Starting phenix.real_space_refine on Sat Mar 2 12:14:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfk_8828/03_2024/5wfk_8828_updated.pdb" } resolution = 3.4 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 1 8.98 5 P 4807 5.49 5 Mg 1413 5.21 5 S 171 5.16 5 C 76955 2.51 5 N 28339 2.21 5 O 42639 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 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ASP 263": "OD1" <-> "OD2" 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 ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" 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 88": "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 "E ASP 176": "OD1" <-> "OD2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ASP 152": "OD1" <-> "OD2" 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 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" 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 "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 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 55": "OD1" <-> "OD2" 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 GLU 5": "OE1" <-> "OE2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" 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 "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 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 "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 166": "OD1" <-> "OD2" Residue "b PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" 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 ASP 49": "OD1" <-> "OD2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" 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 75": "OE1" <-> "OE2" Residue "g ARG 2": "NH1" <-> "NH2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "h TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ARG 113": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "i PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "j ASP 97": "OD1" <-> "OD2" 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 "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 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 "q ARG 5": "NH1" <-> "NH2" 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 "t GLU 14": "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 152": "OE1" <-> "OE2" Residue "z ARG 154": "NH1" <-> "NH2" Residue "z ARG 171": "NH1" <-> "NH2" 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 ARG 269": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z GLU 285": "OE1" <-> "OE2" Residue "z ARG 288": "NH1" <-> "NH2" 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: 154325 Number of models: 1 Model: "" Number of chains: 113 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': 249, 'rna2p_pyr': 119, 'rna3p': 17, 'rna3p_pur': 1418, 'rna3p_pyr': 1089} Link IDs: {'rna2p': 375, 'rna3p': 2524} 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: 33095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 2, 'rna2p_pur': 116, 'rna2p_pyr': 68, 'rna3p': 9, 'rna3p_pur': 753, 'rna3p_pyr': 592} Link IDs: {'rna2p': 186, 'rna3p': 1353} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 2, 'rna2p_pur': 117, 'rna2p_pyr': 68, 'rna3p': 9, 'rna3p_pur': 752, 'rna3p_pyr': 592} Link IDs: {'rna2p': 187, 'rna3p': 1352} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 36951 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: 1164 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} bond proxies already assigned to first conformer: 1160 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: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 976 Unusual residues: {' K': 1, ' MG': 965} Classifications: {'peptide': 1, 'undetermined': 966} Link IDs: {None: 966} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Unusual residues: {' MG': 27} Classifications: {'undetermined': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" 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: "Y" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: "2" 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: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 375 Unusual residues: {' MG': 375} Classifications: {'undetermined': 375} Link IDs: {None: 374} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "l" 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: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "w" 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: "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: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 293 Classifications: {'water': 293} Link IDs: {None: 292} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" 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: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A G a 530 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G a 530 " occ=0.50 residue: pdb=" P A A a1492 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A a1492 " occ=0.50 Time building chain proxies: 71.64, per 1000 atoms: 0.46 Number of scatterers: 154325 At special positions: 0 Unit cell: (278.32, 270.48, 241.08, 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 1 19.00 S 171 16.00 P 4807 15.00 Mg 1413 11.99 O 42639 8.00 N 28339 7.00 C 76955 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: 63.87 Conformation dependent library (CDL) restraints added in 8.0 seconds 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11606 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: 194 helices and 75 sheets defined 38.5% alpha, 18.5% beta 1340 base pairs and 2345 stacking pairs defined. Time for finding SS restraints: 83.82 Creating SS restraints... Processing helix chain 'C' and resid 9 through 16 removed outlier: 7.642A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.652A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.892A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.632A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.026A 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: 6.173A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.695A 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 'C' and resid 196 through 201 removed outlier: 3.962A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.908A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.107A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.544A 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: 3.689A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.537A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.178A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 4.017A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.794A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 5.039A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.624A 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: 4.737A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.682A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 3.986A 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: 4.736A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.738A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.907A 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: 4.063A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.317A 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: 4.189A 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: 3.780A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.739A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 4.359A 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: 3.621A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.725A 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: 5.363A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.119A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.738A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.982A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.588A 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: 4.760A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.554A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.662A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.786A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.934A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.593A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.317A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.186A 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: 3.996A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.525A 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: 5.536A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.531A 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: 3.672A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.680A 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: 3.876A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.885A 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: 3.981A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.947A 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: 5.667A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.549A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.644A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.146A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.180A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 5.388A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.495A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.815A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 3.933A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.914A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.675A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.722A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 12 removed outlier: 3.955A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.581A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.701A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.672A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.596A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.147A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 115 removed outlier: 4.259A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.754A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.530A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.912A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 6.743A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 4 through 11' Processing helix chain 'T' and resid 17 through 26 removed outlier: 4.035A 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: 3.901A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.008A 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: 3.776A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.997A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.630A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.607A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.551A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 8 removed outlier: 4.102A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.659A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 4.402A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.501A pdb=" N LEU Z 23 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 5.166A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.359A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.518A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.807A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.807A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.138A 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: 4.646A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '4' and resid 30 through 35 removed outlier: 4.288A pdb=" N LYS 4 34 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 30 through 35' Processing helix chain '5' and resid 3 through 21 removed outlier: 3.508A pdb=" N ALA 5 10 " --> pdb=" O GLN 5 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.834A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU 5 41 " --> pdb=" O LYS 5 37 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY 5 45 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 70 removed outlier: 4.127A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 59 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) removed outlier: 4.232A 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: 4.238A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.734A 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: 4.101A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.595A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 53 removed outlier: 4.340A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.352A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 3.629A 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: 4.140A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.526A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.528A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.793A 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: 3.946A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.524A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 153 removed outlier: 3.650A pdb=" N LYS b 151 " --> pdb=" O GLY b 148 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 4.003A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU c 11 " --> pdb=" O ASN c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.673A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.886A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.638A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.601A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.006A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.021A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.578A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 5.455A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.575A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.652A 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: 4.207A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 3.605A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.885A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.279A 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: 4.346A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.816A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.360A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.532A pdb=" N VAL e 136 " --> pdb=" O PRO e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.504A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 33 removed outlier: 4.721A pdb=" N GLY f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.500A pdb=" N ASP f 72 " --> pdb=" O GLN f 68 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 6.101A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.061A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.103A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 3.536A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.920A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.793A 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: 3.577A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 removed outlier: 3.555A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 53 removed outlier: 4.643A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.717A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.214A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 98 removed outlier: 3.938A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.625A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.797A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.955A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.170A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 5.055A 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: 4.697A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.547A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (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: 5.046A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.718A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.548A pdb=" N LYS m 30 " --> pdb=" O LYS m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.618A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.635A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.727A pdb=" N ARG m 70 " --> pdb=" O GLY m 66 " (cutoff:3.500A) 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: 3.525A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.802A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.015A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.731A 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: 3.642A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 31 removed outlier: 4.211A pdb=" N ILE n 29 " --> pdb=" O ALA n 24 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.100A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 3.554A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.573A pdb=" N ARG o 52 " --> pdb=" O ASP o 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG o 53 " --> pdb=" O HIS o 49 " (cutoff:3.500A) removed outlier: 3.625A 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 64 removed outlier: 3.557A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP p 60 " --> pdb=" O ARG p 56 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 80 removed outlier: 3.749A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS p 80 " --> pdb=" O LYS p 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.546A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.349A 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: 4.409A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.333A 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: 4.778A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 4.965A 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: 3.831A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 85 removed outlier: 4.319A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.688A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 5.221A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 4.052A 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: 4.625A 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: 3.544A pdb=" N VAL u 52 " --> pdb=" O LYS u 48 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.825A pdb=" N THR z 28 " --> pdb=" O LYS z 24 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR z 33 " --> pdb=" O ALA z 29 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR z 38 " --> pdb=" O VAL z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 45 through 51 removed outlier: 4.126A pdb=" N ILE z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP z 50 " --> pdb=" O PHE z 46 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.038A pdb=" N LYS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG z 58 " --> pdb=" O GLU z 54 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY z 59 " --> pdb=" O GLU z 55 " (cutoff:3.500A) Processing helix chain 'z' and resid 87 through 99 removed outlier: 4.004A pdb=" N THR z 93 " --> pdb=" O LYS z 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP z 99 " --> pdb=" O ALA z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 112 through 126 removed outlier: 3.613A pdb=" N ARG z 116 " --> pdb=" O MET z 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN z 124 " --> pdb=" O LEU z 120 " (cutoff:3.500A) Processing helix chain 'z' and resid 142 through 161 removed outlier: 4.109A pdb=" N LEU z 146 " --> pdb=" O ASP z 142 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU z 147 " --> pdb=" O GLU z 143 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL z 149 " --> pdb=" O LEU z 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU z 150 " --> pdb=" O LEU z 146 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET z 151 " --> pdb=" O GLU z 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU z 152 " --> pdb=" O LEU z 148 " (cutoff:3.500A) Processing helix chain 'z' and resid 173 through 180 removed outlier: 3.556A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU z 179 " --> pdb=" O LEU z 175 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY z 180 " --> pdb=" O LYS z 176 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 198 removed outlier: 3.556A pdb=" N ILE z 188 " --> pdb=" O TRP z 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU z 191 " --> pdb=" O LYS z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 282 through 287 removed outlier: 3.977A pdb=" N ILE z 286 " --> pdb=" O LYS z 282 " (cutoff:3.500A) removed outlier: 5.188A 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: 4.210A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.382A 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: 3.661A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.607A 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: 6.693A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.923A 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: 4.519A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 3.984A 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: 3.883A 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: 3.738A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.163A 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: 