Starting phenix.real_space_refine on Sun Mar 3 01:52:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wdt_8813/03_2024/5wdt_8813_updated.pdb" } resolution = 3.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 5 8.98 5 P 4805 5.49 5 Mg 1904 5.21 5 S 171 5.16 5 C 76935 2.51 5 N 28328 2.21 5 O 43127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "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 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ASP 162": "OD1" <-> "OD2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" 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 GLU 76": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 6": "NH1" <-> "NH2" 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 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 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 ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P GLU 8": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 11": "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 GLU 52": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "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 "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 ASP 193": "OD1" <-> "OD2" 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 "d GLU 77": "OE1" <-> "OE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "g ARG 2": "NH1" <-> "NH2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" 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 "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "k ARG 12": "NH1" <-> "NH2" Residue "k PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 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 ARG 71": "NH1" <-> "NH2" 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 17": "OE1" <-> "OE2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "q GLU 51": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "r ARG 11": "NH1" <-> "NH2" Residue "r PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 15": "OE1" <-> "OE2" 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 33": "NH1" <-> "NH2" 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 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 123": "NH1" <-> "NH2" Residue "z ASP 142": "OD1" <-> "OD2" 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 GLU 267": "OE1" <-> "OE2" Residue "z ARG 269": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z GLU 285": "OE1" <-> "OE2" Residue "z ARG 288": "NH1" <-> "NH2" Residue "z 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: 155275 Number of models: 1 Model: "" Number of chains: 125 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': 253, 'rna2p_pyr': 120, 'rna3p': 17, 'rna3p_pur': 1414, 'rna3p_pyr': 1088} Link IDs: {'rna2p': 380, 'rna3p': 2519} 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': 7, 'rna2p_pyr': 6, 'rna3p_pur': 58, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1557 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1544 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1120 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "S" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 739 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "W" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 33050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 1, 'rna2p_pur': 116, 'rna2p_pyr': 68, 'rna3p': 10, 'rna3p_pur': 753, 'rna3p_pyr': 592} Link IDs: {'rna2p': 185, 'rna3p': 1354} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 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: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1631 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 20 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: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 1340 Unusual residues: {' K': 5, ' MG': 1325} Classifications: {'peptide': 1, 'undetermined': 1330} Link IDs: {None: 1330} 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Unusual residues: {' MG': 36} Classifications: {'undetermined': 36} Link IDs: {None: 35} Chain: "C" 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: "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: "L" 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" 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: "T" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" 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: "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: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 481 Unusual residues: {' MG': 481} Classifications: {'undetermined': 481} Link IDs: {None: 480} 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: "h" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "t" 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: "v" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "z" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Unusual residues: {' MG': 4, 'GNP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Chain: "A" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 653 Classifications: {'water': 653} Link IDs: {None: 652} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 62.66, per 1000 atoms: 0.40 Number of scatterers: 155275 At special positions: 0 Unit cell: (278.32, 269.5, 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 5 19.00 S 171 16.00 P 4805 15.00 Mg 1904 11.99 O 43127 8.00 N 28328 7.00 C 76935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.60 Conformation dependent library (CDL) restraints added in 7.4 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: 195 helices and 74 sheets defined 38.3% alpha, 19.0% beta 1387 base pairs and 2405 stacking pairs defined. Time for finding SS restraints: 83.33 Creating SS restraints... Processing helix chain 'C' and resid 9 through 15 removed outlier: 7.803A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.667A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.057A 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: 3.958A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.694A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.093A 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: 6.225A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.699A 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: 4.046A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.277A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.683A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.169A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.587A 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: 3.596A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.758A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.452A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 4.109A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.649A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.736A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.531A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 4.872A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.611A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.018A 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: 4.718A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.544A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.777A 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: 4.054A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.280A 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: 3.545A pdb=" N LYS G 5 " --> pdb=" O SER G 1 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix No H-bonds generated for 'chain 'G' and resid 1 through 7' Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.279A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.622A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 4.451A 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: 3.687A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.767A 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: 5.340A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.307A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.783A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.983A 