 0.7557 (m-40) cc_final: 0.7262 (m-40) REVERT: k 79 LYS cc_start: 0.8167 (mppt) cc_final: 0.7662 (mmtt) REVERT: k 80 ASN cc_start: 0.6340 (p0) cc_final: 0.6107 (p0) REVERT: k 84 MET cc_start: 0.6761 (mmm) cc_final: 0.6377 (mmt) REVERT: k 115 ILE cc_start: 0.8300 (mt) cc_final: 0.7944 (tp) REVERT: k 125 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7741 (tptm) REVERT: l 69 GLU cc_start: 0.6410 (tt0) cc_final: 0.6070 (mt-10) REVERT: m 65 GLU cc_start: 0.6672 (tp30) cc_final: 0.5831 (mm-30) REVERT: m 92 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.6834 (ttp-170) REVERT: n 22 LYS cc_start: 0.7755 (tptp) cc_final: 0.7366 (mmtt) REVERT: n 42 TRP cc_start: 0.6720 (t-100) cc_final: 0.6320 (t60) REVERT: n 62 ASN cc_start: 0.8182 (t0) cc_final: 0.7862 (t0) REVERT: n 80 SER cc_start: 0.8332 (m) cc_final: 0.8093 (m) REVERT: n 92 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7395 (mp0) REVERT: o 58 MET cc_start: 0.7144 (mtm) cc_final: 0.6853 (mtt) REVERT: o 61 GLN cc_start: 0.8177 (tp40) cc_final: 0.7543 (tt0) REVERT: p 24 SER cc_start: 0.7044 (t) cc_final: 0.6673 (m) REVERT: q 39 ARG cc_start: 0.7075 (mmt90) cc_final: 0.6221 (mmp-170) REVERT: s 43 MET cc_start: 0.7882 (mtp) cc_final: 0.7316 (tpp) REVERT: s 46 LEU cc_start: 0.7302 (mt) cc_final: 0.6645 (mp) REVERT: s 61 VAL cc_start: 0.7050 (t) cc_final: 0.6759 (t) REVERT: s 65 MET cc_start: 0.5903 (ptp) cc_final: 0.5119 (ptp) REVERT: t 58 ASP cc_start: 0.7964 (t0) cc_final: 0.7413 (t0) REVERT: t 68 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6999 (tppt) REVERT: u 20 ARG cc_start: 0.6028 (tpt170) cc_final: 0.5715 (tpt90) outliers start: 206 outliers final: 174 residues processed: 1269 average time/residue: 1.3979 time to fit residues: 3042.5581 Evaluate side-chains 1328 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1136 time to evaluate : 6.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 53 ILE Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 44 PHE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 56 ARG Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain b residue 224 ARG Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 135 ARG Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain d residue 34 GLU Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 4 GLN Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 27 PHE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain t residue 15 LYS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 684 optimal weight: 20.0000 chunk 918 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 795 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 863 optimal weight: 5.9990 chunk 361 optimal weight: 7.9990 chunk 886 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN E 195 GLN H 20 ASN H 73 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN R 43 ASN V 75 GLN X 15 ASN Y 15 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 4 37 GLN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN k 118 ASN ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 81 GLN z 97 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106362 restraints weight = 297205.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106131 restraints weight = 274148.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106250 restraints weight = 239686.510| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 165470 Z= 0.395 Angle : 0.810 15.613 247196 Z= 0.426 Chirality : 0.043 0.395 31417 Planarity : 0.008 0.139 13501 Dihedral : 24.082 179.858 81863 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.36 % Favored : 90.05 % Rotamer: Outliers : 4.84 % Allowed : 24.07 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.95 (0.10), residues: 6218 helix: 0.02 (0.12), residues: 1949 sheet: -1.44 (0.14), residues: 1196 loop : -2.12 (0.10), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 22 HIS 0.012 0.002 HIS C 229 PHE 0.030 0.002 PHE f 8 TYR 0.039 0.003 TYR D 45 ARG 0.010 0.001 ARG n 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44817.17 seconds wall clock time: 780 minutes 51.52 seconds (46851.52 seconds total)