5.907A 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: 5.635A 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: 3.616A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.618A 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: 5.910A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 16 through 20 removed outlier: 5.544A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.131A 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: 6.367A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.138A 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 74 through 78 removed outlier: 7.191A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.086A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.869A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.681A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.366A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.974A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.502A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.547A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.717A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.669A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.698A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.712A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 71 through 78 removed outlier: 3.655A pdb=" N LYS R 76 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.725A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 73 through 79 removed outlier: 5.111A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.070A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'T' and resid 29 through 33 removed outlier: 3.527A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.626A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.308A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 41 through 44 removed outlier: 6.307A pdb=" N ILE W 78 " --> pdb=" O GLY W 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 46 through 50 removed outlier: 7.647A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.854A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 33 through 40 No H-bonds generated for sheet with id= 40 Processing sheet with id= 41, first strand: chain 'Z' and resid 33 through 38 removed outlier: 4.308A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '0' and resid 27 through 30 removed outlier: 6.457A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '1' and resid 19 through 23 removed outlier: 6.535A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '3' and resid 21 through 24 removed outlier: 5.779A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '4' and resid 13 through 19 removed outlier: 8.451A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '5' and resid 24 through 28 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain '6' and resid 21 through 25 Processing sheet with id= 48, first strand: chain 'b' and resid 30 through 33 removed outlier: 4.552A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.914A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.559A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 163 through 168 removed outlier: 3.618A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.592A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N TRP d 169 " --> pdb=" O LYS d 182 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 11 through 15 removed outlier: 4.001A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.642A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.657A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.612A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 43 through 47 removed outlier: 6.298A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 59, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.086A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.550A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.636A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR i 65 " --> pdb=" O ARG i 17 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.501A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'k' and resid 29 through 34 Processing sheet with id= 64, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.041A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.903A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.991A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 37 through 40 removed outlier: 3.549A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 6.089A 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: 7.298A 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: 4.994A 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: 3.784A pdb=" N SER z 65 " --> pdb=" O ASP z 80 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR z 69 " --> pdb=" O TYR z 76 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR z 16 " --> pdb=" O VAL z 79 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS z 81 " --> pdb=" O THR z 16 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY z 18 " --> pdb=" O CYS z 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY z 100 " --> pdb=" O ASN z 13 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY z 15 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL z 105 " --> pdb=" O PHE z 133 " (cutoff:3.500A) removed outlier: 3.775A 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 214 removed outlier: 6.681A pdb=" N PHE z 210 " --> pdb=" O LYS z 294 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLN z 290 " --> pdb=" O ILE z 214 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 216 through 220 removed outlier: 3.915A pdb=" N ASP z 216 " --> pdb=" O THR z 228 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY z 224 " --> pdb=" O ILE z 220 " (cutoff:3.500A) removed outlier: 4.309A 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: 7.313A 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: 3.754A pdb=" N GLY z 339 " --> pdb=" O PRO z 328 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR z 326 " --> pdb=" O ILE z 341 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU z 372 " --> pdb=" O VAL z 388 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3328 hydrogen bonds 5392 hydrogen bond angles 0 basepair planarities 1340 basepair parallelities 2345 stacking parallelities Total time for adding SS restraints: 347.43 Time building geometry restraints manager: 69.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 12628 1.28 - 1.41: 51852 1.41 - 1.55: 89893 1.55 - 1.68: 10859 1.68 - 1.81: 300 Bond restraints: 165532 Sorted by residual: bond pdb=" O3' U w 117 " pdb=" P G w 18 " ideal model delta sigma weight residual 1.607 1.142 0.465 1.50e-02 4.44e+03 9.62e+02 bond pdb=" O4' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.412 1.659 -0.247 1.50e-02 4.44e+03 2.71e+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 2.49e+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 1.489 0.313 2.00e-02 2.50e+03 2.45e+02 ... (remaining 165527 not shown) Histogram of bond angle deviations from ideal: 84.14 - 100.45: 143 100.45 - 116.76: 148543 116.76 - 133.08: 98540 133.08 - 149.39: 70 149.39 - 165.70: 1 Bond angle restraints: 247297 Sorted by residual: angle pdb=" C3' 6MZ A1618 " pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " ideal model delta sigma weight residual 120.20 165.70 -45.50 1.50e+00 4.44e-01 9.20e+02 angle pdb=" C3' U w 117 " pdb=" O3' U w 117 " pdb=" P G w 18 " ideal model delta sigma weight residual 120.20 148.16 -27.96 1.50e+00 4.44e-01 3.47e+02 angle pdb=" O3' U w 117 " pdb=" P G w 18 " pdb=" O5' G w 18 " ideal model delta sigma weight residual 104.00 120.13 -16.13 1.50e+00 4.44e-01 1.16e+02 angle pdb=" O3' G A 51 " pdb=" C3' G A 51 " pdb=" C2' G A 51 " ideal model delta sigma weight residual 109.50 123.73 -14.23 1.50e+00 4.44e-01 9.00e+01 angle pdb=" O3' G a1305 " pdb=" C3' G a1305 " pdb=" C2' G a1305 " ideal model delta sigma weight residual 109.50 123.36 -13.86 1.50e+00 4.44e-01 8.54e+01 ... (remaining 247292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 92589 35.97 - 71.94: 11660 71.94 - 107.91: 1489 107.91 - 143.88: 45 143.88 - 179.85: 47 Dihedral angle restraints: 105830 sinusoidal: 87829 harmonic: 18001 Sorted by residual: dihedral pdb=" C5' G a1432 " pdb=" C4' G a1432 " pdb=" C3' G a1432 " pdb=" O3' G a1432 " ideal model delta sinusoidal sigma weight residual 147.00 68.20 78.80 1 8.00e+00 1.56e-02 1.21e+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 70.91 76.09 1 8.00e+00 1.56e-02 1.14e+02 dihedral pdb=" C5' C a 280 " pdb=" C4' C a 280 " pdb=" C3' C a 280 " pdb=" O3' C a 280 " ideal model delta sinusoidal sigma weight residual 147.00 72.69 74.31 1 8.00e+00 1.56e-02 1.09e+02 ... (remaining 105827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 25856 0.147 - 0.294: 5517 0.294 - 0.442: 31 0.442 - 0.589: 9 0.589 - 0.736: 15 Chirality restraints: 31428 Sorted by residual: chirality pdb=" C3' G A 242 " pdb=" C4' G A 242 " pdb=" O3' G A 242 " pdb=" C2' G A 242 " both_signs ideal model delta sigma weight residual False -2.74 -2.01 -0.74 2.00e-01 2.50e+01 1.35e+01 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 -2.02 -0.72 2.00e-01 2.50e+01 1.31e+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 -2.04 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 31425 not shown) Planarity restraints: 13505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2069 " 0.017 2.00e-02 2.50e+03 6.25e-01 8.80e+03 pdb=" C4' 7MG A2069 " 0.460 2.00e-02 2.50e+03 pdb=" O4' 7MG A2069 " 0.770 2.00e-02 2.50e+03 pdb=" C3' 7MG A2069 " -0.609 2.00e-02 2.50e+03 pdb=" O3' 7MG A2069 " -0.629 2.00e-02 2.50e+03 pdb=" C2' 7MG A2069 " -0.187 2.00e-02 2.50e+03 pdb=" O2' 7MG A2069 " 0.948 2.00e-02 2.50e+03 pdb=" C1' 7MG A2069 " 0.214 2.00e-02 2.50e+03 pdb=" N9 7MG A2069 " -0.985 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.011 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 5MC a1407 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.658 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.625 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.160 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.963 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.234 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " 0.011 2.00e-02 2.50e+03 5.92e-01 7.89e+03 pdb=" C4' 2MG A2445 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.798 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.543 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.231 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.824 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.227 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.937 2.00e-02 2.50e+03 ... (remaining 13502 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.84: 18 1.84 - 2.66: 6241 2.66 - 3.49: 219677 3.49 - 4.31: 591768 4.31 - 5.14: 828182 Nonbonded interactions: 1645886 Sorted by model distance: nonbonded pdb=" O2 C a 392 " pdb=" N7 A a 393 " model vdw 1.013 3.120 nonbonded pdb=" N3 C y 43 " pdb=" O4 U y 45 " model vdw 1.322 3.120 nonbonded pdb=" O4 U a 543 " pdb=" N2 G a 544 " model vdw 1.401 2.520 nonbonded pdb=" O LYS o 46 " pdb=" N ASP o 48 " model vdw 1.411 2.520 nonbonded pdb=" O2 C a 514 " pdb=" N2 G a 538 " model vdw 1.487 2.496 ... (remaining 1645881 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 through 103)) 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 18.320 Check model and map are aligned: 1.750 Set scattering table: 1.040 Process input model: 680.470 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.500 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 711.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.465 165532 Z= 0.490 Angle : 1.110 45.500 247297 Z= 0.734 Chirality : 0.098 0.736 31428 Planarity : 0.023 0.625 13505 Dihedral : 24.201 179.845 94224 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 2.30 % Allowed : 9.73 % Favored : 87.97 % Rotamer: Outliers : 3.19 % Allowed : 7.08 % Favored : 89.72 % 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: -4.14 (0.08), residues: 6219 helix: -2.48 (0.09), residues: 1790 sheet: -3.05 (0.13), residues: 988 loop : -2.85 (0.08), residues: 3441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 212 HIS 0.014 0.001 HIS d 40 PHE 0.018 0.002 PHE u 36 TYR 0.015 0.002 TYR H 25 ARG 0.025 0.001 ARG k 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2155 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1991 time to evaluate : 6.827 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: symmetry clash revert: symmetry clash REVERT: C 12 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7151 (tpt170) REVERT: C 34 GLU cc_start: 0.8012 (pt0) cc_final: 0.7762 (pt0) REVERT: C 78 GLU cc_start: 0.7856 (tt0) cc_final: 0.7612 (tt0) REVERT: C 102 TYR cc_start: 0.8413 (m-80) cc_final: 0.8186 (m-80) REVERT: C 113 ASP cc_start: 0.7235 (m-30) cc_final: 0.7034 (m-30) REVERT: C 123 ILE cc_start: 0.8324 (mm) cc_final: 0.8096 (mm) REVERT: C 139 THR cc_start: 0.8469 (m) cc_final: 0.8194 (p) REVERT: C 200 MET cc_start: 0.8509 (ttp) cc_final: 0.8266 (ttm) REVERT: D 46 ARG cc_start: 0.8301 (ptm160) cc_final: 0.7447 (ttp80) REVERT: D 58 ASN cc_start: 0.8182 (p0) cc_final: 0.7826 (t0) REVERT: D 74 GLU cc_start: 0.7744 (tt0) cc_final: 0.7272 (mm-30) REVERT: D 99 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: D 106 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7325 (mtpt) REVERT: E 46 GLN cc_start: 0.8731 (mp10) cc_final: 0.8311 (mp10) REVERT: E 47 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7548 (mttm) REVERT: E 115 GLN cc_start: 0.7877 (mt0) cc_final: 0.7191 (mt0) REVERT: E 168 ASP cc_start: 0.7792 (t0) cc_final: 0.7462 (t0) REVERT: F 9 ASP cc_start: 0.7322 (m-30) cc_final: 0.6750 (m-30) REVERT: F 14 LYS cc_start: 0.8323 (tptp) cc_final: 0.7979 (mtmt) REVERT: F 16 MET cc_start: 0.8260 (mmm) cc_final: 0.8033 (mmm) REVERT: F 22 ASN cc_start: 0.7130 (m-40) cc_final: 0.6529 (p0) REVERT: F 25 MET cc_start: 0.8804 (mmp) cc_final: 0.8197 (tpp) REVERT: F 51 ASN cc_start: 0.7826 (m-40) cc_final: 0.7607 (t0) REVERT: F 67 THR cc_start: 0.8630 (p) cc_final: 0.8418 (p) REVERT: F 70 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6730 (ptm-80) REVERT: F 103 ILE cc_start: 0.8641 (pt) cc_final: 0.8407 (tt) REVERT: F 109 ARG cc_start: 0.7572 (mtp85) cc_final: 0.6980 (mmm160) REVERT: F 116 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (mp) REVERT: F 162 ASP cc_start: 0.6786 (p0) cc_final: 0.5813 (t0) REVERT: G 61 TRP cc_start: 0.7513 (m100) cc_final: 0.7102 (m-90) REVERT: G 72 ASN cc_start: 0.7622 (t0) cc_final: 0.7421 (t0) REVERT: G 86 LEU cc_start: 0.7986 (mp) cc_final: 0.7459 (mt) REVERT: G 98 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7656 (tptt) REVERT: G 101 VAL cc_start: 0.8682 (t) cc_final: 0.8464 (p) REVERT: G 114 HIS cc_start: 0.7253 (t70) cc_final: 0.7017 (t-170) REVERT: G 129 GLU cc_start: 0.7534 (tt0) cc_final: 0.6922 (tm-30) REVERT: G 138 GLN cc_start: 0.6918 (tp-100) cc_final: 0.6564 (mm-40) REVERT: G 159 LYS cc_start: 0.7746 (mtpp) cc_final: 0.7451 (mtpt) REVERT: G 167 VAL cc_start: 0.7967 (p) cc_final: 0.7604 (m) REVERT: H 116 ARG cc_start: 0.6953 (mmt-90) cc_final: 0.6731 (ptt90) REVERT: I 11 GLN cc_start: -0.1205 (OUTLIER) cc_final: -0.1551 (mp10) REVERT: I 35 MET cc_start: 0.4589 (ttt) cc_final: 0.3642 (mmt) REVERT: J 80 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.5162 (t-90) REVERT: J 86 GLN cc_start: 0.8302 (pt0) cc_final: 0.8066 (pt0) REVERT: J 129 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7972 (mm-30) REVERT: K 7 MET cc_start: 0.8801 (mtt) cc_final: 0.8500 (mtt) REVERT: K 92 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7180 (mp0) REVERT: L 69 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6564 (mmm-85) REVERT: L 78 ARG cc_start: 0.7054 (mtp-110) cc_final: 0.6669 (mtp-110) REVERT: L 79 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8171 (tp) REVERT: L 115 GLU cc_start: 0.7748 (mp0) cc_final: 0.7468 (mp0) REVERT: L 141 LYS cc_start: 0.7242 (mttt) cc_final: 0.6979 (pttm) REVERT: M 5 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8035 (tmtt) REVERT: M 40 ARG cc_start: 0.7891 (ptm160) cc_final: 0.7598 (ptm-80) REVERT: M 84 LYS cc_start: 0.8487 (mttt) cc_final: 0.8032 (mtmt) REVERT: M 95 LEU cc_start: 0.7812 (mt) cc_final: 0.7215 (pt) REVERT: M 104 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7590 (mt-10) REVERT: M 106 ASP cc_start: 0.7999 (t0) cc_final: 0.7723 (t70) REVERT: N 6 SER cc_start: 0.8327 (m) cc_final: 0.8046 (p) REVERT: N 23 ASN cc_start: 0.8274 (m-40) cc_final: 0.8015 (m-40) REVERT: N 30 ARG cc_start: 0.7340 (ttp-110) cc_final: 0.7025 (ttt90) REVERT: N 57 THR cc_start: 0.7292 (m) cc_final: 0.6770 (t) REVERT: N 69 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6733 (mtt90) REVERT: N 110 MET cc_start: 0.8645 (mmp) cc_final: 0.8418 (mmt) REVERT: O 45 SER cc_start: 0.7744 (t) cc_final: 0.7457 (p) REVERT: O 46 GLU cc_start: 0.8191 (pt0) cc_final: 0.7479 (mt-10) REVERT: O 52 SER cc_start: 0.8314 (p) cc_final: 0.8031 (p) REVERT: O 97 PHE cc_start: 0.8511 (m-80) cc_final: 0.8178 (m-80) REVERT: P 70 GLU cc_start: 0.8430 (tt0) cc_final: 0.8111 (mt-10) REVERT: P 88 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5560 (mtt-85) REVERT: Q 24 TYR cc_start: 0.8170 (t80) cc_final: 0.7847 (t80) REVERT: Q 44 TYR cc_start: 0.8268 (m-10) cc_final: 0.8030 (m-10) REVERT: Q 48 ASP cc_start: 0.7799 (m-30) cc_final: 0.7586 (m-30) REVERT: Q 75 TYR cc_start: 0.8401 (t80) cc_final: 0.8141 (t80) REVERT: R 13 ARG cc_start: 0.7381 (ttp80) cc_final: 0.6970 (ttt-90) REVERT: R 39 LEU cc_start: 0.7755 (mp) cc_final: 0.7528 (mp) REVERT: R 73 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8357 (mttm) REVERT: R 84 ARG cc_start: 0.8592 (ptt-90) cc_final: 0.8344 (ptp90) REVERT: S 49 LYS cc_start: 0.7247 (ttmt) cc_final: 0.7022 (mmtp) REVERT: S 72 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8197 (p) REVERT: S 92 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7544 (ptm-80) REVERT: T 33 LYS cc_start: 0.7435 (mtpp) cc_final: 0.7071 (ttmt) REVERT: U 5 ARG cc_start: 0.8183 (ptp-170) cc_final: 0.7761 (mtt180) REVERT: U 65 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: V 2 PHE cc_start: 0.6045 (m-10) cc_final: 0.4480 (m-80) REVERT: V 41 GLU cc_start: 0.7655 (tt0) cc_final: 0.6804 (pt0) REVERT: V 43 ASP cc_start: 0.8307 (t70) cc_final: 0.7558 (t0) REVERT: V 45 ASP cc_start: 0.7807 (m-30) cc_final: 0.7311 (p0) REVERT: V 46 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7747 (mtpt) REVERT: V 50 MET cc_start: 0.6826 (mmm) cc_final: 0.6382 (mtp) REVERT: V 51 GLN cc_start: 0.7779 (pt0) cc_final: 0.7327 (tt0) REVERT: V 80 HIS cc_start: 0.8382 (t-90) cc_final: 0.7924 (t-90) REVERT: V 92 VAL cc_start: 0.8241 (t) cc_final: 0.7855 (m) REVERT: W 15 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7885 (mmtm) REVERT: W 17 LEU cc_start: 0.8808 (mt) cc_final: 0.8586 (mt) REVERT: W 51 ARG cc_start: 0.8462 (ptm-80) cc_final: 0.8259 (ptm-80) REVERT: W 66 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7156 (mm-30) REVERT: X 29 LEU cc_start: 0.9041 (mt) cc_final: 0.8828 (mp) REVERT: X 36 ARG cc_start: 0.7355 (mtp85) cc_final: 0.7115 (mtp180) REVERT: X 71 ARG cc_start: 0.8235 (tpp-160) cc_final: 0.7235 (ttm110) REVERT: Y 5 GLU cc_start: 0.8195 (tt0) cc_final: 0.7800 (tt0) REVERT: Y 7 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7387 (mtp180) REVERT: Y 17 GLU cc_start: 0.7691 (tp30) cc_final: 0.7292 (tp30) REVERT: Y 27 ASN cc_start: 0.7993 (m-40) cc_final: 0.7589 (m110) REVERT: Y 28 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6833 (mt) REVERT: Y 58 ASN cc_start: 0.7264 (t0) cc_final: 0.6605 (t0) REVERT: Z 6 ILE cc_start: 0.8335 (mt) cc_final: 0.8121 (mm) REVERT: Z 36 GLU cc_start: 0.7638 (pt0) cc_final: 0.7414 (pt0) REVERT: Z 55 LYS cc_start: 0.7927 (mttt) cc_final: 0.7340 (mtmm) REVERT: 1 50 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7730 (tm-30) REVERT: 2 1 MET cc_start: 0.7023 (ppp) cc_final: 0.6765 (ppp) REVERT: 2 2 LYS cc_start: 0.8614 (tptm) cc_final: 0.8403 (tptt) REVERT: 2 19 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7778 (mtp85) REVERT: 2 37 LYS cc_start: 0.8279 (tttt) cc_final: 0.7897 (ttpt) REVERT: 2 41 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7691 (mmm160) REVERT: 5 1 MET cc_start: 0.3598 (tpt) cc_final: 0.2372 (mtt) REVERT: 5 86 MET cc_start: -0.2698 (mmm) cc_final: -0.3104 (mmm) REVERT: 6 33 ASN cc_start: 0.6810 (m-40) cc_final: 0.6502 (p0) REVERT: 6 41 HIS cc_start: 0.7850 (t-90) cc_final: 0.7572 (t-90) REVERT: b 26 MET cc_start: 0.7762 (mtp) cc_final: 0.7328 (mtp) REVERT: b 47 PRO cc_start: 0.8264 (Cg_exo) cc_final: 0.7894 (Cg_endo) REVERT: b 51 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7783 (mm-30) REVERT: b 95 TRP cc_start: 0.8197 (t60) cc_final: 0.7673 (t60) REVERT: b 114 LYS cc_start: 0.7091 (ttmt) cc_final: 0.6862 (tptm) REVERT: b 144 GLU cc_start: 0.7713 (tp30) cc_final: 0.7274 (tp30) REVERT: b 151 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8181 (tttp) REVERT: b 153 MET cc_start: 0.6988 (ttm) cc_final: 0.6738 (ttm) REVERT: b 170 ILE cc_start: 0.8306 (pt) cc_final: 0.8026 (mm) REVERT: b 207 ARG cc_start: 0.6587 (ttm170) cc_final: 0.6302 (tpt90) REVERT: b 222 GLU cc_start: 0.6990 (tp30) cc_final: 0.6607 (tp30) REVERT: c 33 ASP cc_start: 0.6992 (t0) cc_final: 0.6005 (t0) REVERT: c 37 