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: 5.212A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.558A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.550A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.768A 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: 3.742A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.746A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.582A 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: 4.228A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.073A 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: 3.836A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.468A 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: 5.753A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.630A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.617A 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: 3.974A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.856A 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: 3.875A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.991A 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: 5.736A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.540A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.624A pdb=" N ARG M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.779A 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 removed outlier: 3.503A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 4.581A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.643A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 5.565A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.579A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 89 removed outlier: 3.767A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.371A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.566A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.525A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.662A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 3.560A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.605A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.035A 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 'P' and resid 104 through 109 removed outlier: 5.904A pdb=" N ILE P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.673A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.627A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.594A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.022A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.857A 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: 4.112A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.820A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.575A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.007A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 6.837A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.512A 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: 3.744A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.866A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.011A 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: 3.520A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.024A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.537A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.679A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.811A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 8 removed outlier: 3.809A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.822A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 4.481A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.514A pdb=" N LEU Z 23 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 4.988A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.262A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.514A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.536A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.728A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.140A 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: 4.829A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 3.505A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.533A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY 5 45 " --> pdb=" O LEU 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 70 removed outlier: 4.150A 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: 4.394A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.664A 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: 3.749A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.590A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 53 removed outlier: 4.288A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.192A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.304A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.562A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.609A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.807A 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: 3.506A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.572A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.854A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.718A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.994A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.617A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.141A pdb=" N ASP c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.780A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.917A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.070A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.516A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.531A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.761A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.715A 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: 4.208A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 3.569A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.955A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.147A 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: 4.476A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.514A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.311A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.502A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 31 removed outlier: 3.701A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.552A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.560A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 6.093A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.516A pdb=" N SER g 40 " --> pdb=" O SER g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 4.224A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.022A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.955A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.718A 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: 3.617A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 removed outlier: 4.251A pdb=" N GLY i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 53 removed outlier: 4.651A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.682A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.987A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 98 removed outlier: 4.148A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.623A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.776A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.707A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.287A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.759A 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: 3.706A pdb=" N ALA k 65 " --> pdb=" O ALA k 61 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.734A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN k 100 " --> pdb=" O ILE k 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.048A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.785A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 removed outlier: 