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8050 (mtmm) REVERT: c 44 LYS cc_start: 0.8165 (tttt) cc_final: 0.7770 (ttpp) REVERT: c 82 ASP cc_start: 0.7848 (m-30) cc_final: 0.7352 (m-30) REVERT: c 84 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7460 (mp0) REVERT: c 125 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7820 (mtm110) REVERT: c 134 LYS cc_start: 0.8119 (mttt) cc_final: 0.7678 (pttp) REVERT: c 141 MET cc_start: 0.7879 (mmm) cc_final: 0.7171 (mmm) REVERT: c 151 GLU cc_start: 0.7584 (tt0) cc_final: 0.7288 (tt0) REVERT: c 169 GLU cc_start: 0.6965 (mt-10) cc_final: 0.5958 (tt0) REVERT: d 3 TYR cc_start: 0.8184 (t80) cc_final: 0.7592 (t80) REVERT: d 50 TYR cc_start: 0.7885 (t80) cc_final: 0.7672 (t80) REVERT: d 56 GLU cc_start: 0.7670 (tp30) cc_final: 0.7208 (tp30) REVERT: d 72 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7429 (tmm160) REVERT: d 135 GLN cc_start: 0.8065 (tp40) cc_final: 0.7605 (mm-40) REVERT: d 162 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6701 (mp0) REVERT: d 169 TRP cc_start: 0.8142 (p90) cc_final: 0.7788 (p90) REVERT: d 195 ASN cc_start: 0.6897 (t0) cc_final: 0.6077 (m-40) REVERT: e 13 LYS cc_start: 0.8430 (ptmt) cc_final: 0.8203 (ptmm) REVERT: e 79 THR cc_start: 0.7916 (t) cc_final: 0.7578 (m) REVERT: e 81 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8568 (mm-40) REVERT: e 145 ASN cc_start: 0.8112 (t0) cc_final: 0.7410 (m-40) REVERT: f 5 GLU cc_start: 0.7178 (tt0) cc_final: 0.6815 (tt0) REVERT: f 25 TYR cc_start: 0.7098 (m-10) cc_final: 0.6343 (m-80) REVERT: f 56 LYS cc_start: 0.7765 (mttp) cc_final: 0.7483 (mtmt) REVERT: f 90 MET cc_start: 0.6979 (mmm) cc_final: 0.6475 (mmm) REVERT: g 11 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6797 (mm) REVERT: g 12 LEU cc_start: 0.6524 (mt) cc_final: 0.6306 (mt) REVERT: g 16 LYS cc_start: 0.7188 (mttt) cc_final: 0.6945 (mmmt) REVERT: g 62 GLU cc_start: 0.7386 (tp30) cc_final: 0.6940 (mm-30) REVERT: g 73 GLU cc_start: 0.7205 (pt0) cc_final: 0.6279 (pt0) REVERT: g 91 ARG cc_start: 0.7014 (mmm160) cc_final: 0.6759 (ttp-110) REVERT: g 117 LEU cc_start: 0.8144 (tp) cc_final: 0.7834 (tt) REVERT: g 121 ASN cc_start: 0.7085 (m-40) cc_final: 0.6776 (m-40) REVERT: g 129 ASN cc_start: 0.7113 (p0) cc_final: 0.6801 (m-40) REVERT: h 24 VAL cc_start: 0.8128 (t) cc_final: 0.7265 (m) REVERT: h 26 MET cc_start: 0.7237 (ptt) cc_final: 0.6717 (pmm) REVERT: h 33 VAL cc_start: 0.8731 (t) cc_final: 0.8478 (m) REVERT: h 87 ARG cc_start: 0.7025 (mtt180) cc_final: 0.6678 (mtp-110) REVERT: h 98 LEU cc_start: 0.8306 (pp) cc_final: 0.7942 (pp) REVERT: h 102 VAL cc_start: 0.9287 (t) cc_final: 0.9017 (p) REVERT: h 107 LYS cc_start: 0.7659 (mmtm) cc_final: 0.7333 (mmmt) REVERT: h 120 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6905 (mp) REVERT: i 32 ARG cc_start: 0.6775 (mmt-90) cc_final: 0.5700 (mmm-85) REVERT: i 60 LEU cc_start: 0.7083 (mt) cc_final: 0.6647 (mt) REVERT: i 109 GLN cc_start: 0.7958 (mt0) cc_final: 0.7748 (mt0) REVERT: j 69 THR cc_start: 0.8589 (m) cc_final: 0.8339 (p) REVERT: k 25 SER cc_start: 0.8353 (t) cc_final: 0.8150 (p) REVERT: k 26 PHE cc_start: 0.7574 (m-80) cc_final: 0.7153 (m-80) REVERT: k 34 THR cc_start: 0.8632 (p) cc_final: 0.8428 (t) REVERT: k 67 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7610 (tp30) REVERT: k 71 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7823 (t0) REVERT: k 81 LEU cc_start: 0.7390 (pp) cc_final: 0.7059 (pt) REVERT: k 121 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7690 (ttt-90) REVERT: l 13 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8125 (mtm110) REVERT: l 23 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7160 (mp) REVERT: l 37 TYR cc_start: 0.7458 (p90) cc_final: 0.7151 (p90) REVERT: l 46 SER cc_start: 0.8313 (t) cc_final: 0.7950 (p) REVERT: l 73 LEU cc_start: 0.7427 (mp) cc_final: 0.7013 (mp) REVERT: l 86 VAL cc_start: 0.8678 (m) cc_final: 0.8203 (t) REVERT: l 107 LYS cc_start: 0.7772 (ttpt) cc_final: 0.6947 (mmmt) REVERT: l 116 TYR cc_start: 0.8681 (m-80) cc_final: 0.8290 (m-80) REVERT: l 119 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7920 (mmtm) REVERT: m 77 LYS cc_start: 0.8298 (tttm) cc_final: 0.8003 (tptm) REVERT: n 9 GLU cc_start: 0.7304 (tp30) cc_final: 0.7029 (mm-30) REVERT: n 19 TYR cc_start: 0.7122 (m-80) cc_final: 0.6276 (m-10) REVERT: n 25 GLU cc_start: 0.7669 (pt0) cc_final: 0.7296 (tm-30) REVERT: n 43 ASN cc_start: 0.8102 (m-40) cc_final: 0.7304 (t0) REVERT: n 53 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6066 (tpt-90) REVERT: n 62 ASN cc_start: 0.9064 (t0) cc_final: 0.8594 (t0) REVERT: n 71 HIS cc_start: 0.8176 (m-70) cc_final: 0.7623 (m-70) REVERT: o 69 LEU cc_start: 0.8442 (tp) cc_final: 0.8105 (tp) REVERT: o 76 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7401 (ttm170) REVERT: p 17 TYR cc_start: 0.7995 (m-80) cc_final: 0.7760 (m-80) REVERT: p 40 ASN cc_start: 0.7208 (t0) cc_final: 0.6920 (t0) REVERT: p 74 LEU cc_start: 0.8134 (mt) cc_final: 0.7515 (tt) REVERT: q 59 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6874 (tt0) REVERT: r 58 ILE cc_start: 0.8760 (mm) cc_final: 0.8556 (mm) REVERT: r 63 TYR cc_start: 0.8542 (t80) cc_final: 0.7714 (t80) REVERT: s 68 HIS cc_start: 0.8469 (m90) cc_final: 0.8225 (m90) REVERT: s 72 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7946 (mt-10) REVERT: s 79 TYR cc_start: 0.7685 (t80) cc_final: 0.7142 (t80) REVERT: t 24 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8487 (ttp-110) REVERT: t 25 SER cc_start: 0.8110 (t) cc_final: 0.7776 (p) REVERT: t 79 THR cc_start: 0.7795 (m) cc_final: 0.7403 (p) REVERT: u 15 LEU cc_start: 0.7634 (tp) cc_final: 0.7260 (tp) REVERT: u 36 PHE cc_start: 0.7333 (t80) cc_final: 0.6773 (t80) REVERT: u 37 TYR cc_start: 0.7844 (t80) cc_final: 0.7282 (t80) REVERT: z 260 MET cc_start: -0.1369 (tpp) cc_final: -0.1887 (tpp) REVERT: z 351 MET cc_start: 0.0816 (mmt) cc_final: 0.0371 (mtp) REVERT: z 368 MET cc_start: 0.0413 (ptp) cc_final: -0.0199 (mmm) outliers start: 164 outliers final: 39 residues processed: 2098 average time/residue: 1.4854 time to fit residues: 5201.8637 Evaluate side-chains 1376 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1317 time to evaluate : 6.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 129 ARG Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 66 LEU 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: 9.9990 chunk 823 optimal weight: 5.9990 chunk 457 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 555 optimal weight: 5.9990 chunk 440 optimal weight: 0.8980 chunk 851 optimal weight: 0.2980 chunk 329 optimal weight: 3.9990 chunk 518 optimal weight: 3.9990 chunk 634 optimal weight: 30.0000 chunk 987 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS C 85 ASN C 127 ASN E 62 GLN E 92 HIS G 72 ASN G 87 GLN G 114 HIS G 142 GLN I 42 ASN J 76 HIS J 128 ASN J 130 HIS J 132 HIS K 13 ASN L 54 GLN N 107 ASN P 11 GLN P 74 GLN P 76 HIS Q 55 GLN R 18 GLN R 43 ASN S 7 HIS S 61 ASN U 65 GLN V 49 ASN W 46 ASN X 19 HIS Y 20 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 6 20 ASN c 7 ASN c 18 ASN c 24 ASN d 70 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN e 11 GLN e 121 ASN f 63 ASN f 68 GLN j 64 GLN k 39 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 GLN o 19 ASN o 27 GLN o 36 ASN ** o 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 18 GLN q 46 HIS r 51 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 56 HIS t 2 ASN t 19 HIS z 135 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 165532 Z= 0.247 Angle : 0.792 15.940 247297 Z= 0.423 Chirality : 0.042 0.531 31428 Planarity : 0.007 0.134 13505 Dihedral : 24.345 177.782 82010 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.80 % Favored : 91.38 % Rotamer: Outliers : 5.23 % Allowed : 15.62 % Favored : 79.15 % 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: -2.84 (0.09), residues: 6219 helix: -0.64 (0.11), residues: 1939 sheet: -2.47 (0.13), residues: 1134 loop : -2.48 (0.09), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 200 HIS 0.014 0.001 HIS z 22 PHE 0.022 0.002 PHE S 75 TYR 0.043 0.002 TYR h 127 ARG 0.012 0.001 ARG l 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1647 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1378 time to evaluate : 6.930 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 12 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6674 (tpt170) REVERT: C 34 GLU cc_start: 0.8332 (pt0) cc_final: 0.7389 (pm20) REVERT: C 113 ASP cc_start: 0.7372 (m-30) cc_final: 0.7043 (m-30) REVERT: C 180 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7151 (mpt) REVERT: C 200 MET cc_start: 0.8695 (ttp) cc_final: 0.8489 (ttm) REVERT: C 263 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7509 (t0) REVERT: D 28 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6837 (tm-30) REVERT: D 74 GLU cc_start: 0.7757 (tt0) cc_final: 0.7307 (mm-30) REVERT: E 24 ASN cc_start: 0.8434 (t0) cc_final: 0.7518 (t0) REVERT: E 47 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7529 (mttm) REVERT: E 141 MET cc_start: 0.7419 (ttm) cc_final: 0.7054 (ttm) REVERT: E 168 ASP cc_start: 0.7615 (t0) cc_final: 0.7263 (t0) REVERT: F 14 LYS cc_start: 0.8331 (tptp) cc_final: 0.7712 (ptmt) REVERT: F 16 MET cc_start: 0.8127 (mmm) cc_final: 0.7860 (mmt) REVERT: F 25 MET cc_start: 0.8305 (mmp) cc_final: 0.7994 (tpp) REVERT: F 109 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7129 (mmm160) REVERT: F 121 PHE cc_start: 0.7421 (m-80) cc_final: 0.7072 (m-10) REVERT: F 162 ASP cc_start: 0.6881 (p0) cc_final: 0.6200 (t0) REVERT: G 61 TRP cc_start: 0.7681 (m100) cc_final: 0.7381 (m-90) REVERT: G 87 GLN cc_start: 0.6494 (pt0) cc_final: 0.5719 (pm20) REVERT: G 114 HIS cc_start: 0.7250 (t-90) cc_final: 0.6731 (t-170) REVERT: G 129 GLU cc_start: 0.7379 (tt0) cc_final: 0.6721 (tm-30) REVERT: H 12 LEU cc_start: 0.6979 (pp) cc_final: 0.6407 (tp) REVERT: I 11 GLN cc_start: -0.0885 (OUTLIER) cc_final: -0.1594 (mp10) REVERT: I 35 MET cc_start: 0.5074 (ttt) cc_final: 0.3942 (mmt) REVERT: J 80 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.5860 (t-90) REVERT: J 129 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8235 (mm-30) REVERT: J 136 GLN cc_start: 0.6898 (mp10) cc_final: 0.6297 (tm-30) REVERT: K 7 MET cc_start: 0.8805 (mtt) cc_final: 0.8443 (mtt) REVERT: K 88 ASN cc_start: 0.7528 (t0) cc_final: 0.7243 (t0) REVERT: K 113 MET cc_start: 0.7363 (mmt) cc_final: 0.6617 (pmm) REVERT: L 79 LEU cc_start: 0.8472 (tt) cc_final: 0.8223 (tp) REVERT: L 141 LYS cc_start: 0.7532 (mttt) cc_final: 0.7235 (ptpp) REVERT: M 5 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8012 (tmtt) REVERT: M 84 LYS cc_start: 0.8753 (mttt) cc_final: 0.8224 (mtmt) REVERT: M 95 LEU cc_start: 0.7931 (mt) cc_final: 0.7216 (pt) REVERT: M 104 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7545 (mt-10) REVERT: N 6 SER cc_start: 0.8310 (m) cc_final: 0.8032 (p) REVERT: N 23 ASN cc_start: 0.8170 (m-40) cc_final: 0.7951 (m-40) REVERT: N 30 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6966 (ttt90) REVERT: N 43 GLU cc_start: 0.8343 (tp30) cc_final: 0.7945 (tp30) REVERT: N 56 LYS cc_start: 0.7005 (mttp) cc_final: 0.6699 (mmmm) REVERT: N 57 THR cc_start: 0.6890 (m) cc_final: 0.6390 (t) REVERT: N 112 TYR cc_start: 0.8728 (m-80) cc_final: 0.8295 (m-80) REVERT: N 113 ILE cc_start: 0.8897 (tt) cc_final: 0.8587 (tt) REVERT: N 116 VAL cc_start: 0.8501 (t) cc_final: 0.7647 (p) REVERT: O 45 SER cc_start: 0.7712 (t) cc_final: 0.7397 (p) REVERT: O 46 GLU cc_start: 0.8310 (pt0) cc_final: 0.7888 (tt0) REVERT: O 62 LEU cc_start: 0.6523 (mm) cc_final: 0.6263 (mt) REVERT: O 97 PHE cc_start: 0.8479 (m-80) cc_final: 0.8124 (m-80) REVERT: P 18 SER cc_start: 0.7675 (t) cc_final: 0.7395 (p) REVERT: P 26 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7277 (tm-30) REVERT: P 65 ASN cc_start: 0.8025 (p0) cc_final: 0.7803 (p0) REVERT: P 70 GLU cc_start: 0.8368 (tt0) cc_final: 0.8069 (mt-10) REVERT: P 96 LEU cc_start: 0.8782 (mp) cc_final: 0.8530 (mm) REVERT: R 13 ARG cc_start: 0.7462 (ttp80) cc_final: 0.6966 (ttt-90) REVERT: R 23 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6084 (pp20) REVERT: R 62 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7130 (tm-30) REVERT: R 84 ARG cc_start: 0.8592 (ptt-90) cc_final: 0.8289 (ptp90) REVERT: S 92 ARG cc_start: 0.7591 (ptp90) cc_final: 0.7352 (ptm-80) REVERT: S 108 SER cc_start: 0.7644 (OUTLIER) cc_final: 0.7075 (p) REVERT: T 3 ARG cc_start: 0.6415 (ptp-110) cc_final: 0.5985 (ptp90) REVERT: T 6 ARG cc_start: 0.7434 (tpt-90) cc_final: 0.7207 (tpp80) REVERT: T 24 MET cc_start: 0.7230 (tpp) cc_final: 0.6820 (tpp) REVERT: T 32 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8309 (pp) REVERT: T 54 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6134 (pm20) REVERT: U 5 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.7805 (mtm180) REVERT: U 17 ASP cc_start: 0.7500 (m-30) cc_final: 0.6953 (m-30) REVERT: U 65 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8270 (mt0) REVERT: U 87 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7809 (mt-10) REVERT: V 46 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7723 (mtpt) REVERT: V 51 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: V 92 VAL cc_start: 0.8253 (t) cc_final: 0.7944 (m) REVERT: W 15 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8143 (mmtm) REVERT: W 35 ARG cc_start: 0.9069 (mmm-85) cc_final: 0.8695 (mtp85) REVERT: X 71 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7315 (ttm110) REVERT: Y 7 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7506 (mtp180) REVERT: Y 17 GLU cc_start: 0.7775 (tp30) cc_final: 0.7293 (tp30) REVERT: Z 36 GLU cc_start: 0.7575 (pt0) cc_final: 0.7355 (pt0) REVERT: Z 55 LYS cc_start: 0.7872 (mttt) cc_final: 0.7416 (mtmm) REVERT: 0 14 MET cc_start: 0.8230 (mtt) cc_final: 0.7956 (mtm) REVERT: 1 31 GLU cc_start: 0.6855 (pp20) cc_final: 0.6640 (pp20) REVERT: 2 37 LYS cc_start: 0.8422 (tttt) cc_final: 0.7865 (ttpt) REVERT: 2 41 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7797 (mmm160) REVERT: 4 12 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7070 (tpm170) REVERT: 4 20 ASP cc_start: 0.8250 (t70) cc_final: 0.7826 (t0) REVERT: 4 37 GLN cc_start: 0.8035 (tt0) cc_final: 0.7512 (tm-30) REVERT: 5 1 MET cc_start: 0.3245 (tpt) cc_final: 0.2709 (tpp) REVERT: 5 86 MET cc_start: -0.2723 (mmm) cc_final: -0.3031 (mmm) REVERT: 6 33 ASN cc_start: 0.6885 (m-40) cc_final: 0.6611 (p0) REVERT: 6 41 HIS cc_start: 0.8082 (t-90) cc_final: 0.7428 (t-90) REVERT: b 8 MET cc_start: 0.5958 (ppp) cc_final: 0.5589 (ppp) REVERT: b 25 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7254 (mtmt) REVERT: b 26 MET cc_start: 0.7556 (mtp) cc_final: 0.6989 (mtp) REVERT: b 29 PHE cc_start: 0.7032 (m-80) cc_final: 0.6821 (m-80) REVERT: b 81 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7607 (t0) REVERT: b 100 LEU cc_start: 0.8618 (mt) cc_final: 0.8402 (tt) REVERT: b 136 ARG cc_start: 0.6185 (mmm-85) cc_final: 0.5646 (ttp-170) REVERT: b 144 GLU cc_start: 0.7723 (tp30) cc_final: 0.7312 (tp30) REVERT: b 207 ARG cc_start: 0.6760 (ttm170) cc_final: 0.6402 (tpt90) REVERT: c 7 ASN cc_start: 0.7876 (t0) cc_final: 0.7453 (t0) REVERT: c 36 PHE cc_start: 0.8201 (t80) cc_final: 0.7836 (t80) REVERT: c 37 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7962 (mtmm) REVERT: c 44 LYS cc_start: 0.8027 (tttt) cc_final: 0.7735 (ttpp) REVERT: c 57 GLU cc_start: 0.7358 (mp0) cc_final: 0.7102 (mp0) REVERT: c 120 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6545 (p) REVERT: c 125 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7941 (mtm110) REVERT: c 130 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8047 (mtt-85) REVERT: c 134 LYS cc_start: 0.8366 (mttt) cc_final: 0.7856 (pttp) REVERT: c 141 MET cc_start: 0.7978 (mmm) cc_final: 0.7617 (mmt) REVERT: c 148 ILE cc_start: 0.7956 (tp) cc_final: 0.7580 (tp) REVERT: c 151 GLU cc_start: 0.7555 (tt0) cc_final: 0.7331 (tt0) REVERT: c 169 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6224 (tt0) REVERT: d 3 TYR cc_start: 0.8204 (t80) cc_final: 0.7637 (t80) REVERT: d 32 LYS cc_start: 0.7024 (mttt) cc_final: 0.6305 (tttm) REVERT: d 75 TYR cc_start: 0.8701 (t80) cc_final: 0.8462 (t80) REVERT: d 146 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7475 (tm-30) REVERT: d 162 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6532 (mp0) REVERT: d 169 TRP cc_start: 0.8044 (p90) cc_final: 0.7676 (p90) REVERT: d 177 MET cc_start: 0.6710 (mmt) cc_final: 0.6074 (mtm) REVERT: d 195 ASN cc_start: 0.6969 (t0) cc_final: 0.5885 (m-40) REVERT: e 11 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: e 145 ASN cc_start: 0.7851 (t0) cc_final: 0.7572 (m-40) REVERT: f 9 MET cc_start: 0.8046 (mtm) cc_final: 0.7814 (mtp) REVERT: f 24 ARG cc_start: 0.7022 (mtp-110) cc_final: 0.6795 (mpp80) REVERT: f 25 TYR cc_start: 0.6607 (m-10) cc_final: 0.6356 (m-80) REVERT: f 38 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5751 (ttp-170) REVERT: f 56 LYS cc_start: 0.7754 (mttp) cc_final: 0.7541 (mtpt) REVERT: f 73 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7787 (mt-10) REVERT: f 90 MET cc_start: 0.6500 (mmm) cc_final: 0.5978 (mmm) REVERT: g 11 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6495 (mm) REVERT: g 14 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7244 (t0) REVERT: g 16 LYS cc_start: 0.7153 (mttt) cc_final: 0.6873 (mmmt) REVERT: g 78 ARG cc_start: 0.2063 (OUTLIER) cc_final: 0.0524 (tmt170) REVERT: g 91 ARG cc_start: 0.6999 (mmm160) cc_final: 0.6617 (ttp-110) REVERT: h 2 MET cc_start: 0.7121 (tpp) cc_final: 0.6880 (tpp) REVERT: h 6 ILE cc_start: 0.8316 (mt) cc_final: 0.8098 (mt) REVERT: h 66 GLN cc_start: 0.6711 (mm-40) cc_final: 0.6249 (mt0) REVERT: h 87 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6592 (ttp80) REVERT: h 98 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7666 (pp) REVERT: h 120 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7148 (mp) REVERT: i 8 THR cc_start: 0.8557 (m) cc_final: 0.8353 (p) REVERT: i 32 ARG cc_start: 0.7158 (mmt-90) cc_final: 0.6047 (mmm-85) REVERT: i 36 GLN cc_start: 0.8018 (pt0) cc_final: 0.7226 (tp-100) REVERT: i 45 MET cc_start: 0.7293 (ppp) cc_final: 0.7080 (ppp) REVERT: i 79 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7254 (ttt-90) REVERT: j 48 ARG cc_start: 0.6709 (mtt90) cc_final: 0.6482 (mtm-85) REVERT: j 69 THR cc_start: 0.8558 (m) cc_final: 0.8164 (p) REVERT: j 88 MET cc_start: 0.5725 (mmm) cc_final: 0.4430 (mtt) REVERT: k 13 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7630 (ptmt) REVERT: k 25 SER cc_start: 0.8621 (t) cc_final: 0.8380 (p) REVERT: k 26 PHE cc_start: 0.7573 (m-80) cc_final: 0.7303 (m-80) REVERT: k 67 GLU cc_start: 0.8658 (mt-10) cc_final: 0.7768 (tp30) REVERT: k 84 MET cc_start: 0.8732 (mmm) cc_final: 0.8396 (mtp) REVERT: k 115 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7622 (tt) REVERT: k 118 ASN cc_start: 0.7270 (m110) cc_final: 0.7024 (m110) REVERT: l 37 TYR cc_start: 0.7665 (p90) cc_final: 0.6998 (p90) REVERT: l 38 THR cc_start: 0.7761 (p) cc_final: 0.6903 (t) REVERT: l 46 SER cc_start: 0.8085 (t) cc_final: 0.7672 (p) REVERT: l 53 ARG cc_start: 0.6089 (mmm-85) cc_final: 0.5409 (tpt90) REVERT: l 107 LYS cc_start: 0.7875 (ttpt) cc_final: 0.6989 (mmmt) REVERT: l 116 TYR cc_start: 0.8804 (m-80) cc_final: 0.8297 (m-80) REVERT: m 49 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8194 (tm-30) REVERT: m 73 SER cc_start: 0.8460 (t) cc_final: 0.7931 (p) REVERT: n 11 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8127 (ttpt) REVERT: n 19 TYR cc_start: 0.6934 (m-80) cc_final: 0.6105 (m-10) REVERT: n 25 GLU cc_start: 0.7744 (pt0) cc_final: 0.7316 (pp20) REVERT: n 53 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7231 (tpt-90) REVERT: n 62 ASN cc_start: 0.9208 (t0) cc_final: 0.8733 (t0) REVERT: n 71 HIS cc_start: 0.8266 (m-70) cc_final: 0.7489 (m-70) REVERT: o 9 LYS cc_start: 0.8604 (tptp) cc_final: 0.8019 (mttt) REVERT: p 32 PHE cc_start: 0.7984 (p90) cc_final: 0.7463 (p90) REVERT: q 59 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6579 (tt0) REVERT: q 72 TRP cc_start: 0.7879 (m100) cc_final: 0.7482 (m100) REVERT: s 36 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7164 (ptp-170) REVERT: s 68 HIS cc_start: 0.8610 (m90) cc_final: 0.8214 (m170) REVERT: s 72 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8192 (mt-10) REVERT: t 23 ARG cc_start: 0.7456 (mmm-85) cc_final: 0.6756 (ptm160) REVERT: t 24 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8225 (ttp-110) REVERT: t 26 MET cc_start: 0.8909 (tmm) cc_final: 0.8454 (tmm) REVERT: t 47 GLN cc_start: 0.8117 (mm110) cc_final: 0.7638 (mm110) REVERT: t 54 GLN cc_start: 0.8104 (tt0) cc_final: 0.7751 (tt0) REVERT: t 60 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7604 (mm-40) REVERT: u 15 LEU cc_start: 0.7696 (tp) cc_final: 0.7363 (tp) REVERT: u 19 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7269 (tptt) REVERT: u 36 PHE cc_start: 0.7005 (t80) cc_final: 0.6497 (t80) REVERT: z 260 MET cc_start: -0.1279 (tpp) cc_final: -0.1849 (tpp) REVERT: z 349 MET cc_start: 0.3030 (mmm) cc_final: -0.0298 (ptp) REVERT: z 351 MET cc_start: 0.1046 (mmt) cc_final: 0.0572 (mtp) REVERT: z 368 MET cc_start: 0.0390 (ptp) cc_final: -0.0182 (mmm) outliers start: 269 outliers final: 156 residues processed: 1533 average time/residue: 1.3923 time to fit residues: 3654.7370 Evaluate side-chains 1395 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1216 time to evaluate : 6.