3.608A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.203A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.476A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 23 removed outlier: 3.500A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.651A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.152A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.760A 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: 3.645A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 31 removed outlier: 4.251A pdb=" N ILE n 29 " --> pdb=" O ALA n 24 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.013A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.409A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.042A 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 GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.504A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.742A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP p 60 " --> pdb=" O ARG p 56 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.735A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.463A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.358A 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 removed outlier: 3.541A pdb=" N SER s 24 " --> pdb=" O LYS s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.378A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.310A 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 7 through 39 removed outlier: 3.566A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 5.026A 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: 3.720A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 85 removed outlier: 4.206A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.787A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 61 Proline residue: u 40 - end of helix removed outlier: 3.553A pdb=" N LYS u 45 " --> pdb=" O THR u 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 32 removed outlier: 4.281A pdb=" N ARG u 32 " --> pdb=" O VAL u 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 27 through 32' Processing helix chain 'z' and resid 24 through 39 removed outlier: 3.674A pdb=" N THR z 28 " --> pdb=" O LYS z 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS z 37 " --> pdb=" O THR z 33 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR z 38 " --> pdb=" O VAL z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 45 through 51 removed outlier: 4.121A pdb=" N ILE z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP z 50 " --> pdb=" O PHE z 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN z 51 " --> pdb=" O ASP 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 57 removed outlier: 4.093A pdb=" N LYS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA z 57 " --> pdb=" O PRO z 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 52 through 57' Processing helix chain 'z' and resid 87 through 99 removed outlier: 3.791A pdb=" N THR z 93 " --> pdb=" O LYS z 89 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASP z 99 " --> pdb=" O ALA z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 112 through 126 removed outlier: 3.860A pdb=" N ARG z 116 " --> pdb=" O MET z 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN z 124 " --> pdb=" O LEU z 120 " (cutoff:3.500A) Processing helix chain 'z' and resid 136 through 141 removed outlier: 6.312A pdb=" N VAL z 140 " --> pdb=" O LYS z 136 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP z 141 " --> pdb=" O CYS z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 136 through 141' Processing helix chain 'z' and resid 142 through 161 removed outlier: 4.277A pdb=" N LEU z 146 " --> pdb=" O ASP z 142 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU z 147 " --> pdb=" O GLU z 143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL z 149 " --> pdb=" O LEU z 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU z 150 " --> pdb=" O LEU z 146 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET z 151 " --> pdb=" O GLU z 147 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU z 152 " --> pdb=" O LEU z 148 " (cutoff:3.500A) Processing helix chain 'z' and resid 173 through 180 removed outlier: 3.583A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU z 179 " --> pdb=" O LEU z 175 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY z 180 " --> pdb=" O LYS z 176 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 198 removed outlier: 3.541A pdb=" N ILE z 188 " --> pdb=" O TRP z 184 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU z 191 " --> pdb=" O LYS z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 282 through 287 removed outlier: 3.682A pdb=" N ILE z 286 " --> pdb=" O LYS z 282 " (cutoff:3.500A) removed outlier: 5.106A 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 1 through 4 Processing sheet with id= 2, first strand: chain 'C' and resid 72 through 77 removed outlier: 4.148A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.636A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.733A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.468A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.906A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.839A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.084A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.586A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.516A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 12, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 13, first strand: chain 'G' and resid 93 through 97 Processing sheet with id= 14, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.915A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LYS G 85 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 16 through 20 removed outlier: 5.563A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.323A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.229A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 6 through 9 removed outlier: 4.090A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 37 through 41 removed outlier: 4.303A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.362A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.687A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.931A 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: 7.181A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.569A 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 36 removed outlier: 5.990A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.087A 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: 3.501A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.465A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER P 84 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.748A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR P 75 " --> pdb=" O SER P 56 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.685A 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: 6.723A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.216A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.799A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.521A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.892A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.179A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS T 70 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 41 through 44 Processing sheet with id= 35, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.554A 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: 6.346A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'W' and resid 25 through 28 removed outlier: 4.530A pdb=" N GLU W 25 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 6.273A 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: 6.978A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.039A 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: 3.682A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.299A 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: 4.242A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.714A 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: 