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 11 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 15 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 51 GLN Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 20 ASN Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 45 LYS Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 548 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 821 optimal weight: 0.7980 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 988 optimal weight: 6.9990 chunk 1068 optimal weight: 0.0980 chunk 880 optimal weight: 4.9990 chunk 980 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 793 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 HIS C 141 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 41 GLN G 138 GLN H 43 ASN K 13 ASN L 35 HIS P 6 GLN P 74 GLN Q 43 GLN Q 58 GLN T 48 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 HIS c 18 ASN d 53 GLN d 70 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN j 35 GLN j 64 GLN k 118 ASN l 72 ASN p 18 GLN p 63 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS t 51 ASN z 51 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 165532 Z= 0.240 Angle : 0.718 14.734 247297 Z= 0.391 Chirality : 0.038 0.608 31428 Planarity : 0.007 0.133 13505 Dihedral : 24.172 179.884 81956 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.25 % Favored : 91.01 % Rotamer: Outliers : 6.10 % Allowed : 17.79 % Favored : 76.11 % 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: -2.16 (0.10), residues: 6219 helix: 0.13 (0.11), residues: 1914 sheet: -1.95 (0.14), residues: 1125 loop : -2.28 (0.10), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 212 HIS 0.075 0.002 HIS t 19 PHE 0.034 0.002 PHE F 174 TYR 0.031 0.002 TYR J 16 ARG 0.016 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1617 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1302 time to evaluate : 6.914 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: C 34 GLU cc_start: 0.8342 (pt0) cc_final: 0.7848 (pt0) REVERT: C 113 ASP cc_start: 0.7503 (m-30) cc_final: 0.7087 (m-30) REVERT: C 180 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7311 (mpt) REVERT: D 28 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7237 (tm-30) REVERT: D 74 GLU cc_start: 0.7752 (tt0) cc_final: 0.7402 (mm-30) REVERT: E 111 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7851 (tm-30) REVERT: E 189 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8245 (p) REVERT: E 197 GLU cc_start: 0.6154 (tt0) cc_final: 0.5936 (tt0) REVERT: F 14 LYS cc_start: 0.8282 (tptp) cc_final: 0.7697 (ptmt) REVERT: F 25 MET cc_start: 0.8365 (mmp) cc_final: 0.8121 (tpp) REVERT: F 34 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.7949 (p) REVERT: F 70 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7124 (ptt90) REVERT: F 95 MET cc_start: 0.8299 (tmm) cc_final: 0.7888 (tmm) REVERT: F 109 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7053 (mmm160) REVERT: F 127 TYR cc_start: 0.8319 (t80) cc_final: 0.7958 (t80) REVERT: F 133 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7895 (tt0) REVERT: F 162 ASP cc_start: 0.6809 (p0) cc_final: 0.6098 (t0) REVERT: G 61 TRP cc_start: 0.7669 (m100) cc_final: 0.6809 (m100) REVERT: G 87 GLN cc_start: 0.6481 (pt0) cc_final: 0.5738 (pm20) REVERT: G 114 HIS cc_start: 0.7215 (t-90) cc_final: 0.6543 (t-170) REVERT: G 129 GLU cc_start: 0.7394 (tt0) cc_final: 0.6638 (tm-30) REVERT: G 166 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6188 (tm-30) REVERT: H 12 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6262 (tp) REVERT: I 11 GLN cc_start: -0.0740 (OUTLIER) cc_final: -0.1499 (mp10) REVERT: I 16 MET cc_start: 0.1641 (OUTLIER) cc_final: 0.0677 (mmm) REVERT: I 35 MET cc_start: 0.5206 (ttt) cc_final: 0.4645 (ptp) REVERT: J 80 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.5882 (t-90) REVERT: J 129 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8307 (mm-30) REVERT: K 7 MET cc_start: 0.8809 (mtt) cc_final: 0.8497 (mtt) REVERT: K 71 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8355 (mmm160) REVERT: K 113 MET cc_start: 0.7195 (mmt) cc_final: 0.6463 (pmm) REVERT: L 79 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (tp) REVERT: L 141 LYS cc_start: 0.7704 (mttt) cc_final: 0.7390 (ptpp) REVERT: M 5 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8105 (tmtt) REVERT: M 60 GLN cc_start: 0.6441 (mm-40) cc_final: 0.5991 (mp10) REVERT: M 84 LYS cc_start: 0.8856 (mttt) cc_final: 0.8133 (mtmt) REVERT: M 95 LEU cc_start: 0.8029 (mt) cc_final: 0.7428 (pt) REVERT: N 23 ASN cc_start: 0.8114 (m-40) cc_final: 0.7873 (m-40) REVERT: N 30 ARG cc_start: 0.7397 (ttp-110) cc_final: 0.7073 (ttt90) REVERT: N 43 GLU cc_start: 0.8354 (tp30) cc_final: 0.7948 (tp30) REVERT: N 56 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6911 (mmtp) REVERT: N 57 THR cc_start: 0.6908 (m) cc_final: 0.6484 (t) REVERT: N 116 VAL cc_start: 0.8101 (t) cc_final: 0.7696 (p) REVERT: O 45 SER cc_start: 0.7773 (t) cc_final: 0.7257 (p) REVERT: O 46 GLU cc_start: 0.8322 (pt0) cc_final: 0.7581 (mt-10) REVERT: O 62 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6312 (mt) REVERT: P 65 ASN cc_start: 0.8148 (p0) cc_final: 0.7929 (p0) REVERT: P 70 GLU cc_start: 0.8325 (tt0) cc_final: 0.8125 (mt-10) REVERT: Q 48 ASP cc_start: 0.7840 (m-30) cc_final: 0.7389 (m-30) REVERT: Q 94 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7188 (mp) REVERT: R 1 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.3938 (ptt) REVERT: R 13 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7244 (ttt-90) REVERT: R 84 ARG cc_start: 0.8564 (ptt-90) cc_final: 0.8350 (ptp90) REVERT: S 12 SER cc_start: 0.8573 (t) cc_final: 0.8269 (t) REVERT: S 59 GLU cc_start: 0.8219 (pp20) cc_final: 0.7929 (pt0) REVERT: S 92 ARG cc_start: 0.7425 (ptp90) cc_final: 0.7216 (ptm-80) REVERT: T 6 ARG cc_start: 0.7502 (tpt-90) cc_final: 0.7221 (tpp80) REVERT: T 12 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7729 (mmt180) REVERT: T 32 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8316 (pp) REVERT: T 54 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6245 (pm20) REVERT: U 5 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.8049 (mtt180) REVERT: V 46 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7602 (mtpt) REVERT: V 51 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: V 57 TYR cc_start: 0.6283 (m-80) cc_final: 0.5888 (m-80) REVERT: V 68 LYS cc_start: 0.7730 (mttt) cc_final: 0.7435 (tmtt) REVERT: V 92 VAL cc_start: 0.8366 (t) cc_final: 0.8069 (m) REVERT: W 11 ASP cc_start: 0.7339 (t0) cc_final: 0.6970 (m-30) REVERT: W 31 SER cc_start: 0.9166 (t) cc_final: 0.8858 (p) REVERT: X 71 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7437 (ttm110) REVERT: Y 7 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7444 (mtm180) REVERT: Y 12 GLU cc_start: 0.6490 (tp30) cc_final: 0.6285 (tm-30) REVERT: Y 17 GLU cc_start: 0.7793 (tp30) cc_final: 0.7274 (tp30) REVERT: Z 36 GLU cc_start: 0.7535 (pt0) cc_final: 0.7232 (pt0) REVERT: Z 55 LYS cc_start: 0.7836 (mttt) cc_final: 0.7347 (mtmm) REVERT: 0 14 MET cc_start: 0.8400 (mtt) cc_final: 0.8181 (mtm) REVERT: 1 19 PHE cc_start: 0.8986 (p90) cc_final: 0.8772 (p90) REVERT: 1 46 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7494 (m) REVERT: 2 37 LYS cc_start: 0.8608 (tttt) cc_final: 0.8031 (ttpt) REVERT: 2 41 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8002 (mmm160) REVERT: 4 12 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7142 (tpm170) REVERT: 4 20 ASP cc_start: 0.8257 (t70) cc_final: 0.7767 (t0) REVERT: 5 1 MET cc_start: 0.2981 (tpt) cc_final: 0.2040 (ttm) REVERT: 5 86 MET cc_start: -0.2710 (mmm) cc_final: -0.3010 (mmm) REVERT: 6 33 ASN cc_start: 0.6981 (m-40) cc_final: 0.6683 (p0) REVERT: 6 41 HIS cc_start: 0.8111 (t-90) cc_final: 0.7413 (t-90) REVERT: b 25 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7205 (mtmt) REVERT: b 26 MET cc_start: 0.7561 (mtp) cc_final: 0.6918 (mtp) REVERT: b 67 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7213 (tt) REVERT: b 99 MET cc_start: 0.6777 (ptm) cc_final: 0.6309 (ptm) REVERT: b 136 ARG cc_start: 0.5721 (mmm-85) cc_final: 0.5366 (ttp-170) REVERT: b 207 ARG cc_start: 0.6866 (ttm170) cc_final: 0.6414 (tpt90) REVERT: c 36 PHE cc_start: 0.8341 (t80) cc_final: 0.7896 (t80) REVERT: c 37 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8045 (mtmm) REVERT: c 125 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7816 (mtm110) REVERT: c 134 LYS cc_start: 0.8389 (mttt) cc_final: 0.7857 (pttp) REVERT: c 141 MET cc_start: 0.7802 (mmm) cc_final: 0.7570 (mmm) REVERT: c 169 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6156 (tt0) REVERT: c 198 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7683 (mttm) REVERT: d 3 TYR cc_start: 0.8138 (t80) cc_final: 0.7664 (t80) REVERT: d 32 LYS cc_start: 0.7169 (mttt) cc_final: 0.6374 (tttm) REVERT: d 146 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7474 (tm-30) REVERT: d 162 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6525 (mp0) REVERT: e 11 GLN cc_start: 0.7590 (tt0) cc_final: 0.7019 (tt0) REVERT: f 9 MET cc_start: 0.7980 (mtm) cc_final: 0.7729 (mtp) REVERT: f 25 TYR cc_start: 0.6683 (m-10) cc_final: 0.6479 (m-80) REVERT: f 38 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5089 (ptp-170) REVERT: f 63 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7248 (t0) REVERT: f 90 MET cc_start: 0.6762 (mmm) cc_final: 0.6173 (mmm) REVERT: g 16 LYS cc_start: 0.7151 (mttt) cc_final: 0.6856 (mmmt) REVERT: g 78 ARG cc_start: 0.1687 (OUTLIER) cc_final: 0.0163 (tmt170) REVERT: g 91 ARG cc_start: 0.6938 (mmm160) cc_final: 0.6699 (ttp-110) REVERT: h 66 GLN cc_start: 0.6552 (mm-40) cc_final: 0.6052 (mt0) REVERT: h 87 ARG cc_start: 0.7433 (mtt180) cc_final: 0.6790 (mtp-110) REVERT: h 110 MET cc_start: 0.7855 (pmm) cc_final: 0.7483 (pmm) REVERT: i 32 ARG cc_start: 0.7104 (mmt-90) cc_final: 0.6165 (mtp180) REVERT: i 36 GLN cc_start: 0.8072 (pt0) cc_final: 0.7422 (mm-40) REVERT: i 49 GLN cc_start: 0.6802 (mt0) cc_final: 0.6424 (mt0) REVERT: i 79 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7262 (ttt90) REVERT: j 37 ARG cc_start: 0.4307 (OUTLIER) cc_final: 0.3522 (mpt90) REVERT: j 69 THR cc_start: 0.8531 (m) cc_final: 0.8117 (p) REVERT: j 88 MET cc_start: 0.5877 (mmm) cc_final: 0.4662 (mtt) REVERT: k 25 SER cc_start: 0.8780 (t) cc_final: 0.8389 (p) REVERT: k 67 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7803 (tp30) REVERT: k 115 ILE cc_start: 0.8267 (mm) cc_final: 0.7639 (tt) REVERT: l 37 TYR cc_start: 0.7807 (p90) cc_final: 0.7118 (p90) REVERT: l 38 THR cc_start: 0.7736 (p) cc_final: 0.7121 (t) REVERT: l 46 SER cc_start: 0.8110 (t) cc_final: 0.7698 (p) REVERT: l 53 ARG cc_start: 0.6110 (mmm-85) cc_final: 0.5815 (ttm110) REVERT: l 116 TYR cc_start: 0.9003 (m-80) cc_final: 0.8433 (m-80) REVERT: m 49 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8226 (tm-30) REVERT: m 109 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8526 (mtpt) REVERT: n 5 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7930 (mpp) REVERT: n 11 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8024 (ttpt) REVERT: n 25 GLU cc_start: 0.7761 (pt0) cc_final: 0.7289 (pp20) REVERT: n 62 ASN cc_start: 0.9194 (t0) cc_final: 0.8767 (t0) REVERT: o 9 LYS cc_start: 0.8608 (tptp) cc_final: 0.8016 (mttt) REVERT: p 32 PHE cc_start: 0.7876 (p90) cc_final: 0.7489 (p90) REVERT: p 35 ARG cc_start: 0.7548 (ptm-80) cc_final: 0.7270 (ptm-80) REVERT: p 56 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7688 (tpp-160) REVERT: q 29 LYS cc_start: 0.7383 (pttt) cc_final: 0.7137 (pttt) REVERT: q 59 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6653 (tt0) REVERT: r 49 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6733 (ttpt) REVERT: s 36 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7299 (ptp-170) REVERT: s 68 HIS cc_start: 0.8647 (m90) cc_final: 0.8312 (m170) REVERT: s 72 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8158 (mt-10) REVERT: t 20 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8278 (m110) REVERT: t 24 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8621 (ttp-110) REVERT: t 47 GLN cc_start: 0.8267 (mm110) cc_final: 0.7656 (mm110) REVERT: u 15 LEU cc_start: 0.7834 (tp) cc_final: 0.7479 (tp) REVERT: u 19 LYS cc_start: 0.8030 (ttpp) cc_final: 0.6912 (tptt) REVERT: u 34 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7616 (tpt90) REVERT: u 36 PHE cc_start: 0.6759 (t80) cc_final: 0.6403 (t80) REVERT: z 351 MET cc_start: 0.1671 (mmt) cc_final: 0.1301 (ptp) outliers start: 315 outliers final: 194 residues processed: 1485 average time/residue: 1.4258 time to fit residues: 3677.7565 Evaluate side-chains 1410 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1187 time to evaluate : 6.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 56 LYS Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 51 GLN Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 20 ASN Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain z residue 61 THR Chi-restraints excluded: chain z residue 67 VAL Chi-restraints excluded: chain z residue 151 MET Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 265 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 977 optimal weight: 0.5980 chunk 743 optimal weight: 20.0000 chunk 513 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 471 optimal weight: 9.9990 chunk 664 optimal weight: 20.0000 chunk 992 optimal weight: 0.9980 chunk 1050 optimal weight: 10.0000 chunk 518 optimal weight: 9.9990 chunk 940 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 overall best weight: 5.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN C 231 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 136 ASN D 150 GLN G 138 GLN I 104 GLN I 106 GLN K 13 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN N 11 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 74 GLN Q 43 GLN T 48 GLN X 15 ASN Z 19 HIS b 169 HIS ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN e 121 ASN f 14 GLN f 68 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN l 72 ASN m 7 ASN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS t 51 ASN t 54 GLN z 66 HIS z 329 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 165532 Z= 0.395 Angle : 0.838 15.370 247297 Z= 0.441 Chirality : 0.044 0.526 31428 Planarity : 0.008 0.132 13505 Dihedral : 24.273 179.942 81924 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.60 % Favored : 90.75 % Rotamer: Outliers : 7.99 % Allowed : 19.13 % Favored : 72.88 % 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: -2.21 (0.10), residues: 6219 helix: -0.07 (0.11), residues: 1901 sheet: -1.89 (0.14), residues: 1119 loop : -2.21 (0.10), residues: 3199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 212 HIS 0.012 0.002 HIS t 19 PHE 0.027 0.003 PHE Q 78 TYR 0.027 0.003 TYR h 127 ARG 0.015 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1679 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 1266 time to evaluate : 6.937 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: C 34 GLU cc_start: 0.8287 (pt0) cc_final: 0.7757 (pt0) REVERT: C 102 TYR cc_start: 0.8813 (m-80) cc_final: 0.8577 (m-80) REVERT: C 120 ASP cc_start: 0.7093 (t70) cc_final: 0.6149 (p0) REVERT: C 149 LYS cc_start: 0.6018 (tttt) cc_final: 0.5600 (tttt) REVERT: C 180 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6823 (mpt) REVERT: C 181 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6152 (ttm-80) REVERT: C 216 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6982 (mtm-85) REVERT: C 255 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8067 (mmtt) REVERT: D 74 GLU cc_start: 0.7844 (tt0) cc_final: 0.7490 (mm-30) REVERT: D 184 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7344 (mtm110) REVERT: E 24 ASN cc_start: 0.8599 (t0) cc_final: 0.7794 (t0) REVERT: E 197 GLU cc_start: 0.6228 (tt0) cc_final: 0.6009 (tt0) REVERT: F 10 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: F 14 LYS cc_start: 0.8275 (tptp) cc_final: 0.7924 (mtpt) REVERT: F 34 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.7860 (p) REVERT: F 70 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7507 (ttt-90) REVERT: F 109 ARG cc_start: 0.7482 (mtp85) cc_final: 0.7163 (mmm160) REVERT: F 162 ASP cc_start: 0.6753 (p0) cc_final: 0.6061 (t0) REVERT: F 164 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8319 (mp0) REVERT: G 41 GLU cc_start: 0.2714 (OUTLIER) cc_final: 0.2338 (mp0) REVERT: G 61 TRP cc_start: 0.7738 (m100) cc_final: 0.6792 (m100) REVERT: G 114 HIS cc_start: 0.7191 (t-90) cc_final: 0.6472 (t-170) REVERT: G 154 GLU cc_start: 0.7725 (tt0) cc_final: 0.7203 (pt0) REVERT: G 166 GLU cc_start: 0.6380 (tm-30) cc_final: 0.6109 (tm-30) REVERT: H 12 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6407 (tp) REVERT: I 11 GLN cc_start: -0.0571 (OUTLIER) cc_final: -0.1206 (mp10) REVERT: I 16 MET cc_start: 0.1236 (tmm) cc_final: 0.0475 (mmp) REVERT: I 35 MET cc_start: 0.5440 (ttt) cc_final: 0.4876 (ptp) REVERT: J 80 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6151 (t-90) REVERT: J 129 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8312 (mm-30) REVERT: J 141 ASP cc_start: 0.6658 (m-30) cc_final: 0.6397 (t70) REVERT: K 7 MET cc_start: 0.8679 (mtt) cc_final: 0.8302 (mtt) REVERT: K 100 PHE cc_start: 0.7819 (m-80) cc_final: 0.7548 (m-80) REVERT: K 113 MET cc_start: 0.7296 (mmt) cc_final: 0.6507 (pmm) REVERT: L 80 SER cc_start: 0.8343 (t) cc_final: 0.7864 (m) REVERT: L 141 LYS cc_start: 0.7958 (mttt) cc_final: 0.7634 (ptpp) REVERT: M 5 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8132 (tttm) REVERT: M 54 THR cc_start: 0.7141 (m) cc_final: 0.6918 (p) REVERT: M 60 GLN cc_start: 0.6440 (mm-40) cc_final: 0.6044 (mp10) REVERT: M 95 LEU cc_start: 0.8029 (mt) cc_final: 0.7420 (pt) REVERT: N 23 ASN cc_start: 0.8127 (m-40) cc_final: 0.7767 (m110) REVERT: N 30 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7093 (ttt180) REVERT: N 57 THR cc_start: 0.7081 (m) cc_final: 0.6693 (t) REVERT: O 45 SER cc_start: 0.7884 (t) cc_final: 0.7438 (p) REVERT: O 46 GLU cc_start: 0.8402 (pt0) cc_final: 0.7592 (mt-10) REVERT: O 85 LYS cc_start: 0.7191 (mmtm) cc_final: 0.6604 (tptt) REVERT: P 9 GLN cc_start: 0.8572 (pp30) cc_final: 0.8086 (pt0) REVERT: Q 94 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7296 (mp) REVERT: Q 96 ASP cc_start: 0.7951 (t0) cc_final: 0.7574 (t0) REVERT: Q 101 ASP cc_start: 0.7820 (m-30) cc_final: 0.7530 (m-30) REVERT: R 1 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4146 (ptt) REVERT: R 13 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7111 (ttt-90) REVERT: R 84 ARG cc_start: 0.8519 (ptt-90) cc_final: 0.8230 (ptp90) REVERT: S 59 GLU cc_start: 0.8343 (pp20) cc_final: 0.8101 (pt0) REVERT: S 92 ARG cc_start: 0.7414 (ptp90) cc_final: 0.7188 (ptm-80) REVERT: T 6 ARG cc_start: 0.7503 (tpt-90) cc_final: 0.7262 (tpp80) REVERT: T 24 MET cc_start: 0.7103 (tpp) cc_final: 0.6670 (tpp) REVERT: T 32 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8210 (pp) REVERT: T 33 LYS cc_start: 0.7596 (mtpp) cc_final: 0.7057 (ttpt) REVERT: T 79 ASP cc_start: 0.8614 (m-30) cc_final: 0.8359 (t0) REVERT: U 5 ARG cc_start: 0.8244 (ptp-170) cc_final: 0.8023 (mtt180) REVERT: U 21 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7815 (ptp-110) REVERT: U 65 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8264 (mt0) REVERT: V 46 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7453 (mtpt) REVERT: V 59 GLU cc_start: 0.5984 (pt0) cc_final: 0.5616 (pt0) REVERT: V 92 VAL cc_start: 0.8463 (t) cc_final: 0.8153 (m) REVERT: W 11 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: W 31 SER cc_start: 0.9107 (t) cc_final: 0.8833 (p) REVERT: W 66 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7537 (mm-30) REVERT: X 71 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7351 (ttm110) REVERT: Y 2 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6469 (pttm) REVERT: Y 7 ARG cc_start: 0.7944 (ttm170) cc_final: 0.7380 (mtm180) REVERT: Y 12 GLU cc_start: 0.6288 (tp30) cc_final: 0.6083 (tm-30) REVERT: Y 17 GLU cc_start: 0.8113 (tp30) cc_final: 0.7740 (tp30) REVERT: Z 36 GLU cc_start: 0.7543 (pt0) cc_final: 0.7168 (pt0) REVERT: Z 55 LYS cc_start: 0.7923 (mttt) cc_final: 0.7409 (mtmm) REVERT: 0 14 MET cc_start: 0.8625 (mtt) cc_final: 0.8377 (mtm) REVERT: 1 19 PHE cc_start: 0.8961 (p90) cc_final: 0.8738 (p90) REVERT: 2 19 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8128 (mtp85) REVERT: 2 37 LYS cc_start: 0.8566 (tttt) cc_final: 0.8078 (ttpt) REVERT: 2 41 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8172 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7152 (tpm170) REVERT: 4 20 ASP cc_start: 0.8425 (t70) cc_final: 0.8019 (t0) REVERT: 5 1 MET cc_start: 0.2838 (tpt) cc_final: 0.1800 (ttm) REVERT: 5 86 MET cc_start: -0.2749 (mmm) cc_final: -0.2988 (mmm) REVERT: 6 41 HIS cc_start: 0.8053 (t-90) cc_final: 0.7165 (t-90) REVERT: b 8 MET cc_start: 0.7283 (ppp) cc_final: 0.6680 (ppp) REVERT: b 14 HIS cc_start: 0.4747 (p-80) cc_final: 0.4281 (p-80) REVERT: b 25 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7171 (mtmt) REVERT: b 26 MET cc_start: 0.7777 (mtp) cc_final: 0.7131 (mtp) REVERT: b 136 ARG cc_start: 0.5962 (mmm-85) cc_final: 0.5499 (ttp-170) REVERT: b 207 ARG cc_start: 0.6861 (ttm170) cc_final: 0.6285 (tpt90) REVERT: c 7 ASN cc_start: 0.7951 (t0) cc_final: 0.7417 (t0) REVERT: c 19 SER cc_start: 0.8757 (m) cc_final: 0.8452 (p) REVERT: c 37 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8087 (mtmm) REVERT: c 134 LYS cc_start: 0.8374 (mttt) cc_final: 0.7771 (pttp) REVERT: d 3 TYR cc_start: 0.8090 (t80) cc_final: 0.7780 (t80) REVERT: d 32 LYS cc_start: 0.7252 (mttt) cc_final: 0.6452 (ttpp) REVERT: d 162 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6321 (mp0) REVERT: e 25 LYS cc_start: 0.8174 (tttt) cc_final: 0.7689 (ttmt) REVERT: f 17 GLN cc_start: 0.7547 (mp10) cc_final: 0.7104 (mp10) REVERT: f 38 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.5109 (ptp-170) REVERT: f 56 LYS cc_start: 0.7518 (mttp) cc_final: 0.7103 (mtmt) REVERT: f 73 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7963 (mt-10) REVERT: f 88 MET cc_start: 0.7991 (ptm) cc_final: 0.7660 (ptm) REVERT: f 90 MET cc_start: 0.6618 (mmm) cc_final: 0.6002 (mmm) REVERT: g 11 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6809 (mm) REVERT: g 14 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7078 (t0) REVERT: g 16 LYS cc_start: 0.7117 (mttt) cc_final: 0.6614 (mmmt) REVERT: g 78 ARG cc_start: 0.1950 (OUTLIER) cc_final: 0.0476 (tmt170) REVERT: g 91 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6495 (ttp-110) REVERT: g 122 GLU cc_start: 0.8291 (tp30) cc_final: 0.8090 (tp30) REVERT: h 85 TYR cc_start: 0.8574 (m-80) cc_final: 0.8307 (m-10) REVERT: h 87 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7096 (mtp-110) REVERT: i 32 ARG cc_start: 0.7187 (mmt-90) cc_final: 0.6390 (mtp180) REVERT: i 36 GLN cc_start: 0.8076 (pt0) cc_final: 0.7217 (mm-40) REVERT: i 62 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6835 (mp) REVERT: i 79 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7160 (ttt90) REVERT: i 89 TYR cc_start: 0.6458 (m-80) cc_final: 0.6003 (m-80) REVERT: i 108 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.5934 (ptm-80) REVERT: j 88 MET cc_start: 0.5668 (mmm) cc_final: 0.4737 (mtt) REVERT: j 91 ASP cc_start: 0.4357 (OUTLIER) cc_final: 0.4142 (t70) REVERT: k 25 SER cc_start: 0.8791 (t) cc_final: 0.8272 (p) REVERT: k 67 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7858 (tp30) REVERT: l 37 TYR cc_start: 0.7869 (p90) cc_final: 0.7140 (p90) REVERT: l 46 SER cc_start: 0.7892 (t) cc_final: 0.7423 (p) REVERT: l 53 ARG cc_start: 0.5950 (mmm-85) cc_final: 0.4931 (tpt90) REVERT: l 107 LYS cc_start: 0.7910 (ttpt) cc_final: 0.6937 (mmmt) REVERT: m 49 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8087 (tm-30) REVERT: m 109 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8443 (mtpt) REVERT: n 5 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: n 11 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7948 (ttpt) REVERT: n 15 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7097 (tt) REVERT: n 20 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: n 25 GLU cc_start: 0.7830 (pt0) cc_final: 0.7355 (pp20) REVERT: n 62 ASN cc_start: 0.9250 (t0) cc_final: 0.8942 (t0) REVERT: n 66 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: p 18 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: p 32 PHE cc_start: 0.7848 (p90) cc_final: 0.7627 (p90) REVERT: p 34 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8179 (pp20) REVERT: p 56 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.7503 (tpp-160) REVERT: q 6 THR cc_start: 0.9030 (p) cc_final: 0.8424 (p) REVERT: q 8 GLN cc_start: 0.7983 (tt0) cc_final: 0.7697 (tm-30) REVERT: q 29 LYS cc_start: 0.7369 (pttt) cc_final: 0.7004 (pttt) REVERT: q 59 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6583 (tt0) REVERT: r 49 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6901 (ttpt) REVERT: s 36 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7301 (ptp-170) REVERT: s 43 MET cc_start: 0.8646 (mtm) cc_final: 0.8405 (mtm) REVERT: t 20 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: t 23 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6845 (ptm-80) REVERT: t 24 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8329 (ttp-110) REVERT: t 47 GLN cc_start: 0.8306 (mm110) cc_final: 0.7771 (mm110) REVERT: t 81 GLN cc_start: 0.7153 (mm110) cc_final: 0.6914 (mm-40) REVERT: t 84 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7794 (tptt) REVERT: u 15 LEU cc_start: 0.7817 (tp) cc_final: 0.7466 (tp) REVERT: u 19 LYS cc_start: 0.7908 (ttpp) cc_final: 0.6796 (tptt) REVERT: u 30 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: z 223 ARG cc_start: 0.4593 (mmm-85) cc_final: 0.4347 (mtt180) REVERT: z 262 ARG cc_start: 0.5330 (mtm-85) cc_final: 0.4890 (mtp180) REVERT: z 349 MET cc_start: 0.1865 (mmp) cc_final: -0.0516 (pmm) REVERT: z 351 MET cc_start: 0.1891 (mmt) cc_final: 0.1232 (mtp) REVERT: z 368 MET cc_start: -0.1518 (ptt) cc_final: -0.2135 (mtt) outliers start: 413 outliers final: 282 residues processed: 1506 average time/residue: 1.3717 time to fit residues: 3554.0417 Evaluate side-chains 1488 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1172 time to evaluate : 6.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 67 THR Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 163 ILE Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 51 GLN Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 13 LYS Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 26 PHE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 84 CYS Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 66 GLN Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 20 ASN Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 30 GLU Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 8 THR Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 50 ASP Chi-restraints excluded: chain z residue 265 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 875 optimal weight: 1.9990 chunk 596 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 782 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 896 optimal weight: 0.8980 chunk 726 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 536 optimal weight: 6.9990 chunk 943 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 130 GLN G 87 GLN H 18 GLN K 13 ASN K 29 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN P 11 GLN V 24 ASN e 11 GLN f 63 ASN i 49 GLN j 64 GLN ** p 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN z 51 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 165532 Z= 0.231 Angle : 0.705 14.709 247297 Z= 0.383 Chirality : 0.037 0.601 31428 Planarity : 0.007 0.127 13505 Dihedral : 24.155 178.589 81917 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.75 % Favored : 91.57 % Rotamer: Outliers : 6.23 % Allowed : 21.82 % Favored : 71.95 % 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: -1.86 (0.10), residues: 6219 helix: 0.29 (0.12), residues: 1917 sheet: -1.73 (0.14), residues: 1165 loop : -2.03 (0.10), residues: 3137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 200 HIS 0.008 0.001 HIS s 13 PHE 0.023 0.002 PHE V 26 TYR 0.021 0.002 TYR h 127 ARG 0.011 0.001 ARG t 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1256 time to evaluate : 6.745 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: C 34 GLU cc_start: 0.8214 (pt0) cc_final: 0.7600 (pt0) REVERT: C 120 ASP cc_start: 0.7107 (t70) cc_final: 0.6115 (p0) REVERT: C 149 LYS cc_start: 0.5922 (tttt) cc_final: 0.5432 (mtpp) REVERT: C 170 TYR cc_start: 0.7444 (m-80) cc_final: 0.7046 (m-80) REVERT: C 180 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7081 (mpt) REVERT: C 216 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7795 (mtm-85) REVERT: C 255 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8012 (mmtt) REVERT: C 269 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6951 (mmp80) REVERT: D 74 GLU cc_start: 0.7604 (tt0) cc_final: 0.7372 (mm-30) REVERT: D 77 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7746 (ptm-80) REVERT: E 24 ASN cc_start: 0.8534 (t0) cc_final: 0.7771 (t0) REVERT: E 111 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7283 (tm-30) REVERT: E 197 GLU cc_start: 0.6204 (tt0) cc_final: 0.5985 (tt0) REVERT: F 14 LYS cc_start: 0.8090 (tptp) cc_final: 0.7501 (mtpt) REVERT: F 15 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7747 (tp) REVERT: F 25 MET cc_start: 0.7703 (mmm) cc_final: 0.6661 (mtp) REVERT: F 34 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7720 (p) REVERT: F 70 ARG cc_start: 0.8162 (mtt-85) cc_final: 0.7361 (ptt90) REVERT: F 95 MET cc_start: 0.8312 (tmm) cc_final: 0.7998 (tmm) REVERT: F 109 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7026 (mmm160) REVERT: F 164 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8344 (mp0) REVERT: G 61 TRP cc_start: 0.7692 (m100) cc_final: 0.6789 (m100) REVERT: G 87 GLN cc_start: 0.5929 (pt0) cc_final: 0.5405 (pm20) REVERT: G 114 HIS cc_start: 0.7138 (t-90) cc_final: 0.6480 (t-170) REVERT: G 154 GLU cc_start: 0.7694 (tt0) cc_final: 0.7198 (pt0) REVERT: G 166 GLU cc_start: 0.6459 (tm-30) cc_final: 0.6167 (tm-30) REVERT: I 11 GLN cc_start: -0.0685 (OUTLIER) cc_final: -0.1326 (mp10) REVERT: I 16 MET cc_start: 0.1050 (tmm) cc_final: -0.0006 (mmm) REVERT: I 35 MET cc_start: 0.5373 (ttt) cc_final: 0.4707 (ptp) REVERT: J 80 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6060 (t-90) REVERT: J 129 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8340 (mm-30) REVERT: J 141 ASP cc_start: 0.6589 (m-30) cc_final: 0.6366 (t70) REVERT: K 7 MET cc_start: 0.8552 (mtt) cc_final: 0.8170 (mtt) REVERT: K 62 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8885 (p) REVERT: K 100 PHE cc_start: 0.7780 (m-80) cc_final: 0.7568 (m-80) REVERT: K 105 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.7042 (mmt90) REVERT: K 113 MET cc_start: 0.7428 (mmt) cc_final: 0.6575 (pmm) REVERT: L 80 SER cc_start: 0.8361 (t) cc_final: 0.7847 (m) REVERT: L 141 LYS cc_start: 0.7898 (mttt) cc_final: 0.7600 (ptpp) REVERT: M 5 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8087 (tttm) REVERT: M 60 GLN cc_start: 0.6548 (mm-40) cc_final: 0.6146 (mp10) REVERT: M 95 LEU cc_start: 0.7970 (mt) cc_final: 0.7356 (pt) REVERT: M 118 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7239 (ttmt) REVERT: N 23 ASN cc_start: 0.8160 (m-40) cc_final: 0.7934 (m-40) REVERT: N 30 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7205 (ttt90) REVERT: N 57 THR cc_start: 0.7102 (m) cc_final: 0.6771 (t) REVERT: N 116 VAL cc_start: 0.8367 (t) cc_final: 0.8033 (p) REVERT: O 45 SER cc_start: 0.7838 (t) cc_final: 0.7409 (p) REVERT: O 46 GLU cc_start: 0.8393 (pt0) cc_final: 0.7524 (mt-10) REVERT: O 85 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6619 (tptt) REVERT: P 9 GLN cc_start: 0.8609 (pp30) cc_final: 0.8179 (pt0) REVERT: Q 48 ASP cc_start: 0.7617 (m-30) cc_final: 0.7221 (m-30) REVERT: Q 96 ASP cc_start: 0.7867 (t0) cc_final: 0.7638 (t0) REVERT: Q 101 ASP cc_start: 0.7718 (m-30) cc_final: 0.7426 (m-30) REVERT: R 1 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.4109 (ptt) REVERT: R 13 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7211 (ttt-90) REVERT: R 84 ARG cc_start: 0.8553 (ptt-90) cc_final: 0.8344 (ptp90) REVERT: R 86 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7685 (mm-40) REVERT: S 8 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7933 (mtp180) REVERT: S 59 GLU cc_start: 0.8310 (pp20) cc_final: 0.8044 (pt0) REVERT: T 6 ARG cc_start: 0.7483 (tpt-90) cc_final: 0.7203 (tpp80) REVERT: T 12 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7917 (mmt180) REVERT: T 24 MET cc_start: 0.7064 (tpp) cc_final: 0.6650 (tpp) REVERT: T 32 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8249 (pp) REVERT: T 79 ASP cc_start: 0.8678 (m-30) cc_final: 0.8454 (t0) REVERT: U 21 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7816 (ptp-110) REVERT: U 65 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8124 (mt0) REVERT: V 46 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7466 (mtpt) REVERT: V 59 GLU cc_start: 0.6336 (pt0) cc_final: 0.5894 (pt0) REVERT: V 68 LYS cc_start: 0.7806 (mttt) cc_final: 0.7454 (tmtt) REVERT: V 92 VAL cc_start: 0.8321 (t) cc_final: 0.8022 (m) REVERT: W 11 ASP cc_start: 0.7307 (t0) cc_final: 0.7086 (m-30) REVERT: W 66 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7556 (mm-30) REVERT: X 71 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7337 (ttm110) REVERT: Y 2 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6250 (pttm) REVERT: Y 6 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6413 (mt) REVERT: Y 7 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7387 (mtm180) REVERT: Y 17 GLU cc_start: 0.8008 (tp30) cc_final: 0.7693 (tp30) REVERT: Z 36 GLU cc_start: 0.7530 (pt0) cc_final: 0.7063 (pt0) REVERT: Z 55 LYS cc_start: 0.7884 (mttt) cc_final: 0.7361 (mtmm) REVERT: 0 14 MET cc_start: 0.8576 (mtt) cc_final: 0.8340 (mtm) REVERT: 1 19 PHE cc_start: 0.8962 (p90) cc_final: 0.8731 (p90) REVERT: 2 1 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6460 (ppp) REVERT: 2 37 LYS cc_start: 0.8541 (tttt) cc_final: 0.8054 (ttpt) REVERT: 2 41 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8080 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7177 (tpm170) REVERT: 4 20 ASP cc_start: 0.8364 (t70) cc_final: 0.7903 (t0) REVERT: 5 1 MET cc_start: 0.2778 (tpt) cc_final: 0.1760 (ttm) REVERT: 6 41 HIS cc_start: 0.8055 (t-90) cc_final: 0.7432 (t70) REVERT: b 8 MET cc_start: 0.7247 (ppp) cc_final: 0.6725 (ppp) REVERT: b 14 HIS cc_start: 0.4742 (p-80) cc_final: 0.4431 (p-80) REVERT: b 25 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7162 (mtmt) REVERT: b 26 MET cc_start: 0.7643 (mtp) cc_final: 0.7045 (mtp) REVERT: b 67 LEU cc_start: 0.7386 (tt) cc_final: 0.7097 (tt) REVERT: b 136 ARG cc_start: 0.5912 (mmm-85) cc_final: 0.5425 (tmm160) REVERT: b 153 MET cc_start: 0.7266 (tpp) cc_final: 0.7002 (tpp) REVERT: b 207 ARG cc_start: 0.6897 (ttm170) cc_final: 0.6238 (tpt90) REVERT: c 20 THR cc_start: 0.7083 (m) cc_final: 0.6858 (t) REVERT: c 37 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8075 (mtmm) REVERT: c 134 LYS cc_start: 0.8326 (mttt) cc_final: 0.7734 (pttp) REVERT: c 198 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7721 (mttm) REVERT: c 205 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6521 (mm-30) REVERT: d 3 TYR cc_start: 0.8045 (t80) cc_final: 0.7720 (t80) REVERT: d 32 LYS cc_start: 0.7270 (mttt) cc_final: 0.6510 (tttm) REVERT: d 110 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6116 (tpp80) REVERT: d 158 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7380 (tt) REVERT: d 162 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6304 (mp0) REVERT: e 11 GLN cc_start: 0.7770 (tt0) cc_final: 0.7467 (tt0) REVERT: e 25 LYS cc_start: 0.8351 (tttt) cc_final: 0.7830 (ttmt) REVERT: e 115 GLU cc_start: 0.8104 (tt0) cc_final: 0.7788 (pt0) REVERT: f 9 MET cc_start: 0.8165 (mtm) cc_final: 0.7920 (mtp) REVERT: f 17 GLN cc_start: 0.7622 (mp10) cc_final: 0.7229 (mp10) REVERT: f 25 TYR cc_start: 0.6759 (m-80) cc_final: 0.6338 (m-80) REVERT: f 38 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.5080 (ptp-170) REVERT: f 73 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7845 (mt-10) REVERT: f 90 MET cc_start: 0.6645 (mmm) cc_final: 0.6365 (mpp) REVERT: g 14 ASP cc_start: 0.7318 (t70) cc_final: 0.7117 (t0) REVERT: g 78 ARG cc_start: 0.1854 (OUTLIER) cc_final: 0.0352 (tmt170) REVERT: g 91 ARG cc_start: 0.6899 (mmm160) cc_final: 0.6486 (ttp-110) REVERT: g 122 GLU cc_start: 0.8292 (tp30) cc_final: 0.8045 (tp30) REVERT: h 66 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6261 (mt0) REVERT: h 87 ARG cc_start: 0.7527 (mtt180) cc_final: 0.6948 (mtp-110) REVERT: i 32 ARG cc_start: 0.7177 (mmt-90) cc_final: 0.6491 (mtp180) REVERT: i 36 GLN cc_start: 0.8129 (pt0) cc_final: 0.7276 (mm-40) REVERT: i 89 TYR cc_start: 0.6505 (m-80) cc_final: 0.6049 (m-80) REVERT: j 88 MET cc_start: 0.5399 (mmm) cc_final: 0.4444 (mtt) REVERT: k 25 SER cc_start: 0.8786 (t) cc_final: 0.8337 (p) REVERT: k 67 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7814 (tp30) REVERT: k 96 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6906 (mm) REVERT: k 125 LYS cc_start: 0.8012 (tttt) cc_final: 0.7744 (ttpp) REVERT: l 37 TYR cc_start: 0.7786 (p90) cc_final: 0.7016 (p90) REVERT: l 46 SER cc_start: 0.7830 (t) cc_final: 0.7453 (p) REVERT: l 116 TYR cc_start: 0.9019 (m-80) cc_final: 0.8636 (m-80) REVERT: m 99 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: m 109 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8502 (mtpt) REVERT: n 5 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: n 15 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6982 (tt) REVERT: n 25 GLU cc_start: 0.7775 (pt0) cc_final: 0.7355 (pp20) REVERT: n 62 ASN cc_start: 0.9219 (t0) cc_final: 0.8815 (t0) REVERT: o 88 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.4411 (pmt-80) REVERT: p 32 PHE cc_start: 0.7888 (p90) cc_final: 0.7602 (p90) REVERT: p 56 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7786 (tpp-160) REVERT: q 6 THR cc_start: 0.9091 (p) cc_final: 0.8459 (p) REVERT: q 8 GLN cc_start: 0.7972 (tt0) cc_final: 0.7665 (tm-30) REVERT: q 29 LYS cc_start: 0.7383 (pttt) cc_final: 0.7029 (pttt) REVERT: q 59 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6591 (tt0) REVERT: q 76 ARG cc_start: 0.7072 (ptt90) cc_final: 0.6689 (ptt90) REVERT: r 49 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7012 (ttpt) REVERT: s 36 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7332 (ptp-170) REVERT: s 43 MET cc_start: 0.8496 (mtm) cc_final: 0.8278 (mtm) REVERT: t 23 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.6893 (ptm160) REVERT: t 24 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8406 (ttp-110) REVERT: t 47 GLN cc_start: 0.8201 (mm110) cc_final: 0.7599 (mm110) REVERT: t 67 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.6301 (t-170) REVERT: u 15 LEU cc_start: 0.7713 (tp) cc_final: 0.7368 (tp) REVERT: u 19 LYS cc_start: 0.7697 (ttpp) cc_final: 0.6600 (tptt) REVERT: u 32 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7370 (ptm160) REVERT: u 34 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7438 (tpt90) REVERT: z 223 ARG cc_start: 0.4506 (mmm-85) cc_final: 0.4201 (mtt180) REVERT: z 262 ARG cc_start: 0.5344 (mtm-85) cc_final: 0.4833 (mtt180) REVERT: z 349 MET cc_start: 0.2251 (mmp) cc_final: -0.0352 (pmm) REVERT: z 351 MET cc_start: 0.1822 (mmt) cc_final: 0.1342 (ptp) outliers start: 322 outliers final: 218 residues processed: 1436 average time/residue: 1.3572 time to fit residues: 3371.5295 Evaluate side-chains 1430 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1181 time to evaluate : 6.