6.420A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 5.507A 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 Processing sheet with id= 44, first strand: chain '3' and resid 21 through 24 removed outlier: 5.694A 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: 8.499A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (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 20 through 25 removed outlier: 4.621A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER 6 15 " --> pdb=" O LEU 6 32 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 6 34 " --> pdb=" O SER 6 15 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.685A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN b 41 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 4.664A 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: 3.929A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.696A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.997A 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 170 removed outlier: 3.712A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.534A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 11 through 15 removed outlier: 3.971A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.869A 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: 7.547A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY e 86 " --> pdb=" O VAL e 93 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL e 122 " --> pdb=" O GLY e 103 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.663A 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 43 removed outlier: 3.749A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 44 through 47 removed outlier: 6.305A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.284A 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: 6.174A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 4.655A 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: 6.703A 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: 4.594A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.852A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 4.177A 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 removed outlier: 4.519A pdb=" N ASN k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.032A 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: 4.935A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.279A 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: 5.968A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN p 40 " --> pdb=" O GLY p 49 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 6 through 10 removed outlier: 7.374A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 's' and resid 29 through 33 removed outlier: 4.194A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN s 55 " --> pdb=" O ASN s 52 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'z' and resid 64 through 70 removed outlier: 3.536A pdb=" N SER z 65 " --> pdb=" O ASP z 80 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR z 69 " --> pdb=" O TYR z 76 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS z 81 " --> pdb=" O THR z 16 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY z 18 " --> pdb=" O CYS z 81 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY z 15 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL z 105 " --> pdb=" O PHE z 133 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN z 135 " --> pdb=" O VAL z 105 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 210 through 214 removed outlier: 6.666A pdb=" N PHE z 210 " --> pdb=" O LYS z 294 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN z 290 " --> pdb=" O ILE z 214 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'z' and resid 216 through 220 removed outlier: 3.867A pdb=" N ASP z 216 " --> pdb=" O THR z 228 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 234 through 237 removed outlier: 7.302A pdb=" N GLY z 234 " --> pdb=" O ALA z 270 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'z' and resid 336 through 340 removed outlier: 3.730A pdb=" N GLY z 339 " --> pdb=" O PRO z 328 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU z 372 " --> pdb=" O VAL z 387 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL z 387 " --> pdb=" O LEU z 372 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE z 374 " --> pdb=" O ALA z 385 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA z 385 " --> pdb=" O PHE z 374 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE z 376 " --> pdb=" O VAL z 383 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG z 381 " --> pdb=" O GLU z 378 " (cutoff:3.500A) 1780 hydrogen bonds defined for protein. 5240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3440 hydrogen bonds 5536 hydrogen bond angles 0 basepair planarities 1387 basepair parallelities 2405 stacking parallelities Total time for adding SS restraints: 433.86 Time building geometry restraints manager: 69.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 62089 1.40 - 1.62: 103036 1.62 - 1.84: 352 1.84 - 2.06: 0 2.06 - 2.28: 1 Bond restraints: 165478 Sorted by residual: bond pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " ideal model delta sigma weight residual 1.607 2.280 -0.673 1.50e-02 4.44e+03 2.01e+03 bond pdb=" O4' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.412 1.663 -0.251 1.50e-02 4.44e+03 2.80e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.484 0.318 2.00e-02 2.50e+03 2.53e+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 165473 not shown) Histogram of bond angle deviations from ideal: 62.92 - 83.68: 3 83.68 - 104.44: 20235 104.44 - 125.21: 207793 125.21 - 145.97: 19173 145.97 - 166.73: 2 Bond angle restraints: 247206 Sorted by residual: angle pdb=" O3' C w 17 " pdb=" P U w 117 " pdb=" O5' U w 117 " ideal model delta sigma weight residual 104.00 148.04 -44.04 1.50e+00 4.44e-01 8.62e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP1 A A2031 " ideal model delta sigma weight residual 108.00 166.73 -58.73 3.00e+00 1.11e-01 3.83e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP2 A A2031 " ideal model delta sigma weight residual 108.00 62.92 45.08 3.00e+00 1.11e-01 2.26e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" O5' A A2031 " ideal model delta sigma weight residual 104.00 81.98 22.02 1.50e+00 4.44e-01 2.15e+02 angle pdb=" C3' 6MZ A1618 " pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " ideal model delta sigma weight residual 120.20 142.10 -21.90 1.50e+00 4.44e-01 2.13e+02 ... (remaining 247201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 92332 35.82 - 71.64: 11927 71.64 - 107.46: 1454 107.46 - 143.27: 46 143.27 - 179.09: 43 Dihedral angle restraints: 105802 sinusoidal: 87801 harmonic: 18001 Sorted by residual: 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 70.00 77.00 1 8.00e+00 1.56e-02 1.16e+02 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 70.25 76.75 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C5' U w 27 " pdb=" C4' U w 27 " pdb=" C3' U w 27 " pdb=" O3' U w 27 " ideal model delta sinusoidal sigma weight residual 147.00 74.06 72.94 1 8.00e+00 1.56e-02 1.06e+02 ... (remaining 105799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 26597 0.158 - 0.315: 4769 0.315 - 0.473: 25 0.473 - 0.631: 12 0.631 - 0.788: 11 Chirality restraints: 31414 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 -1.96 -0.79 2.00e-01 2.50e+01 1.55e+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 -2.02 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C3' G A 859 " pdb=" C4' G A 859 " pdb=" O3' G A 859 " pdb=" C2' G A 859 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 31411 not shown) Planarity restraints: 13504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2069 " 0.037 2.00e-02 2.50e+03 6.24e-01 8.77e+03 pdb=" C4' 7MG A2069 " 0.450 2.00e-02 2.50e+03 pdb=" O4' 7MG A2069 " 0.728 2.00e-02 2.50e+03 pdb=" C3' 7MG A2069 " -0.622 2.00e-02 2.50e+03 pdb=" O3' 7MG A2069 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 7MG A2069 " -0.170 2.00e-02 2.50e+03 pdb=" O2' 7MG A2069 " 0.973 2.00e-02 2.50e+03 pdb=" C1' 7MG A2069 " 0.223 2.00e-02 2.50e+03 pdb=" N9 7MG A2069 " -0.974 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.038 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' 5MC a1407 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.661 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.655 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.153 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.992 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.225 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " -0.020 2.00e-02 2.50e+03 6.09e-01 8.34e+03 pdb=" C4' 2MG A2445 " -0.466 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.794 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.592 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.867 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.221 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.967 2.00e-02 2.50e+03 ... (remaining 13501 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.25: 331 2.25 - 2.97: 64183 2.97 - 3.69: 321451 3.69 - 4.42: 542585 4.42 - 5.14: 752947 Nonbonded interactions: 1681497 Sorted by model distance: nonbonded pdb=" O6 G B 21 " pdb=" N3 C B 62 " model vdw 1.527 2.496 nonbonded pdb=" N1 A A1021 " pdb=" O4 U A1141 " model vdw 1.536 2.496 nonbonded pdb=" O6 G A 283 " pdb=" O6 G A 356 " model vdw 1.569 3.040 nonbonded pdb=" O2 U A2489 " pdb=" O4 U A2491 " model vdw 1.616 3.040 nonbonded pdb=" N1 G A1867 " pdb=" N3 C A1874 " model vdw 1.677 2.600 ... (remaining 1681492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'v' and (resid 0 through 76 or resid 101)) selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 18.220 Check model and map are aligned: 1.790 Set scattering table: 1.050 Process input model: 751.830 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.460 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 792.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.673 165478 Z= 0.501 Angle : 1.132 58.733 247206 Z= 0.743 Chirality : 0.098 0.788 31414 Planarity : 0.024 0.624 13504 Dihedral : 24.242 179.093 94196 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 2.25 % Allowed : 9.68 % Favored : 88.07 % Rotamer: Outliers : 3.29 % Allowed : 6.85 % Favored : 89.86 % Cbeta Deviations : 0.03 % 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: -4.08 (0.08), residues: 6219 helix: -2.60 (0.09), residues: 1774 sheet: -2.92 (0.13), residues: 965 loop : -2.75 (0.09), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 212 HIS 0.010 0.001 HIS S 9 PHE 0.018 0.002 PHE M 31 TYR 0.021 0.002 TYR Q 31 ARG 0.024 0.001 ARG d 153 *********************** 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 1998 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1828 time to evaluate : 6.588 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: C 3 VAL cc_start: 0.8326 (t) cc_final: 0.8011 (p) REVERT: C 25 LYS cc_start: 0.6816 (mttt) cc_final: 0.6546 (mptp) REVERT: C 27 LYS cc_start: 0.7534 (mttt) cc_final: 0.6876 (mmtm) REVERT: C 104 LEU cc_start: 0.8974 (mt) cc_final: 0.8676 (mt) REVERT: C 110 LYS cc_start: 0.7903 (mttt) cc_final: 0.7515 (mtpp) REVERT: C 113 ASP cc_start: 0.6791 (m-30) cc_final: 0.6363 (m-30) REVERT: C 114 GLN cc_start: 0.7022 (tt0) cc_final: 0.6733 (mt0) REVERT: C 235 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6692 (mt-10) REVERT: C 241 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (ptpt) REVERT: C 249 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7653 (p) REVERT: C 269 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7317 (mtp-110) REVERT: D 81 GLU cc_start: 0.7416 (tt0) cc_final: 0.7135 (mt-10) REVERT: D 105 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7407 (mmpt) REVERT: D 168 GLU cc_start: 0.7586 (tt0) cc_final: 0.7355 (tt0) REVERT: D 183 GLU cc_start: 0.7801 (tt0) cc_final: 0.7398 (pt0) REVERT: D 200 ASP cc_start: 0.7678 (m-30) cc_final: 0.7247 (p0) REVERT: E 117 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7531 (mpp80) REVERT: E 197 GLU cc_start: 0.6914 (tp30) cc_final: 0.6690 (tp30) REVERT: F 47 LYS cc_start: 0.7390 (ptmt) cc_final: 0.6936 (mmmt) REVERT: F 67 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8150 (p) REVERT: F 79 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7154 (mtp-110) REVERT: F 101 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7903 (ttp80) REVERT: F 104 THR cc_start: 0.7820 (m) cc_final: 0.7528 (t) REVERT: F 126 ASN cc_start: 0.8365 (m-40) cc_final: 0.7946 (m-40) REVERT: F 166 ARG cc_start: 0.6862 (ttm110) cc_final: 0.6270 (ttp-110) REVERT: G 11 PRO cc_start: 0.6569 (Cg_exo) cc_final: 0.6309 (Cg_endo) REVERT: G 36 LEU cc_start: 0.6792 (tp) cc_final: 0.6492 (tt) REVERT: G 82 PHE cc_start: 0.6724 (m-80) cc_final: 0.6432 (m-80) REVERT: G 83 THR cc_start: 0.5731 (m) cc_final: 0.5474 (t) REVERT: G 85 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7788 (mppt) REVERT: G 105 SER cc_start: 0.6987 (t) cc_final: 0.6777 (p) REVERT: H 22 LYS cc_start: 0.6670 (mttp) cc_final: 0.6458 (mtmt) REVERT: I 10 LEU cc_start: 0.1762 (OUTLIER) cc_final: 0.1162 (tt) REVERT: I 11 GLN cc_start: 0.2266 (OUTLIER) cc_final: 0.0709 (mm110) REVERT: I 30 GLN cc_start: -0.0222 (OUTLIER) cc_final: -0.0653 (pm20) REVERT: I 116 MET cc_start: -0.0341 (mmp) cc_final: -0.1063 (tpt) REVERT: I 135 MET cc_start: 0.1665 (OUTLIER) cc_final: 0.0308 (tmt) REVERT: K 18 ARG cc_start: 0.7592 (mmt180) cc_final: 0.7320 (mtp85) REVERT: K 45 GLU cc_start: 0.7517 (tt0) cc_final: 0.7163 (tp30) REVERT: K 53 LYS cc_start: 0.7960 (pttp) cc_final: 0.7252 (mmtt) REVERT: K 86 LEU cc_start: 0.9033 (mt) cc_final: 0.8809 (mt) REVERT: K 100 PHE cc_start: 0.8427 (m-10) cc_final: 0.8199 (m-80) REVERT: L 25 SER cc_start: 0.9089 (t) cc_final: 0.8886 (t) REVERT: L 60 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7196 (ptt90) REVERT: L 70 LYS cc_start: 0.8267 (tttp) cc_final: 0.8034 (tttt) REVERT: L 77 ILE cc_start: 0.7870 (mt) cc_final: 0.7648 (mt) REVERT: L 78 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6688 (mmm160) REVERT: L 80 SER cc_start: 0.8508 (t) cc_final: 0.8018 (p) REVERT: M 6 ARG cc_start: 0.7662 (ttt90) cc_final: 0.7157 (ttp-110) REVERT: M 25 ASP cc_start: 0.7674 (m-30) cc_final: 0.7440 (m-30) REVERT: M 51 ARG cc_start: 0.7470 (mtt90) cc_final: 0.7060 (mtp85) REVERT: M 127 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7440 (tptm) REVERT: M 133 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7584 (tttt) REVERT: N 18 GLN cc_start: 0.8281 (tt0) cc_final: 0.8063 (tt0) REVERT: N 27 SER cc_start: 0.8404 (m) cc_final: 0.8120 (m) REVERT: N 43 GLU cc_start: 0.8570 (tp30) cc_final: 0.8339 (tp30) REVERT: O 16 ARG cc_start: 0.8143 (mmt-90) cc_final: 0.7387 (mmm-85) REVERT: O 29 HIS cc_start: 0.7836 (t-90) cc_final: 0.7355 (t-170) REVERT: O 65 THR cc_start: 0.7441 (p) cc_final: 0.7147 (t) REVERT: O 85 LYS cc_start: 0.7425 (mmtm) cc_final: 0.7132 (ttmt) REVERT: P 8 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6832 (mm-30) REVERT: P 12 MET cc_start: 0.7957 (mtp) cc_final: 0.7621 (mtp) REVERT: P 23 ASP cc_start: 0.7215 (m-30) cc_final: 0.7014 (m-30) REVERT: P 29 VAL cc_start: 0.8328 (t) cc_final: 0.7810 (p) REVERT: P 43 GLU cc_start: 0.7940 (tt0) cc_final: 0.7360 (pm20) REVERT: P 56 SER cc_start: 0.8221 (p) cc_final: 0.7732 (p) REVERT: P 71 ARG cc_start: 0.7826 (ttt180) cc_final: 0.7493 (mtp180) REVERT: P 75 THR cc_start: 0.8974 (m) cc_final: 0.8629 (p) REVERT: P 112 ARG cc_start: 0.6124 (mtp85) cc_final: 0.5422 (mtm-85) REVERT: Q 83 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7880 (mttp) REVERT: Q 106 THR cc_start: 0.7544 (m) cc_final: 0.7191 (p) REVERT: Q 110 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6923 (mm-30) REVERT: R 18 GLN cc_start: 0.7332 (pt0) cc_final: 0.6921 (pt0) REVERT: R 66 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7655 (m90) REVERT: R 95 ASP cc_start: 0.7560 (m-30) cc_final: 0.7133 (t70) REVERT: S 34 ASP cc_start: 0.6043 (m-30) cc_final: 0.5228 (m-30) REVERT: S 77 ASP cc_start: 0.8495 (m-30) cc_final: 0.8255 (m-30) REVERT: S 78 GLU cc_start: 0.7674 (pt0) cc_final: 0.7367 (pt0) REVERT: S 92 ARG