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 11 GLN Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 31 GLU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 20 ASN Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 20 ASN Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain z residue 69 TYR Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 353 optimal weight: 4.9990 chunk 946 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 616 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 1051 optimal weight: 20.0000 chunk 873 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 552 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS D 130 GLN D 136 ASN F 62 GLN G 138 GLN K 13 ASN K 29 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN N 3 HIS P 114 ASN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** b 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN f 63 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN n 66 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 165532 Z= 0.327 Angle : 0.775 14.986 247297 Z= 0.412 Chirality : 0.040 0.553 31428 Planarity : 0.007 0.130 13505 Dihedral : 24.160 179.955 81908 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.22 % Favored : 90.21 % Rotamer: Outliers : 7.49 % Allowed : 21.60 % Favored : 70.91 % 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: 6219 helix: 0.17 (0.12), residues: 1918 sheet: -1.69 (0.14), residues: 1156 loop : -2.08 (0.10), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 200 HIS 0.010 0.001 HIS s 13 PHE 0.025 0.002 PHE V 26 TYR 0.039 0.002 TYR d 75 ARG 0.025 0.001 ARG d 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1218 time to evaluate : 6.942 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: C 34 GLU cc_start: 0.8121 (pt0) cc_final: 0.7406 (pt0) REVERT: C 120 ASP cc_start: 0.7219 (t70) cc_final: 0.6240 (p0) REVERT: C 149 LYS cc_start: 0.6055 (tttt) cc_final: 0.5557 (mtpp) REVERT: C 180 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6857 (mpt) REVERT: C 181 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6942 (ptm-80) REVERT: C 216 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7041 (mtm-85) REVERT: C 255 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8068 (mmtt) REVERT: C 261 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8038 (ptt-90) REVERT: D 74 GLU cc_start: 0.7600 (tt0) cc_final: 0.7312 (mm-30) REVERT: E 24 ASN cc_start: 0.8539 (t0) cc_final: 0.7653 (t0) REVERT: E 111 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7167 (tm-30) REVERT: E 197 GLU cc_start: 0.6409 (tt0) cc_final: 0.6180 (tt0) REVERT: F 14 LYS cc_start: 0.8284 (tptp) cc_final: 0.7858 (mtpt) REVERT: F 25 MET cc_start: 0.7806 (mmm) cc_final: 0.6532 (mtp) REVERT: F 34 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7709 (p) REVERT: F 70 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.7379 (ttt-90) REVERT: F 95 MET cc_start: 0.8307 (tmm) cc_final: 0.8064 (tmm) REVERT: F 109 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7185 (mmm160) REVERT: F 131 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7500 (p) REVERT: F 132 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6453 (mpp-170) REVERT: F 164 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8376 (mp0) REVERT: G 37 ASN cc_start: 0.7299 (t0) cc_final: 0.7080 (t0) REVERT: G 41 GLU cc_start: 0.2865 (OUTLIER) cc_final: 0.2582 (mp0) REVERT: G 61 TRP cc_start: 0.7567 (m100) cc_final: 0.7340 (m100) REVERT: G 87 GLN cc_start: 0.6108 (pt0) cc_final: 0.5326 (pm20) REVERT: G 114 HIS cc_start: 0.7152 (t-90) cc_final: 0.6476 (t-170) REVERT: G 138 GLN cc_start: 0.6836 (mt0) cc_final: 0.6543 (mt0) REVERT: G 166 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6258 (tm-30) REVERT: I 11 GLN cc_start: -0.0973 (OUTLIER) cc_final: -0.1483 (mp10) REVERT: I 16 MET cc_start: 0.0757 (tmm) cc_final: -0.0253 (mmm) REVERT: I 35 MET cc_start: 0.5789 (ttt) cc_final: 0.5002 (ptp) REVERT: J 80 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.6211 (t-90) REVERT: J 108 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: J 129 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8441 (mm-30) REVERT: K 7 MET cc_start: 0.8572 (mtt) cc_final: 0.8243 (mtt) REVERT: K 20 MET cc_start: 0.8581 (ttp) cc_final: 0.8213 (ttm) REVERT: K 113 MET cc_start: 0.7558 (mmt) cc_final: 0.6657 (pmm) REVERT: L 141 LYS cc_start: 0.7839 (mttt) cc_final: 0.7590 (pttm) REVERT: M 5 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7933 (tttm) REVERT: M 54 THR cc_start: 0.7121 (m) cc_final: 0.6889 (p) REVERT: M 60 GLN cc_start: 0.6486 (mm-40) cc_final: 0.6107 (mp10) REVERT: M 84 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.7843 (mtmt) REVERT: M 95 LEU cc_start: 0.8015 (mt) cc_final: 0.7325 (pt) REVERT: M 118 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7239 (ttmt) REVERT: N 23 ASN cc_start: 0.8090 (m-40) cc_final: 0.7865 (m-40) REVERT: N 30 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7177 (ttt90) REVERT: N 57 THR cc_start: 0.7158 (m) cc_final: 0.6800 (t) REVERT: O 45 SER cc_start: 0.7992 (t) cc_final: 0.7569 (p) REVERT: O 46 GLU cc_start: 0.8509 (pt0) cc_final: 0.8180 (pt0) REVERT: O 85 LYS cc_start: 0.7335 (mmtm) cc_final: 0.6775 (tptt) REVERT: O 88 LYS cc_start: 0.7234 (tppp) cc_final: 0.6933 (tppp) REVERT: P 9 GLN cc_start: 0.8594 (pp30) cc_final: 0.8169 (pt0) REVERT: Q 101 ASP cc_start: 0.7814 (m-30) cc_final: 0.7566 (m-30) REVERT: R 1 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4010 (ptt) REVERT: R 13 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7127 (ttt-90) REVERT: R 84 ARG cc_start: 0.8586 (ptt-90) cc_final: 0.8374 (ptp90) REVERT: R 86 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7664 (mm-40) REVERT: S 59 GLU cc_start: 0.8286 (pp20) cc_final: 0.7969 (pt0) REVERT: T 6 ARG cc_start: 0.7524 (tpt-90) cc_final: 0.7233 (tpp80) REVERT: T 12 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7671 (mmt180) REVERT: T 32 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8239 (pp) REVERT: T 33 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7126 (ttpt) REVERT: T 77 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7343 (mtt-85) REVERT: T 79 ASP cc_start: 0.8686 (m-30) cc_final: 0.8427 (t0) REVERT: U 5 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8145 (mtt90) REVERT: U 21 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7801 (ptp-110) REVERT: U 65 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8114 (mt0) REVERT: V 46 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7420 (mtpt) REVERT: V 59 GLU cc_start: 0.6485 (pt0) cc_final: 0.6116 (pt0) REVERT: V 68 LYS cc_start: 0.7863 (mttt) cc_final: 0.7420 (tmtt) REVERT: V 92 VAL cc_start: 0.8309 (t) cc_final: 0.8031 (m) REVERT: W 11 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: W 66 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7446 (mm-30) REVERT: X 71 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.7354 (ttm110) REVERT: Y 2 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6353 (pttm) REVERT: Y 6 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6694 (mt) REVERT: Y 7 ARG cc_start: 0.7876 (ttm170) cc_final: 0.7410 (mtm180) REVERT: Y 17 GLU cc_start: 0.8070 (tp30) cc_final: 0.7756 (tp30) REVERT: Y 54 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (mmtp) REVERT: Z 36 GLU cc_start: 0.7532 (pt0) cc_final: 0.7046 (pt0) REVERT: Z 55 LYS cc_start: 0.7902 (mttt) cc_final: 0.7383 (mtmm) REVERT: 0 14 MET cc_start: 0.8598 (mtt) cc_final: 0.8359 (mtm) REVERT: 1 19 PHE cc_start: 0.8978 (p90) cc_final: 0.8768 (p90) REVERT: 2 1 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6374 (ppp) REVERT: 2 37 LYS cc_start: 0.8556 (tttt) cc_final: 0.8053 (ttpt) REVERT: 2 41 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8159 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7207 (tpm170) REVERT: 4 20 ASP cc_start: 0.8378 (t70) cc_final: 0.7928 (t0) REVERT: 5 1 MET cc_start: 0.2336 (tpt) cc_final: 0.1504 (ttm) REVERT: 6 41 HIS cc_start: 0.7893 (t-90) cc_final: 0.7133 (t70) REVERT: b 14 HIS cc_start: 0.4888 (p-80) cc_final: 0.4562 (p-80) REVERT: b 25 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7187 (mtmt) REVERT: b 26 MET cc_start: 0.7474 (mtp) cc_final: 0.6679 (mtp) REVERT: b 29 PHE cc_start: 0.7354 (m-10) cc_final: 0.7069 (m-80) REVERT: b 136 ARG cc_start: 0.6045 (mmm-85) cc_final: 0.5590 (tmm160) REVERT: b 207 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6275 (tpt90) REVERT: c 20 THR cc_start: 0.7300 (m) cc_final: 0.7000 (t) REVERT: c 37 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8078 (mtmm) REVERT: c 134 LYS cc_start: 0.8262 (mttt) cc_final: 0.7844 (pttp) REVERT: c 198 LYS cc_start: 0.8284 (mtmt) cc_final: 0.8022 (mttp) REVERT: c 205 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6572 (mm-30) REVERT: d 3 TYR cc_start: 0.8069 (t80) cc_final: 0.7813 (t80) REVERT: d 32 LYS cc_start: 0.7207 (mttt) cc_final: 0.6404 (ttpp) REVERT: d 158 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7543 (tt) REVERT: e 11 GLN cc_start: 0.7712 (tt0) cc_final: 0.7462 (tt0) REVERT: e 25 LYS cc_start: 0.8312 (tttt) cc_final: 0.7808 (ttmt) REVERT: e 54 GLU cc_start: 0.7843 (pm20) cc_final: 0.7560 (pm20) REVERT: f 17 GLN cc_start: 0.7585 (mp10) cc_final: 0.7349 (mp10) REVERT: f 25 TYR cc_start: 0.6788 (m-80) cc_final: 0.6433 (m-80) REVERT: f 38 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.5282 (ptp-170) REVERT: f 73 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8037 (mt-10) REVERT: f 88 MET cc_start: 0.8137 (ptm) cc_final: 0.7528 (ptm) REVERT: f 90 MET cc_start: 0.6638 (mmm) cc_final: 0.6415 (mpp) REVERT: g 11 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6939 (mm) REVERT: g 14 ASP cc_start: 0.7376 (t70) cc_final: 0.7047 (t0) REVERT: g 91 ARG cc_start: 0.6600 (mmm160) cc_final: 0.6314 (ttp-110) REVERT: g 122 GLU cc_start: 0.8257 (tp30) cc_final: 0.8026 (tp30) REVERT: h 87 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7025 (mtp-110) REVERT: h 95 MET cc_start: 0.7874 (mtp) cc_final: 0.7469 (mtp) REVERT: i 13 SER cc_start: 0.9415 (t) cc_final: 0.9198 (t) REVERT: i 32 ARG cc_start: 0.7195 (mmt-90) cc_final: 0.6402 (mtp180) REVERT: i 89 TYR cc_start: 0.6646 (m-80) cc_final: 0.6158 (m-80) REVERT: i 108 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.5723 (ptm-80) REVERT: j 88 MET cc_start: 0.5354 (mmm) cc_final: 0.4696 (mtt) REVERT: j 101 SER cc_start: 0.6960 (t) cc_final: 0.6717 (p) REVERT: k 25 SER cc_start: 0.8879 (t) cc_final: 0.8379 (p) REVERT: k 67 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7847 (tp30) REVERT: k 96 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7060 (mm) REVERT: k 125 LYS cc_start: 0.8139 (tttt) cc_final: 0.7838 (ttpp) REVERT: l 37 TYR cc_start: 0.7887 (p90) cc_final: 0.7079 (p90) REVERT: l 46 SER cc_start: 0.7891 (t) cc_final: 0.7428 (p) REVERT: l 93 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8135 (ttp-110) REVERT: l 116 TYR cc_start: 0.9013 (m-80) cc_final: 0.8638 (m-80) REVERT: m 99 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: m 109 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8558 (mtpt) REVERT: n 5 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7952 (mpp) REVERT: n 15 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7083 (tt) REVERT: n 25 GLU cc_start: 0.7773 (pt0) cc_final: 0.7393 (pp20) REVERT: n 62 ASN cc_start: 0.9232 (t0) cc_final: 0.8881 (t0) REVERT: o 9 LYS cc_start: 0.8660 (tptm) cc_final: 0.8068 (mttt) REVERT: o 48 ASP cc_start: 0.8587 (t70) cc_final: 0.8354 (t70) REVERT: o 51 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8742 (p) REVERT: p 56 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7848 (tpp-160) REVERT: p 74 LEU cc_start: 0.7800 (mt) cc_final: 0.7548 (mt) REVERT: q 6 THR cc_start: 0.9042 (p) cc_final: 0.8695 (p) REVERT: q 8 GLN cc_start: 0.7961 (tt0) cc_final: 0.7733 (tt0) REVERT: q 29 LYS cc_start: 0.7374 (pttt) cc_final: 0.7004 (pttt) REVERT: q 59 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6549 (tt0) REVERT: q 76 ARG cc_start: 0.7208 (ptt90) cc_final: 0.6782 (ptt90) REVERT: r 49 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7090 (ttpt) REVERT: s 36 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7199 (ptp-170) REVERT: s 43 MET cc_start: 0.8670 (mtm) cc_final: 0.8321 (mtm) REVERT: t 20 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8326 (m-40) REVERT: t 23 ARG cc_start: 0.7475 (mmm-85) cc_final: 0.7044 (mmt-90) REVERT: t 47 GLN cc_start: 0.8214 (mm110) cc_final: 0.7689 (mm110) REVERT: t 84 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7813 (tptt) REVERT: u 19 LYS cc_start: 0.7690 (ttpp) cc_final: 0.6518 (tptt) REVERT: u 34 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7407 (tpt90) REVERT: z 262 ARG cc_start: 0.5318 (mtm-85) cc_final: 0.4716 (mtt180) REVERT: z 265 LEU cc_start: 0.2422 (OUTLIER) cc_final: 0.2123 (tp) REVERT: z 349 MET cc_start: 0.1692 (mmp) cc_final: -0.0436 (pmm) REVERT: z 351 MET cc_start: 0.2037 (mmt) cc_final: 0.1522 (ptp) REVERT: z 383 VAL cc_start: 0.1169 (t) cc_final: 0.0847 (t) outliers start: 387 outliers final: 277 residues processed: 1445 average time/residue: 1.3558 time to fit residues: 3395.8219 Evaluate side-chains 1485 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1170 time to evaluate : 6.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 54 LYS Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 40 GLU Chi-restraints excluded: chain 5 residue 67 THR Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 163 ILE Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 20 ASN Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 69 TYR Chi-restraints excluded: chain z residue 151 MET Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 265 LEU Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 1013 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 599 optimal weight: 0.0980 chunk 768 optimal weight: 10.0000 chunk 595 optimal weight: 8.9990 chunk 885 optimal weight: 5.9990 chunk 587 optimal weight: 3.9990 chunk 1047 optimal weight: 30.0000 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 9.9990 chunk 483 optimal weight: 0.0270 overall best weight: 3.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN D 130 GLN E 41 GLN K 13 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN P 11 GLN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 165532 Z= 0.215 Angle : 0.693 16.422 247297 Z= 0.376 Chirality : 0.036 0.578 31428 Planarity : 0.007 0.126 13505 Dihedral : 24.092 179.575 81904 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.80 % Favored : 91.62 % Rotamer: Outliers : 6.54 % Allowed : 23.27 % Favored : 70.19 % 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: -1.76 (0.10), residues: 6219 helix: 0.32 (0.12), residues: 1925 sheet: -1.55 (0.14), residues: 1162 loop : -1.99 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 21 HIS 0.008 0.001 HIS s 13 PHE 0.023 0.002 PHE V 26 TYR 0.033 0.002 TYR d 75 ARG 0.014 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1211 time to evaluate : 6.763 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: C 34 GLU cc_start: 0.8171 (pt0) cc_final: 0.7405 (pt0) REVERT: C 120 ASP cc_start: 0.7057 (t70) cc_final: 0.6082 (p0) REVERT: C 149 LYS cc_start: 0.5962 (tttt) cc_final: 0.5574 (mtpp) REVERT: C 170 TYR cc_start: 0.7460 (m-80) cc_final: 0.7003 (m-80) REVERT: C 180 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6949 (mpt) REVERT: C 181 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.5982 (ttm-80) REVERT: C 216 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7784 (mtm-85) REVERT: C 255 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7977 (mmtt) REVERT: C 261 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8060 (ptt-90) REVERT: C 269 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6920 (mmp80) REVERT: D 77 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7632 (ptm-80) REVERT: D 184 ARG cc_start: 0.7376 (mtm110) cc_final: 0.6788 (mtm-85) REVERT: E 24 ASN cc_start: 0.8514 (t0) cc_final: 0.7659 (t0) REVERT: E 111 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7122 (tm-30) REVERT: E 197 GLU cc_start: 0.6397 (tt0) cc_final: 0.6181 (tt0) REVERT: F 8 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7889 (ptmm) REVERT: F 25 MET cc_start: 0.7724 (mmm) cc_final: 0.6489 (mtp) REVERT: F 34 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7707 (p) REVERT: F 70 ARG cc_start: 0.8099 (ttt-90) cc_final: 0.7400 (ttt-90) REVERT: F 82 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: F 95 MET cc_start: 0.8287 (tmm) cc_final: 0.8010 (tmm) REVERT: F 109 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7241 (mmm160) REVERT: F 131 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7494 (p) REVERT: G 36 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6861 (mp) REVERT: G 41 GLU cc_start: 0.3000 (OUTLIER) cc_final: 0.2779 (mp0) REVERT: G 61 TRP cc_start: 0.7556 (m100) cc_final: 0.7344 (m100) REVERT: G 68 ARG cc_start: 0.6153 (tmt-80) cc_final: 0.5803 (ttp80) REVERT: G 87 GLN cc_start: 0.6020 (pt0) cc_final: 0.5487 (pm20) REVERT: G 114 HIS cc_start: 0.7166 (t-90) cc_final: 0.6496 (t-170) REVERT: G 154 GLU cc_start: 0.7746 (tt0) cc_final: 0.7248 (pt0) REVERT: H 12 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6416 (tp) REVERT: I 11 GLN cc_start: -0.1163 (OUTLIER) cc_final: -0.1572 (mp10) REVERT: I 16 MET cc_start: 0.0457 (tmm) cc_final: -0.0426 (mmm) REVERT: I 35 MET cc_start: 0.5845 (ttt) cc_final: 0.5175 (ptp) REVERT: J 80 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6142 (t-90) REVERT: J 129 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8425 (mm-30) REVERT: J 141 ASP cc_start: 0.6177 (m-30) cc_final: 0.5962 (t70) REVERT: K 7 MET cc_start: 0.8522 (mtt) cc_final: 0.8174 (mtt) REVERT: K 20 MET cc_start: 0.8553 (ttp) cc_final: 0.7948 (ttm) REVERT: K 113 MET cc_start: 0.7608 (mmt) cc_final: 0.6681 (pmm) REVERT: L 141 LYS cc_start: 0.7859 (mttt) cc_final: 0.7642 (pttm) REVERT: M 60 GLN cc_start: 0.6421 (mm-40) cc_final: 0.6119 (mp10) REVERT: M 95 LEU cc_start: 0.7995 (mt) cc_final: 0.7324 (pt) REVERT: M 118 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7149 (ttmt) REVERT: N 23 ASN cc_start: 0.8148 (m-40) cc_final: 0.7944 (m-40) REVERT: N 30 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7205 (ttt90) REVERT: N 57 THR cc_start: 0.7119 (m) cc_final: 0.6811 (t) REVERT: O 45 SER cc_start: 0.7730 (t) cc_final: 0.7199 (p) REVERT: O 46 GLU cc_start: 0.8465 (pt0) cc_final: 0.7680 (mt-10) REVERT: O 67 ASN cc_start: 0.7252 (p0) cc_final: 0.6938 (p0) REVERT: O 85 LYS cc_start: 0.7275 (mmtm) cc_final: 0.6720 (tptt) REVERT: P 9 GLN cc_start: 0.8633 (pp30) cc_final: 0.8213 (pt0) REVERT: Q 101 ASP cc_start: 0.7825 (m-30) cc_final: 0.7582 (m-30) REVERT: R 1 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.3993 (ptt) REVERT: R 13 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7208 (ttt180) REVERT: R 86 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7634 (mm-40) REVERT: S 59 GLU cc_start: 0.8293 (pp20) cc_final: 0.7946 (pt0) REVERT: T 6 ARG cc_start: 0.7537 (tpt-90) cc_final: 0.7270 (tpp80) REVERT: T 12 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7810 (mmt180) REVERT: T 24 MET cc_start: 0.7093 (tpp) cc_final: 0.6506 (tpp) REVERT: T 32 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8238 (pp) REVERT: U 5 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8042 (mtt90) REVERT: U 21 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7833 (ptp-110) REVERT: U 65 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8030 (mt0) REVERT: V 46 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7463 (mtpt) REVERT: V 59 GLU cc_start: 0.6593 (pt0) cc_final: 0.6291 (pt0) REVERT: V 68 LYS cc_start: 0.7834 (mttt) cc_final: 0.7407 (tmtt) REVERT: V 92 VAL cc_start: 0.8147 (t) cc_final: 0.7862 (m) REVERT: W 11 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: W 54 THR cc_start: 0.9258 (m) cc_final: 0.8743 (p) REVERT: W 66 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7415 (mm-30) REVERT: X 71 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7368 (ttm110) REVERT: Y 2 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6241 (pttm) REVERT: Y 6 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6474 (mt) REVERT: Y 7 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7367 (mtp-110) REVERT: Y 17 GLU cc_start: 0.7996 (tp30) cc_final: 0.7637 (tp30) REVERT: Z 36 GLU cc_start: 0.7440 (pt0) cc_final: 0.6912 (pt0) REVERT: Z 55 LYS cc_start: 0.7889 (mttt) cc_final: 0.7378 (mtmm) REVERT: 0 14 MET cc_start: 0.8589 (mtt) cc_final: 0.8355 (mtm) REVERT: 2 1 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6373 (ppp) REVERT: 2 37 LYS cc_start: 0.8529 (tttt) cc_final: 0.8057 (ttpt) REVERT: 2 41 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8148 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7199 (tpm170) REVERT: 4 20 ASP cc_start: 0.8386 (t70) cc_final: 0.7887 (t0) REVERT: 5 1 MET cc_start: 0.2247 (tpt) cc_final: 0.1443 (ttm) REVERT: 6 41 HIS cc_start: 0.7975 (t-90) cc_final: 0.7216 (t70) REVERT: b 8 MET cc_start: 0.6963 (ppp) cc_final: 0.6563 (ppp) REVERT: b 25 LYS cc_start: 0.7625 (mmtt) cc_final: 0.7174 (mtmt) REVERT: b 26 MET cc_start: 0.7406 (mtp) cc_final: 0.6733 (mtp) REVERT: b 62 ARG cc_start: 0.8140 (ptm-80) cc_final: 0.7642 (mmm160) REVERT: b 67 LEU cc_start: 0.7404 (tt) cc_final: 0.7115 (tt) REVERT: b 136 ARG cc_start: 0.6060 (mmm-85) cc_final: 0.5579 (tmm160) REVERT: b 207 ARG cc_start: 0.6934 (ttm170) cc_final: 0.6252 (tpt90) REVERT: c 18 ASN cc_start: 0.7202 (m-40) cc_final: 0.6634 (t0) REVERT: c 20 THR cc_start: 0.7332 (m) cc_final: 0.7054 (t) REVERT: c 37 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8059 (mtmm) REVERT: c 134 LYS cc_start: 0.8212 (mttt) cc_final: 0.7767 (pttp) REVERT: c 198 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8136 (mttp) REVERT: c 205 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6569 (tp30) REVERT: d 3 TYR cc_start: 0.8040 (t80) cc_final: 0.7777 (t80) REVERT: d 32 LYS cc_start: 0.7166 (mttt) cc_final: 0.6472 (tttm) REVERT: e 11 GLN cc_start: 0.7657 (tt0) cc_final: 0.7385 (tt0) REVERT: e 25 LYS cc_start: 0.8392 (tttt) cc_final: 0.7885 (ttmt) REVERT: e 54 GLU cc_start: 0.7799 (pm20) cc_final: 0.7531 (pm20) REVERT: f 17 GLN cc_start: 0.7541 (mp10) cc_final: 0.7224 (mp10) REVERT: f 24 ARG cc_start: 0.7120 (mtp-110) cc_final: 0.6800 (mtp-110) REVERT: f 25 TYR cc_start: 0.6747 (m-80) cc_final: 0.6451 (m-80) REVERT: f 38 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.4937 (ptp-170) REVERT: f 73 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8023 (mt-10) REVERT: f 88 MET cc_start: 0.8002 (ptm) cc_final: 0.7427 (ptm) REVERT: f 90 MET cc_start: 0.6726 (mmm) cc_final: 0.6241 (mmm) REVERT: g 11 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6809 (mm) REVERT: g 14 ASP cc_start: 0.7322 (t70) cc_final: 0.7009 (t0) REVERT: g 78 ARG cc_start: 0.1798 (OUTLIER) cc_final: 0.0515 (tmt170) REVERT: g 91 ARG cc_start: 0.6641 (mmm160) cc_final: 0.6413 (ttp-110) REVERT: g 122 GLU cc_start: 0.8284 (tp30) cc_final: 0.8068 (tp30) REVERT: h 2 MET cc_start: 0.7244 (tpp) cc_final: 0.6884 (tpp) REVERT: h 66 GLN cc_start: 0.6774 (mm-40) cc_final: 0.6327 (mt0) REVERT: h 87 ARG cc_start: 0.7470 (mtt180) cc_final: 0.6941 (mtp-110) REVERT: i 13 SER cc_start: 0.9377 (t) cc_final: 0.9115 (t) REVERT: i 32 ARG cc_start: 0.7304 (mmt-90) cc_final: 0.6537 (mtp180) REVERT: i 63 TYR cc_start: 0.6207 (t80) cc_final: 0.5999 (t80) REVERT: i 89 TYR cc_start: 0.6598 (m-80) cc_final: 0.6144 (m-80) REVERT: i 108 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.5754 (ptm-80) REVERT: j 83 THR cc_start: 0.5580 (OUTLIER) cc_final: 0.5305 (p) REVERT: j 88 MET cc_start: 0.5766 (mmm) cc_final: 0.4997 (mtt) REVERT: k 25 SER cc_start: 0.8866 (t) cc_final: 0.8389 (p) REVERT: k 67 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7833 (tp30) REVERT: k 96 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6897 (mm) REVERT: k 125 LYS cc_start: 0.8055 (tttt) cc_final: 0.7760 (ttpp) REVERT: l 37 TYR cc_start: 0.7772 (p90) cc_final: 0.6978 (p90) REVERT: l 46 SER cc_start: 0.7932 (t) cc_final: 0.7568 (p) REVERT: l 116 TYR cc_start: 0.9054 (m-80) cc_final: 0.8749 (m-80) REVERT: m 99 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: m 109 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8504 (mtpt) REVERT: n 5 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8069 (mtm) REVERT: n 15 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7099 (tt) REVERT: n 25 GLU cc_start: 0.7875 (pt0) cc_final: 0.7438 (pp20) REVERT: n 62 ASN cc_start: 0.9231 (t0) cc_final: 0.8841 (t0) REVERT: o 48 ASP cc_start: 0.8654 (t70) cc_final: 0.8449 (t70) REVERT: o 51 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8768 (p) REVERT: o 88 ARG cc_start: 0.4468 (OUTLIER) cc_final: 0.3716 (pmt-80) REVERT: p 56 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7906 (tpp-160) REVERT: q 6 THR cc_start: 0.9070 (p) cc_final: 0.8450 (p) REVERT: q 8 GLN cc_start: 0.7950 (tt0) cc_final: 0.7669 (tt0) REVERT: q 29 LYS cc_start: 0.7365 (pttt) cc_final: 0.7002 (pttt) REVERT: q 59 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6561 (tt0) REVERT: q 76 ARG cc_start: 0.7300 (ptt90) cc_final: 0.6944 (ptt90) REVERT: r 49 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7025 (ttpt) REVERT: s 43 MET cc_start: 0.8488 (mtm) cc_final: 0.8168 (ttp) REVERT: t 24 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8383 (ttp-110) REVERT: t 47 GLN cc_start: 0.8174 (mm110) cc_final: 0.7629 (mm110) REVERT: t 84 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7829 (tptt) REVERT: u 19 LYS cc_start: 0.7666 (ttpp) cc_final: 0.6495 (tptt) REVERT: u 32 ARG cc_start: 0.7548 (ptm160) cc_final: 0.6785 (ptm160) REVERT: z 262 ARG cc_start: 0.5513 (mtm-85) cc_final: 0.4878 (mtt180) REVERT: z 349 MET cc_start: 0.1715 (mmp) cc_final: -0.0363 (pmm) REVERT: z 351 MET cc_start: 0.1988 (mmt) cc_final: 0.1476 (ptp) outliers start: 338 outliers final: 242 residues processed: 1409 average time/residue: 1.3460 time to fit residues: 3274.3791 Evaluate side-chains 1447 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1169 time to evaluate : 6.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 40 GLU Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 65 ARG Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 69 TYR Chi-restraints excluded: chain z residue 151 MET Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 265 LEU Chi-restraints excluded: chain z residue 276 VAL 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: 0.0020 chunk 625 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 666 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 517 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 823 optimal weight: 3.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN E 41 GLN G 138 GLN K 13 ASN L 4 ASN L 104 GLN R 89 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN l 111 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 165532 Z= 0.354 Angle : 0.798 17.819 247297 Z= 0.421 Chirality : 0.041 0.548 31428 Planarity : 0.008 0.131 13505 Dihedral : 24.133 179.512 81900 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.99 % Favored : 89.47 % Rotamer: Outliers : 7.34 % Allowed : 22.94 % Favored : 69.73 % 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: -1.97 (0.10), residues: 6219 helix: 0.06 (0.12), residues: 1922 sheet: -1.59 (0.14), residues: 1167 loop : -2.11 (0.10), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.021 0.002 HIS t 67 PHE 0.026 0.002 PHE V 26 TYR 0.028 0.002 TYR b 212 ARG 0.016 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 1181 time to evaluate : 6.764 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: C 34 GLU cc_start: 0.8162 (pt0) cc_final: 0.7366 (pt0) REVERT: C 120 ASP cc_start: 0.7312 (t70) cc_final: 0.6315 (p0) REVERT: C 149 LYS cc_start: 0.6049 (tttt) cc_final: 0.5699 (mtpp) REVERT: C 180 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6878 (mpt) REVERT: C 181 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.5934 (ttm-80) REVERT: C 216 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7030 (mtm-85) REVERT: C 255 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8166 (mmtt) REVERT: C 261 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8041 (ptt-90) REVERT: D 77 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7493 (ptm-80) REVERT: D 184 ARG cc_start: 0.7474 (mtm110) cc_final: 0.6896 (ptp90) REVERT: E 24 ASN cc_start: 0.8555 (t0) cc_final: 0.7738 (t0) REVERT: E 111 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7206 (tm-30) REVERT: E 197 GLU cc_start: 0.6500 (tt0) cc_final: 0.6295 (tt0) REVERT: F 8 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7886 (ptmm) REVERT: F 25 MET cc_start: 0.7664 (mmm) cc_final: 0.6479 (mtp) REVERT: F 34 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7697 (p) REVERT: F 70 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7434 (ttt-90) REVERT: F 95 MET cc_start: 0.8289 (tmm) cc_final: 0.8033 (tmm) REVERT: F 131 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7552 (p) REVERT: F 132 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6449 (mpp-170) REVERT: F 143 ASP cc_start: 0.8008 (m-30) cc_final: 0.6661 (p0) REVERT: G 36 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7034 (mp) REVERT: G 41 GLU cc_start: 0.3089 (OUTLIER) cc_final: 0.2788 (mp0) REVERT: G 87 GLN cc_start: 0.6212 (pt0) cc_final: 0.5573 (pm20) REVERT: G 114 HIS cc_start: 0.7224 (t-90) cc_final: 0.6440 (t-170) REVERT: G 154 GLU cc_start: 0.7717 (tt0) cc_final: 0.7169 (pt0) REVERT: H 12 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6500 (tp) REVERT: I 11 GLN cc_start: -0.1335 (OUTLIER) cc_final: -0.1760 (mt0) REVERT: I 16 MET cc_start: 0.0261 (tmm) cc_final: -0.0575 (mmm) REVERT: I 35 MET cc_start: 0.5722 (ttt) cc_final: 0.5422 (pmm) REVERT: J 80 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6217 (t-90) REVERT: J 86 GLN cc_start: 0.8350 (pt0) cc_final: 0.8092 (pt0) REVERT: J 108 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8013 (mmt) REVERT: J 129 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8638 (mm-30) REVERT: J 141 ASP cc_start: 0.6397 (m-30) cc_final: 0.5587 (t70) REVERT: K 7 MET cc_start: 0.8524 (mtt) cc_final: 0.8190 (mtt) REVERT: K 20 MET cc_start: 0.8561 (ttp) cc_final: 0.8214 (ttm) REVERT: L 141 LYS cc_start: 0.7918 (mttt) cc_final: 0.7712 (ptpp) REVERT: M 5 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7928 (tttm) REVERT: M 60 GLN cc_start: 0.6439 (mm-40) cc_final: 0.6113 (mp10) REVERT: M 84 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: M 95 LEU cc_start: 0.8090 (mt) cc_final: 0.7417 (pt) REVERT: M 118 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7228 (ttmt) REVERT: N 23 ASN cc_start: 0.8035 (m-40) cc_final: 0.7770 (m-40) REVERT: N 30 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7132 (ttt90) REVERT: N 57 THR cc_start: 0.7192 (m) cc_final: 0.6841 (t) REVERT: O 45 SER cc_start: 0.7905 (t) cc_final: 0.7497 (p) REVERT: O 46 GLU cc_start: 0.8433 (pt0) cc_final: 0.8197 (pt0) REVERT: P 9 GLN cc_start: 0.8612 (pp30) cc_final: 0.8162 (pt0) REVERT: Q 101 ASP cc_start: 0.7632 (m-30) cc_final: 0.7422 (m-30) REVERT: R 1 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.4081 (ptt) REVERT: R 13 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7389 (ttt-90) REVERT: R 86 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7648 (mm-40) REVERT: S 59 GLU cc_start: 0.8305 (pp20) cc_final: 0.8049 (pt0) REVERT: T 6 ARG cc_start: 0.7573 (tpt-90) cc_final: 0.7294 (tpp80) REVERT: T 12 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7735 (mmt180) REVERT: T 32 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8225 (pp) REVERT: T 33 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7136 (ttpt) REVERT: T 77 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7381 (mtt-85) REVERT: T 79 ASP cc_start: 0.8673 (m-30) cc_final: 0.8399 (t0) REVERT: U 5 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8056 (mtt90) REVERT: U 20 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7419 (mtpt) REVERT: U 21 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7777 (ptp-110) REVERT: U 65 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8302 (mt0) REVERT: V 46 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7491 (mtpt) REVERT: V 59 GLU cc_start: 0.6588 (pt0) cc_final: 0.6278 (pt0) REVERT: V 68 LYS cc_start: 0.7806 (mttt) cc_final: 0.7353 (tmtt) REVERT: V 92 VAL cc_start: 0.8171 (t) cc_final: 0.7878 (m) REVERT: W 11 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: W 54 THR cc_start: 0.9342 (m) cc_final: 0.8871 (p) REVERT: W 66 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7396 (mm-30) REVERT: X 44 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7737 (ptm-80) REVERT: X 71 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7394 (ttm110) REVERT: Y 6 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6689 (mt) REVERT: Y 7 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7383 (ttp-110) REVERT: Z 36 GLU cc_start: 0.7477 (pt0) cc_final: 0.6947 (pt0) REVERT: Z 55 LYS cc_start: 0.7914 (mttt) cc_final: 0.7391 (mtmm) REVERT: 0 14 MET cc_start: 0.8581 (mtt) cc_final: 0.8354 (mtm) REVERT: 2 1 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6360 (ppp) REVERT: 2 37 LYS cc_start: 0.8578 (tttt) cc_final: 0.8041 (ttpt) REVERT: 2 41 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8168 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7245 (tpm170) REVERT: 4 20 ASP cc_start: 0.8379 (t70) cc_final: 0.7945 (t0) REVERT: 5 1 MET cc_start: 0.2295 (tpt) cc_final: 0.1640 (ttm) REVERT: 6 41 HIS cc_start: 0.7891 (t-90) cc_final: 0.6990 (t-90) REVERT: b 25 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7211 (mtmt) REVERT: b 26 MET cc_start: 0.7614 (mtp) cc_final: 0.6925 (mtp) REVERT: b 62 ARG cc_start: 0.8151 (ptm-80) cc_final: 0.7698 (mmm160) REVERT: b 88 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7281 (mm-40) REVERT: b 136 ARG cc_start: 0.6078 (mmm-85) cc_final: 0.5625 (ttp-170) REVERT: b 207 ARG cc_start: 0.6914 (ttm170) cc_final: 0.6267 (tpt90) REVERT: c 18 ASN cc_start: 0.7234 (m-40) cc_final: 0.6725 (t0) REVERT: c 20 THR cc_start: 0.7384 (m) cc_final: 0.7161 (t) REVERT: c 37 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8084 (mtmm) REVERT: c 134 LYS cc_start: 0.8182 (mttt) cc_final: 0.7829 (pttp) REVERT: c 198 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8202 (mttp) REVERT: c 205 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6881 (tp30) REVERT: d 3 TYR cc_start: 0.8031 (t80) cc_final: 0.7792 (t80) REVERT: d 32 LYS cc_start: 0.7226 (mttt) cc_final: 0.6437 (ttpp) REVERT: e 25 LYS cc_start: 0.8285 (tttt) cc_final: 0.7792 (ttmt) REVERT: e 54 GLU cc_start: 0.7840 (pm20) cc_final: 0.7575 (pm20) REVERT: e 77 ASN cc_start: 0.8063 (m-40) cc_final: 0.7805 (m110) REVERT: f 17 GLN cc_start: 0.7534 (mp10) cc_final: 0.7205 (mp10) REVERT: f 25 TYR cc_start: 0.6922 (m-80) cc_final: 0.6676 (m-80) REVERT: f 38 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.4918 (ptp-170) REVERT: f 73 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8051 (mt-10) REVERT: f 88 MET cc_start: 0.8089 (ptm) cc_final: 0.7617 (ptm) REVERT: f 90 MET cc_start: 0.6691 (mmm) cc_final: 0.6400 (tpp) REVERT: g 11 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7068 (mm) REVERT: g 14 ASP cc_start: 0.7409 (t70) cc_final: 0.7053 (t0) REVERT: g 91 ARG cc_start: 0.6490 (mmm160) cc_final: 0.6273 (ttp-110) REVERT: g 122 GLU cc_start: 0.8236 (tp30) cc_final: 0.8011 (tp30) REVERT: h 87 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7014 (mtp-110) REVERT: i 13 SER cc_start: 0.9470 (t) cc_final: 0.9166 (t) REVERT: i 32 ARG cc_start: 0.7250 (mmt-90) cc_final: 0.6527 (mtp180) REVERT: i 89 TYR cc_start: 0.6795 (m-80) cc_final: 0.6315 (m-80) REVERT: i 106 ASP cc_start: 0.7985 (t0) cc_final: 0.7460 (t0) REVERT: i 108 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.5464 (ptm-80) REVERT: j 83 THR cc_start: 0.5540 (OUTLIER) cc_final: 0.5211 (p) REVERT: j 88 MET cc_start: 0.5689 (mmm) cc_final: 0.4994 (mtt) REVERT: k 25 SER cc_start: 0.8930 (t) cc_final: 0.8417 (p) REVERT: k 67 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7766 (tp30) REVERT: k 96 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6997 (mm) REVERT: k 115 ILE cc_start: 0.7902 (tp) cc_final: 0.7391 (pt) REVERT: l 37 TYR cc_start: 0.7831 (p90) cc_final: 0.7094 (p90) REVERT: l 46 SER cc_start: 0.7898 (t) cc_final: 0.7428 (p) REVERT: l 53 ARG cc_start: 0.6246 (mmm-85) cc_final: 0.5109 (tpt90) REVERT: l 93 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8213 (ttp-110) REVERT: l 116 TYR cc_start: 0.9009 (m-80) cc_final: 0.8597 (m-80) REVERT: l 120 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6946 (tmt170) REVERT: m 99 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: m 109 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8519 (mtpt) REVERT: n 5 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7995 (mtm) REVERT: n 15 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7196 (tt) REVERT: n 25 GLU cc_start: 0.7905 (pt0) cc_final: 0.7455 (pp20) REVERT: n 62 ASN cc_start: 0.9226 (t0) cc_final: 0.8878 (t0) REVERT: o 88 ARG cc_start: 0.4639 (OUTLIER) cc_final: 0.3946 (pmt-80) REVERT: p 56 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7749 (tpp-160) REVERT: q 6 THR cc_start: 0.9037 (p) cc_final: 0.8683 (p) REVERT: q 8 GLN cc_start: 0.8042 (tt0) cc_final: 0.7759 (tt0) REVERT: q 29 LYS cc_start: 0.7398 (pttt) cc_final: 0.7021 (pttt) REVERT: q 59 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6539 (tt0) REVERT: q 61 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7565 (ttp-110) REVERT: q 76 ARG cc_start: 0.7322 (ptt90) cc_final: 0.6924 (ptt90) REVERT: r 49 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7124 (ttpt) REVERT: s 43 MET cc_start: 0.8630 (mtm) cc_final: 0.8362 (ttp) REVERT: t 20 ASN cc_start: 0.8728 (m-40) cc_final: 0.8413 (m-40) REVERT: t 47 GLN cc_start: 0.8202 (mm110) cc_final: 0.7727 (mm110) REVERT: t 67 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5863 (t70) REVERT: t 84 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7850 (tptt) REVERT: u 19 LYS cc_start: 0.7757 (ttpp) cc_final: 0.6552 (tptt) REVERT: u 32 ARG cc_start: 0.7689 (ptm160) cc_final: 0.7115 (ptm160) REVERT: u 34 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7565 (tpt90) REVERT: z 262 ARG cc_start: 0.5389 (mtm-85) cc_final: 0.4735 (mtt180) REVERT: z 278 LEU cc_start: 0.3533 (mm) cc_final: 0.3289 (mt) REVERT: z 349 MET cc_start: 0.1726 (mmp) cc_final: -0.0629 (pmm) REVERT: z 351 MET cc_start: 0.1754 (mmt) cc_final: 0.1120 (ptp) outliers start: 379 outliers final: 297 residues processed: 1411 average time/residue: 1.4649 time to fit residues: 3604.2834 Evaluate side-chains 1479 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1143 time to evaluate : 6.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 44 ARG Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 92 ASP Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 26 PHE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 50 ASP Chi-restraints excluded: chain z residue 69 TYR Chi-restraints excluded: chain z residue 151 MET Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 265 LEU Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 953 optimal weight: 8.9990 chunk 1003 optimal weight: 2.9990 chunk 915 optimal weight: 8.9990 chunk 976 optimal weight: 8.9990 chunk 587 optimal weight: 2.9990 chunk 425 optimal weight: 7.9990 chunk 766 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 882 optimal weight: 20.0000 chunk 923 optimal weight: 6.9990 chunk 972 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN G 138 GLN K 13 ASN K 29 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN X 15 ASN 3 42 HIS ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 11 GLN e 121 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN j 35 GLN t 67 HIS t 81 GLN z 251 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 165532 Z= 0.347 Angle : 0.783 17.459 247297 Z= 0.415 Chirality : 0.041 0.540 31428 Planarity : 0.007 0.130 13505 Dihedral : 24.174 179.515 81896 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.55 % Favored : 89.90 % Rotamer: Outliers : 7.20 % Allowed : 23.48 % Favored : 69.32 % 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: -2.04 (0.10), residues: 6219 helix: -0.00 (0.12), residues: 1911 sheet: -1.66 (0.14), residues: 1167 loop : -2.11 (0.10), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 212 HIS 0.022 0.002 HIS e 120 PHE 0.026 0.002 PHE V 26 TYR 0.031 0.002 TYR d 75 ARG 0.018 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1182 time to evaluate : 6.883 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: C 120 ASP cc_start: 0.7319 (t70) cc_final: 0.6317 (p0) REVERT: C 145 MET cc_start: 0.7391 (tpp) cc_final: 0.7104 (tpp) REVERT: C 149 LYS cc_start: 0.6092 (tttt) cc_final: 0.5765 (mtpp) REVERT: C 180 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6867 (mpt) REVERT: C 181 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.5930 (ttm-80) REVERT: C 216 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: C 255 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8150 (mmtt) REVERT: C 261 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8062 (ptt-90) REVERT: D 77 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7468 (ptm-80) REVERT: D 184 ARG cc_start: 0.7546 (mtm110) cc_final: 0.6985 (ptp90) REVERT: E 24 ASN cc_start: 0.8544 (t0) cc_final: 0.7586 (t0) REVERT: E 111 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 197 GLU cc_start: 0.6521 (tt0) cc_final: 0.6320 (tt0) REVERT: F 25 MET cc_start: 0.7684 (mmm) cc_final: 0.6454 (mtp) REVERT: F 34 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.7642 (p) REVERT: F 70 ARG cc_start: 0.8136 (ttt-90) cc_final: 0.7478 (ttt-90) REVERT: F 95 MET cc_start: 0.8266 (tmm) cc_final: 0.8009 (tmm) REVERT: F 131 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7570 (p) REVERT: F 132 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6508 (mpp-170) REVERT: F 143 ASP cc_start: 0.7912 (m-30) cc_final: 0.6599 (p0) REVERT: F 162 ASP cc_start: 0.6579 (p0) cc_final: 0.5838 (t0) REVERT: G 36 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6939 (mp) REVERT: G 41 GLU cc_start: 0.2965 (OUTLIER) cc_final: 0.2694 (mp0) REVERT: G 87 GLN cc_start: 0.6132 (pt0) cc_final: 0.5556 (pm20) REVERT: G 154 GLU cc_start: 0.7765 (tt0) cc_final: 0.7212 (pt0) REVERT: H 12 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6485 (tp) REVERT: I 11 GLN cc_start: -0.1530 (OUTLIER) cc_final: -0.1872 (mt0) REVERT: J 80 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6313 (t-90) REVERT: J 108 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7918 (mmt) REVERT: J 129 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8630 (mm-30) REVERT: K 7 MET cc_start: 0.8526 (mtt) cc_final: 0.8193 (mtt) REVERT: K 20 MET cc_start: 0.8548 (ttp) cc_final: 0.8203 (ttm) REVERT: L 141 LYS cc_start: 0.7958 (mttt) cc_final: 0.7635 (ptpp) REVERT: M 60 GLN cc_start: 0.6408 (mm-40) cc_final: 0.6093 (mp10) REVERT: M 84 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: M 95 LEU cc_start: 0.8060 (mt) cc_final: 0.7385 (pt) REVERT: M 118 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7238 (ttmt) REVERT: N 11 ASN cc_start: 0.8525 (m110) cc_final: 0.8186 (m-40) REVERT: N 23 ASN cc_start: 0.8158 (m-40) cc_final: 0.7863 (m-40) REVERT: N 30 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7212 (ttt90) REVERT: N 57 THR cc_start: 0.7208 (m) cc_final: 0.6867 (t) REVERT: O 45 SER cc_start: 0.7892 (t) cc_final: 0.7470 (p) REVERT: O 46 GLU cc_start: 0.8463 (pt0) cc_final: 0.8228 (pt0) REVERT: P 9 GLN cc_start: 0.8598 (pp30) cc_final: 0.8241 (pt0) REVERT: R 13 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7476 (ttt180) REVERT: R 86 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7668 (mm-40) REVERT: S 59 GLU cc_start: 0.8316 (pp20) cc_final: 0.8025 (pt0) REVERT: T 6 ARG cc_start: 0.7579 (tpt-90) cc_final: 0.7304 (tpp80) REVERT: T 12 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7632 (mmt180) REVERT: T 24 MET cc_start: 0.7132 (tpp) cc_final: 0.6633 (tpp) REVERT: T 32 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8263 (pp) REVERT: T 33 LYS cc_start: 0.7619 (mtpp) cc_final: 0.7125 (ttpt) REVERT: T 77 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.7322 (mtt-85) REVERT: T 79 ASP cc_start: 0.8683 (m-30) cc_final: 0.8412 (t0) REVERT: U 5 ARG cc_start: 0.8548 (mtt180) cc_final: 0.8093 (mtt90) REVERT: U 65 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8270 (mt0) REVERT: V 46 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7510 (mtpt) REVERT: V 59 GLU cc_start: 0.6603 (pt0) cc_final: 0.6285 (pt0) REVERT: V 68 LYS cc_start: 0.7785 (mttt) cc_final: 0.7276 (tmtt) REVERT: V 71 LYS cc_start: 0.6737 (mtpp) cc_final: 0.6401 (mtpp) REVERT: V 92 VAL cc_start: 0.8297 (t) cc_final: 0.7987 (m) REVERT: W 11 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: W 54 THR cc_start: 0.9357 (m) cc_final: 0.8866 (p) REVERT: W 66 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7393 (mm-30) REVERT: X 44 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7813 (ptm-80) REVERT: X 71 