cc_start: 0.6681 (ptp90) cc_final: 0.6399 (ptm160) REVERT: T 9 LYS cc_start: 0.7466 (mttt) cc_final: 0.7162 (mttp) REVERT: T 66 LYS cc_start: 0.7395 (mtpt) cc_final: 0.7060 (mtmm) REVERT: U 5 ARG cc_start: 0.7348 (ptp-170) cc_final: 0.6921 (ptp-170) REVERT: U 21 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7275 (mtm110) REVERT: U 25 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6492 (mtmm) REVERT: U 46 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7695 (pttt) REVERT: U 59 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7316 (tp30) REVERT: U 73 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6479 (t160) REVERT: U 78 LYS cc_start: 0.7623 (pttp) cc_final: 0.6348 (ptpp) REVERT: U 90 LYS cc_start: 0.7354 (mmtp) cc_final: 0.6878 (mtmt) REVERT: V 7 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7455 (tm-30) REVERT: V 19 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7763 (mtm180) REVERT: V 50 MET cc_start: 0.7000 (mmm) cc_final: 0.6424 (mtm) REVERT: V 71 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7586 (tptt) REVERT: W 25 GLU cc_start: 0.7777 (tt0) cc_final: 0.7374 (mt-10) REVERT: W 35 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7658 (mtp85) REVERT: W 74 LYS cc_start: 0.7958 (mttt) cc_final: 0.7348 (mmmt) REVERT: X 16 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7915 (p0) REVERT: X 27 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7887 (mtm180) REVERT: Y 5 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6945 (mt-10) REVERT: Y 13 GLU cc_start: 0.7367 (tt0) cc_final: 0.7011 (tp30) REVERT: Y 17 GLU cc_start: 0.8478 (tp30) cc_final: 0.7858 (tt0) REVERT: Y 19 LEU cc_start: 0.7512 (mt) cc_final: 0.7288 (mt) REVERT: Y 27 ASN cc_start: 0.7958 (m-40) cc_final: 0.7755 (m-40) REVERT: Y 54 LYS cc_start: 0.8350 (tttm) cc_final: 0.8145 (tttt) REVERT: Y 55 THR cc_start: 0.8371 (m) cc_final: 0.8162 (p) REVERT: 0 36 LYS cc_start: 0.7961 (mttt) cc_final: 0.7711 (mtmt) REVERT: 0 49 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7455 (mmm160) REVERT: 1 29 LYS cc_start: 0.7309 (mmmt) cc_final: 0.6705 (mmmt) REVERT: 1 32 LYS cc_start: 0.7593 (mttt) cc_final: 0.7210 (mttp) REVERT: 2 1 MET cc_start: 0.7203 (ppp) cc_final: 0.6848 (pp-130) REVERT: 2 41 ARG cc_start: 0.7809 (mmt180) cc_final: 0.7210 (ttt-90) REVERT: 4 30 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7438 (mm-30) REVERT: 6 9 TYR cc_start: 0.7878 (t80) cc_final: 0.7564 (t80) REVERT: 6 12 ILE cc_start: 0.6989 (pt) cc_final: 0.6751 (pp) REVERT: b 21 TYR cc_start: 0.6723 (p90) cc_final: 0.4792 (p90) REVERT: b 22 TRP cc_start: 0.7734 (p-90) cc_final: 0.6837 (p-90) REVERT: b 27 LYS cc_start: 0.7204 (tttt) cc_final: 0.6816 (ttmt) REVERT: b 41 ASN cc_start: 0.5412 (t0) cc_final: 0.5203 (p0) REVERT: b 104 LYS cc_start: 0.7999 (pttp) cc_final: 0.7719 (pttp) REVERT: b 107 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6995 (ttp-170) REVERT: b 108 GLN cc_start: 0.7719 (pt0) cc_final: 0.7371 (mm-40) REVERT: b 110 ILE cc_start: 0.7811 (mt) cc_final: 0.7433 (pt) REVERT: b 164 ASP cc_start: 0.7413 (t0) cc_final: 0.6598 (t70) REVERT: b 170 ILE cc_start: 0.8368 (pt) cc_final: 0.7960 (mm) REVERT: c 81 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6667 (mt-10) REVERT: c 99 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.5301 (tm-30) REVERT: c 101 ASN cc_start: 0.6697 (m-40) cc_final: 0.6381 (m-40) REVERT: c 121 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7641 (p) REVERT: c 134 LYS cc_start: 0.6635 (mttt) cc_final: 0.6314 (mttt) REVERT: c 165 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7198 (mt-10) REVERT: c 195 ILE cc_start: 0.8670 (mt) cc_final: 0.8370 (mm) REVERT: d 47 LEU cc_start: 0.7309 (tp) cc_final: 0.6976 (pp) REVERT: d 64 TYR cc_start: 0.8172 (m-80) cc_final: 0.7680 (m-80) REVERT: d 69 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7350 (tpt170) REVERT: d 71 PHE cc_start: 0.8677 (t80) cc_final: 0.8328 (t80) REVERT: d 99 ASN cc_start: 0.8692 (t0) cc_final: 0.8376 (t0) REVERT: d 102 TYR cc_start: 0.7486 (t80) cc_final: 0.7260 (t80) REVERT: d 120 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7472 (mptm) REVERT: d 123 MET cc_start: 0.7692 (ttt) cc_final: 0.7420 (ttt) REVERT: d 130 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6758 (m110) REVERT: d 131 ILE cc_start: 0.8043 (mp) cc_final: 0.7756 (mm) REVERT: d 177 MET cc_start: 0.6910 (mmp) cc_final: 0.5901 (mpp) REVERT: d 178 GLU cc_start: 0.7252 (tt0) cc_final: 0.6680 (tp30) REVERT: d 181 PHE cc_start: 0.6945 (t80) cc_final: 0.6546 (t80) REVERT: d 182 LYS cc_start: 0.6743 (ttmt) cc_final: 0.6379 (mmpt) REVERT: d 188 SER cc_start: 0.8132 (p) cc_final: 0.7924 (m) REVERT: d 201 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6536 (mt-10) REVERT: e 12 GLU cc_start: 0.6367 (pt0) cc_final: 0.5956 (pm20) REVERT: f 58 HIS cc_start: 0.7780 (t70) cc_final: 0.7558 (t70) REVERT: f 90 MET cc_start: 0.7961 (mmm) cc_final: 0.7548 (mpp) REVERT: g 21 LEU cc_start: 0.7250 (tp) cc_final: 0.6749 (tm) REVERT: g 25 PHE cc_start: 0.8855 (t80) cc_final: 0.8402 (t80) REVERT: g 39 GLU cc_start: 0.7488 (tt0) cc_final: 0.7282 (tp30) REVERT: g 62 GLU cc_start: 0.7003 (tp30) cc_final: 0.6642 (mp0) REVERT: g 71 THR cc_start: 0.7770 (m) cc_final: 0.7239 (t) REVERT: g 77 ARG cc_start: 0.3561 (ttt-90) cc_final: 0.2836 (ptt180) REVERT: g 89 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: g 95 ARG cc_start: 0.6961 (ttt180) cc_final: 0.6637 (ttp-170) REVERT: g 125 ASP cc_start: 0.7969 (m-30) cc_final: 0.7751 (m-30) REVERT: h 49 LYS cc_start: 0.7995 (mttp) cc_final: 0.7676 (pttm) REVERT: h 51 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7079 (pm20) REVERT: h 93 LYS cc_start: 0.6626 (ptpt) cc_final: 0.6153 (mmtp) REVERT: h 110 MET cc_start: 0.7342 (ptp) cc_final: 0.7101 (ptm) REVERT: i 106 ASP cc_start: 0.7981 (t70) cc_final: 0.7766 (t70) REVERT: i 123 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7488 (mtm-85) REVERT: j 9 ARG cc_start: 0.6760 (ttp80) cc_final: 0.6523 (ttp80) REVERT: j 25 ILE cc_start: 0.7662 (tt) cc_final: 0.7375 (tp) REVERT: j 45 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7094 (tmt-80) REVERT: j 48 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7723 (mtt-85) REVERT: j 51 VAL cc_start: 0.8909 (m) cc_final: 0.8465 (p) REVERT: j 88 MET cc_start: 0.6883 (mmm) cc_final: 0.6586 (ttp) REVERT: k 17 ASP cc_start: 0.7143 (p0) cc_final: 0.6411 (m-30) REVERT: k 76 TYR cc_start: 0.7036 (m-80) cc_final: 0.6822 (m-80) REVERT: k 125 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6565 (tptt) REVERT: l 8 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7811 (mtm180) REVERT: m 26 LYS cc_start: 0.7805 (tttp) cc_final: 0.7538 (tptt) REVERT: m 38 ILE cc_start: 0.7495 (mm) cc_final: 0.7259 (mp) REVERT: m 77 LYS cc_start: 0.7745 (tttm) cc_final: 0.7247 (tptt) REVERT: n 41 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.6999 (ttm110) REVERT: n 62 ASN cc_start: 0.8211 (t0) cc_final: 0.7729 (t0) REVERT: o 61 GLN cc_start: 0.8033 (tp40) cc_final: 0.7833 (tp40) REVERT: p 35 ARG cc_start: 0.7718 (ptm-80) cc_final: 0.7480 (ttt-90) REVERT: q 17 GLU cc_start: 0.7907 (tt0) cc_final: 0.7630 (tt0) REVERT: q 20 ILE cc_start: 0.8002 (tt) cc_final: 0.7790 (pt) REVERT: q 24 ILE cc_start: 0.8525 (mt) cc_final: 0.8250 (mp) REVERT: q 61 ARG cc_start: 0.7079 (ttp-170) cc_final: 0.6538 (ptt180) REVERT: q 72 TRP cc_start: 0.8581 (m100) cc_final: 0.8102 (m100) REVERT: q 76 ARG cc_start: 0.7622 (ptt-90) cc_final: 0.7109 (ppt90) REVERT: r 20 ILE cc_start: 0.7756 (mm) cc_final: 0.7532 (mt) REVERT: r 49 LYS cc_start: 0.7573 (ttpp) cc_final: 0.7302 (ttmm) REVERT: s 5 LYS cc_start: 0.4498 (OUTLIER) cc_final: 0.3725 (tmmt) REVERT: s 22 VAL cc_start: 0.7162 (t) cc_final: 0.6893 (p) REVERT: s 42 ASN cc_start: 0.7703 (p0) cc_final: 0.7463 (t0) REVERT: s 43 MET cc_start: 0.8626 (mtp) cc_final: 0.8258 (mtp) REVERT: t 47 GLN cc_start: 0.7178 (tt0) cc_final: 0.6637 (tm-30) REVERT: u 19 LYS cc_start: 0.6173 (tttt) cc_final: 0.5430 (tptt) REVERT: u 33 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6638 (ttp-170) REVERT: u 37 TYR cc_start: 0.6855 (t80) cc_final: 0.6501 (t80) REVERT: z 11 HIS cc_start: 0.7422 (t70) cc_final: 0.6907 (t70) REVERT: z 22 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7693 (m-70) REVERT: z 24 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7979 (ttpt) REVERT: z 62 ILE cc_start: 0.7931 (mt) cc_final: 0.7657 (mp) REVERT: z 75 HIS cc_start: 0.7235 (t70) cc_final: 0.6023 (t-90) REVERT: z 80 ASP cc_start: 0.7030 (t70) cc_final: 0.6678 (t70) REVERT: z 136 LYS cc_start: 0.5610 (OUTLIER) cc_final: 0.4536 (mmtt) REVERT: z 217 VAL cc_start: 0.8151 (t) cc_final: 0.7931 (p) REVERT: z 267 GLU cc_start: 0.6259 (mt-10) cc_final: 0.5801 (pt0) REVERT: z 282 LYS cc_start: 0.7419 (mttt) cc_final: 0.6946 (mptt) REVERT: z 284 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6706 (pp20) REVERT: z 294 LYS cc_start: 0.7014 (ttpp) cc_final: 0.6579 (tptm) REVERT: z 305 GLU cc_start: 0.6216 (mt-10) cc_final: 0.5890 (tm-30) REVERT: z 322 PHE cc_start: 0.2836 (p90) cc_final: 0.1672 (p90) REVERT: z 381 ARG cc_start: 0.4431 (ptm160) cc_final: 0.3777 (ppt170) REVERT: z 390 LYS cc_start: 0.7032 (ttmt) cc_final: 0.6796 (tppt) outliers start: 170 outliers final: 16 residues processed: 1945 average time/residue: 2.4016 time to fit residues: 6616.4070 Evaluate side-chains 1277 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1237 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 83 LYS Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain o residue 87 ARG Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain z residue 22 HIS Chi-restraints excluded: chain z residue 24 LYS Chi-restraints excluded: chain z residue 136 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 917 optimal weight: 4.9990 chunk 823 optimal weight: 8.9990 chunk 457 optimal weight: 0.9990 chunk 281 optimal weight: 8.9990 chunk 555 optimal weight: 8.9990 chunk 440 optimal weight: 7.9990 chunk 851 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 518 optimal weight: 3.9990 chunk 634 optimal weight: 7.9990 chunk 987 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 116 GLN C 141 HIS D 67 HIS E 136 GLN E 156 ASN E 165 HIS E 195 GLN F 36 ASN F 134 GLN G 63 GLN G 87 GLN J 40 HIS J 77 HIS J 128 ASN L 54 GLN N 62 ASN Q 19 GLN Q 71 ASN Q 80 ASN R 6 GLN R 86 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS U 73 ASN V 49 ASN W 72 ASN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN 6 41 HIS b 102 ASN c 7 ASN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 70 GLN d 115 GLN e 77 ASN e 121 ASN f 3 HIS f 81 ASN g 67 ASN g 141 HIS h 75 GLN i 74 GLN k 23 HIS k 80 ASN n 43 ASN n 60 GLN o 27 GLN p 40 ASN p 79 ASN t 69 ASN z 114 GLN z 329 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 165478 Z= 0.333 Angle : 0.840 21.080 247206 Z= 0.441 Chirality : 0.044 0.409 31414 Planarity : 0.008 0.134 13504 Dihedral : 24.274 179.576 81938 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.64 % Favored : 91.49 % Rotamer: Outliers : 7.14 % Allowed : 19.42 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.09), residues: 6219 helix: -0.50 (0.11), residues: 1913 sheet: -2.28 (0.13), residues: 1139 loop : -2.38 (0.10), residues: 3167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.012 0.002 HIS C 24 PHE 0.023 0.002 PHE e 47 TYR 0.023 0.002 TYR L 58 ARG 0.010 0.001 ARG L 123 *********************** 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 1697 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1328 time to evaluate : 6.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 VAL cc_start: 0.8537 (t) cc_final: 0.8302 (m) REVERT: C 25 LYS cc_start: 0.7249 (mttt) cc_final: 0.6726 (mptp) REVERT: C 27 LYS cc_start: 0.7759 (mttt) cc_final: 0.7046 (mmtm) REVERT: C 99 GLU cc_start: 0.7799 (tt0) cc_final: 0.7586 (tt0) REVERT: C 104 LEU cc_start: 0.9054 (mt) cc_final: 0.8769 (mt) REVERT: C 110 LYS cc_start: 0.7860 (mttt) cc_final: 0.7507 (mtpp) REVERT: C 113 ASP cc_start: 0.6992 (m-30) cc_final: 0.6532 (m-30) REVERT: C 114 GLN cc_start: 0.7339 (tt0) cc_final: 0.6851 (mt0) REVERT: C 139 THR cc_start: 0.8568 (m) cc_final: 0.8190 (p) REVERT: C 152 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.6382 (mp10) REVERT: C 159 THR cc_start: 0.9151 (m) cc_final: 0.8777 (p) REVERT: C 179 GLU cc_start: 0.7730 (tt0) cc_final: 0.7501 (tt0) REVERT: C 180 MET cc_start: 0.8515 (mtp) cc_final: 0.8298 (mmt) REVERT: C 182 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7528 (mtpp) REVERT: C 186 ASP cc_start: 0.7758 (m-30) cc_final: 0.7451 (t0) REVERT: C 266 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8380 (mm) REVERT: C 269 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7431 (mtp-110) REVERT: D 99 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7976 (mt-10) REVERT: D 105 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7288 (mmpt) REVERT: D 168 GLU cc_start: 0.7590 (tt0) cc_final: 0.7310 (tt0) REVERT: D 169 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7178 (ttt180) REVERT: D 183 GLU cc_start: 0.7855 (tt0) cc_final: 0.7507 (pt0) REVERT: D 200 ASP cc_start: 0.7857 (m-30) cc_final: 0.7328 (p0) REVERT: E 27 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7987 (mt) REVERT: E 88 ARG cc_start: 0.7434 (mmm160) cc_final: 0.7023 (mtt-85) REVERT: F 25 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6811 (mpm) REVERT: F 47 LYS cc_start: 0.7379 (ptmt) cc_final: 0.6638 (mmmt) REVERT: F 51 ASN cc_start: 0.7327 (m-40) cc_final: 0.6712 (m110) REVERT: F 67 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (p) REVERT: F 97 GLU cc_start: 0.6896 (tp30) cc_final: 0.6439 (tp30) REVERT: F 111 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6566 (mmm-85) REVERT: F 126 ASN cc_start: 0.8644 (m-40) cc_final: 0.8276 (m-40) REVERT: F 142 TYR cc_start: 0.6562 (t80) cc_final: 0.6020 (t80) REVERT: F 177 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5212 (mtm180) REVERT: G 5 LYS cc_start: 0.5922 (mtmm) cc_final: 0.5211 (ptmm) REVERT: G 11 PRO cc_start: 0.6698 (Cg_exo) cc_final: 0.6482 (Cg_endo) REVERT: G 36 LEU cc_start: 0.6792 (tp) cc_final: 0.6378 (tt) REVERT: G 70 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6920 (mp) REVERT: G 82 PHE cc_start: 0.7166 (m-80) cc_final: 0.6884 (m-80) REVERT: G 129 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7542 (tm-30) REVERT: H 45 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6083 (pp20) REVERT: I 72 THR cc_start: 0.1542 (OUTLIER) cc_final: 0.1294 (p) REVERT: I 135 MET cc_start: 0.0571 (mtp) cc_final: 0.0329 (tmt) REVERT: J 57 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8180 (pp) REVERT: K 17 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7331 (mmt90) REVERT: K 44 LYS cc_start: 0.8240 (mmtp) cc_final: 0.7987 (mmtt) REVERT: K 45 GLU cc_start: 0.7685 (tt0) cc_final: 0.7186 (tp30) REVERT: K 53 LYS cc_start: 0.7746 (pttp) cc_final: 0.7076 (mmtt) REVERT: K 88 ASN cc_start: 0.7164 (t0) cc_final: 0.6804 (t0) REVERT: K 100 PHE cc_start: 0.8373 (m-10) cc_final: 0.7926 (m-80) REVERT: K 121 GLU cc_start: 0.8487 (tt0) cc_final: 0.8196 (tt0) REVERT: L 41 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8189 (mmt90) REVERT: L 60 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7440 (ptt90) REVERT: L 80 SER cc_start: 0.8176 (t) cc_final: 0.7541 (p) REVERT: L 84 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6747 (mttt) REVERT: M 6 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7000 (ttp-110) REVERT: M 25 ASP cc_start: 0.7796 (m-30) cc_final: 0.7551 (m-30) REVERT: M 47 GLU cc_start: 0.7437 (tp30) cc_final: 0.7137 (tp30) REVERT: M 51 ARG cc_start: 0.7300 (mtt90) cc_final: 0.7019 (mtp85) REVERT: M 127 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7374 (tptm) REVERT: M 133 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7721 (tttt) REVERT: M 136 MET cc_start: 0.5898 (tmm) cc_final: 0.5688 (tmm) REVERT: N 18 GLN cc_start: 0.8212 (tt0) cc_final: 0.7897 (tt0) REVERT: N 27 SER cc_start: 0.8037 (m) cc_final: 0.7833 (m) REVERT: N 32 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: N 34 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8306 (mm) REVERT: N 43 