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7430 (ttm110) REVERT: Y 7 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7372 (ttp-110) REVERT: Z 36 GLU cc_start: 0.7631 (pt0) cc_final: 0.7035 (pt0) REVERT: Z 55 LYS cc_start: 0.7913 (mttt) cc_final: 0.7406 (mtmm) REVERT: 0 14 MET cc_start: 0.8603 (mtt) cc_final: 0.8366 (mtm) REVERT: 2 1 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6372 (ppp) REVERT: 2 37 LYS cc_start: 0.8528 (tttt) cc_final: 0.8082 (ttpp) REVERT: 2 41 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8172 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7307 (tpm170) REVERT: 4 20 ASP cc_start: 0.8384 (t70) cc_final: 0.7949 (t0) REVERT: 5 1 MET cc_start: 0.2272 (tpt) cc_final: 0.1621 (ttm) REVERT: 6 41 HIS cc_start: 0.7936 (t-90) cc_final: 0.7146 (t70) REVERT: b 25 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7220 (mtmt) REVERT: b 26 MET cc_start: 0.7501 (mtp) cc_final: 0.6854 (mtp) REVERT: b 62 ARG cc_start: 0.8143 (ptm-80) cc_final: 0.7704 (mmm160) REVERT: b 88 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7298 (mm-40) REVERT: b 136 ARG cc_start: 0.6216 (mmm-85) cc_final: 0.5636 (ttp-170) REVERT: b 140 LEU cc_start: 0.7129 (tt) cc_final: 0.6575 (mt) REVERT: b 207 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6312 (tpt90) REVERT: c 37 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8120 (mtmm) REVERT: c 134 LYS cc_start: 0.8192 (mttt) cc_final: 0.7828 (pttp) REVERT: c 198 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8231 (mttp) REVERT: c 205 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6950 (mm-30) REVERT: d 32 LYS cc_start: 0.7221 (mttt) cc_final: 0.6467 (ttpp) REVERT: d 116 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7678 (tp) REVERT: d 163 GLN cc_start: 0.7135 (mt0) cc_final: 0.6724 (tm-30) REVERT: e 11 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: e 25 LYS cc_start: 0.8415 (tttt) cc_final: 0.7854 (ttmt) REVERT: e 54 GLU cc_start: 0.7805 (pm20) cc_final: 0.7557 (pm20) REVERT: e 77 ASN cc_start: 0.8051 (m-40) cc_final: 0.7814 (m110) REVERT: f 25 TYR cc_start: 0.6927 (m-80) cc_final: 0.6626 (m-80) REVERT: f 38 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.4907 (ptp-170) REVERT: f 88 MET cc_start: 0.8082 (ptm) cc_final: 0.7458 (ptm) REVERT: f 90 MET cc_start: 0.6715 (mmm) cc_final: 0.6412 (tpp) REVERT: g 14 ASP cc_start: 0.7384 (t70) cc_final: 0.7072 (t0) REVERT: g 91 ARG cc_start: 0.6501 (mmm160) cc_final: 0.6283 (ttp-110) REVERT: g 122 GLU cc_start: 0.8209 (tp30) cc_final: 0.7999 (tp30) REVERT: h 87 ARG cc_start: 0.7460 (mtt180) cc_final: 0.6977 (mtp-110) REVERT: i 13 SER cc_start: 0.9449 (t) cc_final: 0.9116 (t) REVERT: i 32 ARG cc_start: 0.7241 (mmt-90) cc_final: 0.6475 (mtp180) REVERT: i 89 TYR cc_start: 0.6928 (m-80) cc_final: 0.6475 (m-80) REVERT: i 106 ASP cc_start: 0.8007 (t0) cc_final: 0.7501 (t0) REVERT: i 108 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.5391 (ptm-80) REVERT: j 83 THR cc_start: 0.5563 (OUTLIER) cc_final: 0.5263 (p) REVERT: j 88 MET cc_start: 0.5660 (mmm) cc_final: 0.5027 (mtt) REVERT: k 25 SER cc_start: 0.8953 (t) cc_final: 0.8470 (p) REVERT: k 67 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7781 (tp30) REVERT: k 96 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7049 (mm) REVERT: l 37 TYR cc_start: 0.7734 (p90) cc_final: 0.6969 (p90) REVERT: l 46 SER cc_start: 0.7842 (t) cc_final: 0.7415 (p) REVERT: l 93 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8233 (ttp-110) REVERT: l 111 GLN cc_start: 0.7193 (mt0) cc_final: 0.6428 (mt0) REVERT: l 116 TYR cc_start: 0.9106 (m-80) cc_final: 0.8750 (m-80) REVERT: l 120 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6940 (tmt170) REVERT: m 99 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: m 109 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8509 (mtpt) REVERT: n 5 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: n 15 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7253 (tt) REVERT: n 25 GLU cc_start: 0.7761 (pt0) cc_final: 0.7352 (pp20) REVERT: n 51 LEU cc_start: 0.8299 (mt) cc_final: 0.7194 (pp) REVERT: n 62 ASN cc_start: 0.9225 (t0) cc_final: 0.8876 (t0) REVERT: o 9 LYS cc_start: 0.8498 (tptp) cc_final: 0.7915 (mttt) REVERT: o 88 ARG cc_start: 0.4529 (OUTLIER) cc_final: 0.3848 (pmt-80) REVERT: p 56 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7846 (tpp-160) REVERT: q 6 THR cc_start: 0.9038 (p) cc_final: 0.8278 (p) REVERT: q 8 GLN cc_start: 0.8057 (tt0) cc_final: 0.7696 (tt0) REVERT: q 29 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7019 (pttt) REVERT: q 59 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6614 (tt0) REVERT: q 61 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7534 (ttp-110) REVERT: q 76 ARG cc_start: 0.7335 (ptt90) cc_final: 0.6977 (ptt90) REVERT: r 49 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7080 (ttpt) REVERT: s 43 MET cc_start: 0.8539 (mtm) cc_final: 0.8270 (ttp) REVERT: t 20 ASN cc_start: 0.8612 (m-40) cc_final: 0.8257 (m-40) REVERT: t 47 GLN cc_start: 0.8248 (mm110) cc_final: 0.7841 (mm110) REVERT: t 67 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6722 (t-170) REVERT: t 84 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7818 (tptt) REVERT: u 19 LYS cc_start: 0.7674 (ttpp) cc_final: 0.6458 (tptt) REVERT: u 28 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.5187 (tp) REVERT: u 32 ARG cc_start: 0.7722 (ptm160) cc_final: 0.6923 (ptm160) REVERT: u 34 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7521 (tpt90) REVERT: z 262 ARG cc_start: 0.5157 (mtm-85) cc_final: 0.4542 (mtp180) REVERT: z 349 MET cc_start: 0.1706 (mmp) cc_final: -0.0798 (pmm) REVERT: z 351 MET cc_start: 0.1848 (mmt) cc_final: 0.1608 (mmm) outliers start: 372 outliers final: 298 residues processed: 1407 average time/residue: 1.3477 time to fit residues: 3281.1999 Evaluate side-chains 1498 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1160 time to evaluate : 6.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 44 ARG Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 26 PHE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 29 LYS Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 50 ASP Chi-restraints excluded: chain z residue 69 TYR Chi-restraints excluded: chain z residue 151 MET Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 265 LEU Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 641 optimal weight: 3.9990 chunk 1032 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 489 optimal weight: 0.5980 chunk 717 optimal weight: 10.0000 chunk 1082 optimal weight: 8.9990 chunk 996 optimal weight: 2.9990 chunk 862 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN K 13 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN 6 20 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 165532 Z= 0.295 Angle : 0.750 17.782 247297 Z= 0.400 Chirality : 0.039 0.558 31428 Planarity : 0.007 0.128 13505 Dihedral : 24.162 179.881 81896 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.62 % Favored : 89.80 % Rotamer: Outliers : 6.52 % Allowed : 24.29 % Favored : 69.18 % 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: -1.97 (0.10), residues: 6219 helix: 0.05 (0.12), residues: 1911 sheet: -1.60 (0.15), residues: 1162 loop : -2.08 (0.10), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 21 HIS 0.023 0.001 HIS t 67 PHE 0.024 0.002 PHE V 26 TYR 0.030 0.002 TYR b 212 ARG 0.017 0.001 ARG C 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1182 time to evaluate : 6.897 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: C 120 ASP cc_start: 0.7293 (t70) cc_final: 0.6330 (p0) REVERT: C 145 MET cc_start: 0.7270 (tpp) cc_final: 0.7015 (tpp) REVERT: C 149 LYS cc_start: 0.6090 (tttt) cc_final: 0.5766 (mtpp) REVERT: C 180 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6956 (mpt) REVERT: C 181 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.5996 (ttm-80) REVERT: C 216 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7103 (mtm-85) REVERT: C 255 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8124 (mmtt) REVERT: C 261 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8058 (ptt-90) REVERT: D 77 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7480 (ptm-80) REVERT: E 24 ASN cc_start: 0.8537 (t0) cc_final: 0.7638 (t0) REVERT: E 111 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7279 (tm-30) REVERT: E 143 LEU cc_start: 0.7882 (tp) cc_final: 0.7608 (tp) REVERT: E 197 GLU cc_start: 0.6489 (tt0) cc_final: 0.6284 (tt0) REVERT: F 25 MET cc_start: 0.7643 (mmm) cc_final: 0.6408 (mtp) REVERT: F 34 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7691 (p) REVERT: F 70 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7479 (ttt-90) REVERT: F 95 MET cc_start: 0.8231 (tmm) cc_final: 0.7959 (tmm) REVERT: F 131 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7560 (p) REVERT: F 132 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6473 (mpp-170) REVERT: F 133 GLU cc_start: 0.8445 (tt0) cc_final: 0.8025 (tt0) REVERT: F 162 ASP cc_start: 0.6546 (p0) cc_final: 0.5901 (t0) REVERT: G 36 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7100 (mp) REVERT: G 41 GLU cc_start: 0.3018 (OUTLIER) cc_final: 0.2773 (mp0) REVERT: G 68 ARG cc_start: 0.6210 (tmt-80) cc_final: 0.5852 (ttp80) REVERT: G 87 GLN cc_start: 0.6115 (pt0) cc_final: 0.5550 (pm20) REVERT: G 154 GLU cc_start: 0.7740 (tt0) cc_final: 0.7201 (pt0) REVERT: H 12 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6478 (tp) REVERT: I 11 GLN cc_start: -0.1564 (OUTLIER) cc_final: -0.1905 (mp10) REVERT: I 16 MET cc_start: -0.0144 (tmm) cc_final: -0.0909 (mmm) REVERT: J 80 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6295 (t-90) REVERT: J 108 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8003 (mmt) REVERT: J 129 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8623 (mm-30) REVERT: K 7 MET cc_start: 0.8574 (mtt) cc_final: 0.8262 (mtt) REVERT: K 20 MET cc_start: 0.8569 (ttp) cc_final: 0.7981 (ttm) REVERT: L 141 LYS cc_start: 0.7863 (mttt) cc_final: 0.7560 (ptpp) REVERT: M 60 GLN cc_start: 0.6375 (mm-40) cc_final: 0.6079 (mp10) REVERT: M 84 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: M 95 LEU cc_start: 0.8019 (mt) cc_final: 0.7327 (pt) REVERT: M 118 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7235 (ttmt) REVERT: N 23 ASN cc_start: 0.8063 (m-40) cc_final: 0.7833 (m-40) REVERT: N 30 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7222 (ttt90) REVERT: N 57 THR cc_start: 0.7196 (m) cc_final: 0.6868 (t) REVERT: O 45 SER cc_start: 0.7868 (t) cc_final: 0.7461 (p) REVERT: O 46 GLU cc_start: 0.8381 (pt0) cc_final: 0.8168 (pt0) REVERT: P 9 GLN cc_start: 0.8616 (pp30) cc_final: 0.8300 (pt0) REVERT: P 88 ARG cc_start: 0.6449 (mtp180) cc_final: 0.5854 (mtt-85) REVERT: R 13 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7451 (ttt-90) REVERT: R 86 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7637 (mm-40) REVERT: S 59 GLU cc_start: 0.8355 (pp20) cc_final: 0.8102 (pt0) REVERT: S 108 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7245 (p) REVERT: T 6 ARG cc_start: 0.7585 (tpt-90) cc_final: 0.7317 (tpp80) REVERT: T 12 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7766 (mmt180) REVERT: T 24 MET cc_start: 0.7154 (tpp) cc_final: 0.6635 (tpp) REVERT: T 32 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8238 (pp) REVERT: T 33 LYS cc_start: 0.7574 (mtpp) cc_final: 0.7105 (ttpt) REVERT: U 5 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8108 (mtt90) REVERT: U 65 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8002 (mt0) REVERT: V 46 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7562 (mtpt) REVERT: V 59 GLU cc_start: 0.6570 (pt0) cc_final: 0.6254 (pt0) REVERT: V 68 LYS cc_start: 0.7715 (mttt) cc_final: 0.7350 (tmtt) REVERT: V 71 LYS cc_start: 0.6799 (mtpp) cc_final: 0.6472 (mtpp) REVERT: V 92 VAL cc_start: 0.8281 (t) cc_final: 0.7969 (m) REVERT: W 11 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: W 54 THR cc_start: 0.9393 (m) cc_final: 0.8915 (p) REVERT: W 66 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7398 (mm-30) REVERT: X 44 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7795 (ptm-80) REVERT: X 71 ARG cc_start: 0.7983 (tpp-160) cc_final: 0.7364 (ttm110) REVERT: Y 7 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7378 (mtm110) REVERT: Z 55 LYS cc_start: 0.7954 (mttt) cc_final: 0.7433 (mtmm) REVERT: 0 14 MET cc_start: 0.8600 (mtt) cc_final: 0.8361 (mtm) REVERT: 2 1 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6392 (ppp) REVERT: 2 37 LYS cc_start: 0.8551 (tttt) cc_final: 0.8085 (ttpp) REVERT: 2 41 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8176 (mtp-110) REVERT: 4 12 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7259 (tpm170) REVERT: 4 20 ASP cc_start: 0.8365 (t70) cc_final: 0.7934 (t0) REVERT: 5 1 MET cc_start: 0.2115 (tpt) cc_final: 0.1518 (ttm) REVERT: 6 41 HIS cc_start: 0.8058 (t-90) cc_final: 0.7429 (t70) REVERT: b 25 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7236 (mtmt) REVERT: b 26 MET cc_start: 0.7649 (mtp) cc_final: 0.6978 (mtp) REVERT: b 62 ARG cc_start: 0.8137 (ptm-80) cc_final: 0.7708 (mmm160) REVERT: b 88 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7346 (mm-40) REVERT: b 136 ARG cc_start: 0.6376 (mmm-85) cc_final: 0.5784 (ttp-170) REVERT: b 207 ARG cc_start: 0.6867 (ttm170) cc_final: 0.6300 (tpt90) REVERT: c 37 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8097 (mtmm) REVERT: c 134 LYS cc_start: 0.8198 (mttt) cc_final: 0.7826 (pttp) REVERT: c 198 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8233 (mttp) REVERT: c 205 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6830 (tp30) REVERT: d 32 LYS cc_start: 0.7117 (mttt) cc_final: 0.6391 (ttpp) REVERT: d 116 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7624 (tp) REVERT: d 146 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: d 163 GLN cc_start: 0.7137 (mt0) cc_final: 0.6708 (tm-30) REVERT: e 11 GLN cc_start: 0.7720 (tt0) cc_final: 0.7381 (tt0) REVERT: e 25 LYS cc_start: 0.8396 (tttt) cc_final: 0.7840 (ttmt) REVERT: e 54 GLU cc_start: 0.7774 (pm20) cc_final: 0.7552 (pm20) REVERT: e 77 ASN cc_start: 0.8023 (m-40) cc_final: 0.7784 (m110) REVERT: f 17 GLN cc_start: 0.7413 (mp10) cc_final: 0.7132 (mp10) REVERT: f 25 TYR cc_start: 0.6933 (m-80) cc_final: 0.6682 (m-80) REVERT: f 38 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.4796 (ptp-170) REVERT: f 88 MET cc_start: 0.8102 (ptm) cc_final: 0.7437 (ptm) REVERT: f 90 MET cc_start: 0.6672 (mmm) cc_final: 0.6218 (mmm) REVERT: g 14 ASP cc_start: 0.7348 (t70) cc_final: 0.7014 (t0) REVERT: g 91 ARG cc_start: 0.6512 (mmm160) cc_final: 0.6290 (ttp-110) REVERT: h 87 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6934 (mtp-110) REVERT: i 13 SER cc_start: 0.9345 (t) cc_final: 0.8993 (t) REVERT: i 32 ARG cc_start: 0.7165 (mmt-90) cc_final: 0.6453 (mtp180) REVERT: i 89 TYR cc_start: 0.6918 (m-80) cc_final: 0.6546 (m-80) REVERT: i 106 ASP cc_start: 0.7988 (t0) cc_final: 0.7529 (t0) REVERT: i 108 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.5418 (ptm-80) REVERT: j 83 THR cc_start: 0.5388 (OUTLIER) cc_final: 0.5107 (p) REVERT: j 88 MET cc_start: 0.5590 (mmm) cc_final: 0.5026 (mtt) REVERT: k 25 SER cc_start: 0.8917 (t) cc_final: 0.8430 (p) REVERT: k 67 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7780 (tp30) REVERT: l 37 TYR cc_start: 0.7707 (p90) cc_final: 0.6998 (p90) REVERT: l 46 SER cc_start: 0.7828 (t) cc_final: 0.7394 (p) REVERT: l 53 ARG cc_start: 0.6244 (mmm-85) cc_final: 0.5139 (tpt90) REVERT: l 87 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6862 (tppt) REVERT: l 93 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (ttp-110) REVERT: l 111 GLN cc_start: 0.7293 (mt0) cc_final: 0.6530 (mt0) REVERT: l 116 TYR cc_start: 0.9104 (m-80) cc_final: 0.8777 (m-80) REVERT: l 120 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6929 (tmt170) REVERT: m 99 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: m 109 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8535 (mtpt) REVERT: n 5 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: n 15 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7323 (tt) REVERT: n 25 GLU cc_start: 0.7817 (pt0) cc_final: 0.7394 (pp20) REVERT: n 51 LEU cc_start: 0.8299 (mt) cc_final: 0.7250 (pp) REVERT: n 62 ASN cc_start: 0.9254 (t0) cc_final: 0.8905 (t0) REVERT: o 9 LYS cc_start: 0.8486 (tptp) cc_final: 0.7943 (mttt) REVERT: o 58 MET cc_start: 0.8342 (mtm) cc_final: 0.7569 (mtm) REVERT: o 88 ARG cc_start: 0.4675 (OUTLIER) cc_final: 0.3962 (pmt-80) REVERT: p 56 ARG cc_start: 0.8131 (tpp-160) cc_final: 0.7889 (tpp-160) REVERT: q 6 THR cc_start: 0.9038 (p) cc_final: 0.8708 (p) REVERT: q 8 GLN cc_start: 0.7952 (tt0) cc_final: 0.7631 (tt0) REVERT: q 29 LYS cc_start: 0.7373 (pttt) cc_final: 0.7007 (pttt) REVERT: q 59 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6590 (tt0) REVERT: q 61 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7450 (ttp-110) REVERT: q 76 ARG cc_start: 0.7335 (ptt90) cc_final: 0.6993 (ptt90) REVERT: r 49 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7073 (ttpt) REVERT: s 43 MET cc_start: 0.8505 (mtm) cc_final: 0.8237 (ttp) REVERT: s 72 GLU cc_start: 0.8688 (tp30) cc_final: 0.8372 (tp30) REVERT: t 20 ASN cc_start: 0.8624 (m-40) cc_final: 0.8171 (m-40) REVERT: t 23 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7067 (mmt-90) REVERT: t 47 GLN cc_start: 0.8237 (mm110) cc_final: 0.7830 (mm110) REVERT: t 84 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7806 (tptt) REVERT: u 19 LYS cc_start: 0.7698 (ttpp) cc_final: 0.6512 (tptt) REVERT: u 28 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5191 (tp) REVERT: u 32 ARG cc_start: 0.7573 (ptm160) cc_final: 0.6943 (ptm160) REVERT: u 34 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7480 (tpt90) REVERT: z 262 ARG cc_start: 0.5261 (mtm-85) cc_final: 0.4622 (mtt180) REVERT: z 263 LYS cc_start: 0.2441 (mtmm) cc_final: 0.2211 (mtpt) REVERT: z 349 MET cc_start: 0.1316 (mmp) cc_final: -0.1304 (pmm) REVERT: z 351 MET cc_start: 0.1638 (mmt) cc_final: 0.1415 (mmm) outliers start: 337 outliers final: 278 residues processed: 1386 average time/residue: 1.3686 time to fit residues: 3278.5972 Evaluate side-chains 1474 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1157 time to evaluate : 6.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 2 ASN Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 12 ARG Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 44 ARG Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 37 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 118 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 181 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 48 SER Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 87 GLU Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 146 GLU Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 21 SER Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 38 ARG Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 108 ARG Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 26 PHE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain n residue 5 MET Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 3 LYS Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 63 CYS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 49 LYS Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 32 THR Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 30 PHE Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain z residue 12 VAL Chi-restraints excluded: chain z residue 16 THR Chi-restraints excluded: chain z residue 50 ASP Chi-restraints excluded: chain z residue 69 TYR Chi-restraints excluded: chain z residue 115 THR Chi-restraints excluded: chain z residue 151 MET Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 265 LEU Chi-restraints excluded: chain z residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 684 optimal weight: 10.0000 chunk 918 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 795 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 863 optimal weight: 3.9990 chunk 361 optimal weight: 9.9990 chunk 886 optimal weight: 5.9990 chunk 109 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 47 ASN G 138 GLN K 13 ASN L 4 ASN ** L 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN V 24 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 GLN t 67 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108681 restraints weight = 371101.111| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.49 r_work: 0.3342 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 165532 Z= 0.460 Angle : 0.881 18.954 247297 Z= 0.458 Chirality : 0.045 0.484 31428 Planarity : 0.008 0.134 13505 Dihedral : 24.272 179.401 81896 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.34 % Favored : 88.08 % Rotamer: Outliers : 7.32 % Allowed : 23.69 % Favored : 68.99 % 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: -2.31 (0.10), residues: 6219 helix: -0.35 (0.11), residues: 1911 sheet: -1.74 (0.15), residues: 1158 loop : -2.22 (0.10), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP z 184 HIS 0.011 0.002 HIS G 44 PHE 0.029 0.003 PHE 6 60 TYR 0.038 0.003 TYR h 127 ARG 0.019 0.001 ARG C 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49355.79 seconds wall clock time: 858 minutes 6.30 seconds (51486.30 seconds total)