GLU cc_start: 0.8668 (tp30) cc_final: 0.8340 (tp30) REVERT: N 74 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: N 114 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: O 16 ARG cc_start: 0.8060 (mmt-90) cc_final: 0.7199 (mmm-85) REVERT: O 115 LEU cc_start: 0.7106 (tp) cc_final: 0.6707 (mp) REVERT: P 5 LYS cc_start: 0.6519 (ttpt) cc_final: 0.6216 (mtpp) REVERT: P 29 VAL cc_start: 0.8577 (t) cc_final: 0.8173 (p) REVERT: P 112 ARG cc_start: 0.5977 (mtp85) cc_final: 0.5185 (mtm-85) REVERT: Q 86 SER cc_start: 0.7201 (OUTLIER) cc_final: 0.6807 (p) REVERT: Q 106 THR cc_start: 0.7737 (m) cc_final: 0.7357 (p) REVERT: Q 110 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6976 (mm-30) REVERT: R 18 GLN cc_start: 0.7576 (pt0) cc_final: 0.7199 (pt0) REVERT: R 60 LYS cc_start: 0.8593 (tppp) cc_final: 0.8031 (mptt) REVERT: R 95 ASP cc_start: 0.7600 (m-30) cc_final: 0.7049 (m-30) REVERT: S 4 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8099 (tt) REVERT: S 29 VAL cc_start: 0.7676 (t) cc_final: 0.7382 (m) REVERT: S 31 GLN cc_start: 0.7044 (tt0) cc_final: 0.6600 (pt0) REVERT: S 52 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7925 (mm-30) REVERT: S 82 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7727 (mtp) REVERT: S 92 ARG cc_start: 0.6565 (ptp90) cc_final: 0.6334 (ptm160) REVERT: T 66 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6907 (mtmm) REVERT: U 21 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7594 (mtm110) REVERT: U 25 LYS cc_start: 0.7069 (mmmt) cc_final: 0.6483 (mtmm) REVERT: U 46 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7667 (pttt) REVERT: U 59 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7735 (tp30) REVERT: U 78 LYS cc_start: 0.7405 (pttp) cc_final: 0.6255 (ptpp) REVERT: U 90 LYS cc_start: 0.7303 (mmtp) cc_final: 0.6696 (mtmt) REVERT: V 7 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7513 (tm-30) REVERT: V 49 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7314 (t0) REVERT: V 62 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7630 (t) REVERT: V 71 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7519 (mptm) REVERT: W 7 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7469 (mmm-85) REVERT: W 36 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: W 72 ASN cc_start: 0.7923 (m-40) cc_final: 0.7721 (m110) REVERT: W 73 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7735 (mtt180) REVERT: W 74 LYS cc_start: 0.7901 (mttt) cc_final: 0.7426 (mmmt) REVERT: W 79 GLU cc_start: 0.6832 (pm20) cc_final: 0.6593 (pm20) REVERT: X 49 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.6881 (ttt-90) REVERT: Y 5 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6885 (mt-10) REVERT: Y 17 GLU cc_start: 0.8436 (tp30) cc_final: 0.8219 (tp30) REVERT: Y 19 LEU cc_start: 0.7511 (mt) cc_final: 0.7246 (mt) REVERT: Y 21 LEU cc_start: 0.6704 (mt) cc_final: 0.6435 (mt) REVERT: Y 36 GLN cc_start: 0.6489 (mt0) cc_final: 0.5736 (mm-40) REVERT: Y 54 LYS cc_start: 0.8229 (tttm) cc_final: 0.7941 (mtpt) REVERT: Z 5 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7668 (mtpm) REVERT: 0 49 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7331 (mmm160) REVERT: 1 29 LYS cc_start: 0.7327 (mmmt) cc_final: 0.7066 (mptm) REVERT: 1 49 LYS cc_start: 0.7653 (mttt) cc_final: 0.6828 (tppt) REVERT: 2 25 LYS cc_start: 0.8362 (tppt) cc_final: 0.8155 (ttmp) REVERT: 2 28 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8294 (mtm-85) REVERT: 2 41 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7298 (ttt-90) REVERT: 4 37 GLN cc_start: 0.7951 (tt0) cc_final: 0.7557 (tm-30) REVERT: 5 38 MET cc_start: 0.0964 (mtt) cc_final: 0.0674 (mtp) REVERT: 5 60 LEU cc_start: 0.0123 (OUTLIER) cc_final: -0.0114 (mp) REVERT: b 8 MET cc_start: 0.5326 (pp-130) cc_final: 0.4917 (ppp) REVERT: b 21 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.4971 (p90) REVERT: b 27 LYS cc_start: 0.7147 (tttt) cc_final: 0.6925 (ttmt) REVERT: b 40 ILE cc_start: 0.7716 (mt) cc_final: 0.7290 (tt) REVERT: b 41 ASN cc_start: 0.5777 (t0) cc_final: 0.4954 (m-40) REVERT: b 42 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7113 (tm) REVERT: b 46 VAL cc_start: 0.6477 (OUTLIER) cc_final: 0.6265 (t) REVERT: b 80 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6801 (tppt) REVERT: b 107 ARG cc_start: 0.7274 (ttp-170) cc_final: 0.6972 (ttp-170) REVERT: b 108 GLN cc_start: 0.7728 (pt0) cc_final: 0.7192 (mm-40) REVERT: b 139 GLU cc_start: 0.7803 (tp30) cc_final: 0.7276 (tp30) REVERT: b 164 ASP cc_start: 0.6657 (t0) cc_final: 0.6301 (t70) REVERT: b 172 ILE cc_start: 0.7643 (mt) cc_final: 0.7415 (mm) REVERT: b 199 ILE cc_start: 0.7961 (mt) cc_final: 0.7746 (mp) REVERT: c 37 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7683 (mptt) REVERT: c 126 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7334 (mmm160) REVERT: c 134 LYS cc_start: 0.7179 (mttt) cc_final: 0.6699 (mtmt) REVERT: d 30 LYS cc_start: 0.4806 (OUTLIER) cc_final: 0.4404 (pttt) REVERT: d 64 TYR cc_start: 0.8096 (m-80) cc_final: 0.7888 (m-80) REVERT: d 66 VAL cc_start: 0.8105 (t) cc_final: 0.7831 (m) REVERT: d 77 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7112 (tp30) REVERT: d 102 TYR cc_start: 0.7452 (t80) cc_final: 0.6985 (t80) REVERT: d 123 MET cc_start: 0.7517 (ttt) cc_final: 0.7224 (ttp) REVERT: d 169 TRP cc_start: 0.7845 (p90) cc_final: 0.7536 (p90) REVERT: d 176 LYS cc_start: 0.6678 (pmtt) cc_final: 0.6189 (pmtt) REVERT: d 177 MET cc_start: 0.6933 (mmp) cc_final: 0.6208 (mpp) REVERT: d 178 GLU cc_start: 0.7091 (tt0) cc_final: 0.6740 (tp30) REVERT: d 181 PHE cc_start: 0.6857 (t80) cc_final: 0.6591 (t80) REVERT: d 182 LYS cc_start: 0.6948 (ttmt) cc_final: 0.6634 (mtmt) REVERT: d 184 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6837 (mtpt) REVERT: d 201 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6604 (mt-10) REVERT: e 12 GLU cc_start: 0.6536 (pt0) cc_final: 0.6266 (pm20) REVERT: e 121 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7812 (p0) REVERT: f 21 MET cc_start: 0.7176 (mtm) cc_final: 0.6637 (mtm) REVERT: f 40 GLU cc_start: 0.6436 (tt0) cc_final: 0.5849 (mt-10) REVERT: g 55 LYS cc_start: 0.6555 (ttmt) cc_final: 0.6173 (ttmp) REVERT: g 62 GLU cc_start: 0.7193 (tp30) cc_final: 0.6819 (tp30) REVERT: g 66 GLU cc_start: 0.7817 (pt0) cc_final: 0.7454 (mm-30) REVERT: g 67 ASN cc_start: 0.7574 (m-40) cc_final: 0.7300 (m110) REVERT: g 71 THR cc_start: 0.7543 (m) cc_final: 0.7207 (t) REVERT: g 77 ARG cc_start: 0.3911 (ttt-90) cc_final: 0.2764 (ptt180) REVERT: g 89 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: g 114 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7162 (t) REVERT: g 125 ASP cc_start: 0.8252 (m-30) cc_final: 0.7965 (m-30) REVERT: g 148 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7614 (ttpp) REVERT: h 26 MET cc_start: 0.7613 (ptp) cc_final: 0.7337 (ptp) REVERT: h 30 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7129 (mtpp) REVERT: h 49 LYS cc_start: 0.8125 (mttp) cc_final: 0.7782 (mppt) REVERT: h 91 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (mp) REVERT: h 93 LYS cc_start: 0.6885 (ptpt) cc_final: 0.6192 (mmtp) REVERT: h 110 MET cc_start: 0.7607 (ptp) cc_final: 0.7387 (ptm) REVERT: i 32 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5648 (mpp80) REVERT: i 41 GLU cc_start: 0.3864 (OUTLIER) cc_final: 0.2149 (tm-30) REVERT: i 45 MET cc_start: 0.5736 (pp-130) cc_final: 0.5382 (pp-130) REVERT: i 63 TYR cc_start: 0.7993 (t80) cc_final: 0.7645 (t80) REVERT: i 118 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6522 (ttp-110) REVERT: j 10 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7647 (pp) REVERT: j 37 ARG cc_start: 0.5029 (mpt90) cc_final: 0.4781 (mmm160) REVERT: j 45 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6934 (tmt-80) REVERT: j 48 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7703 (mtt-85) REVERT: j 63 ASP cc_start: 0.8339 (m-30) cc_final: 0.8127 (m-30) REVERT: j 88 MET cc_start: 0.6747 (mmm) cc_final: 0.6467 (ttp) REVERT: k 17 ASP cc_start: 0.7299 (p0) cc_final: 0.6276 (m-30) REVERT: k 39 ASN cc_start: 0.7745 (t0) cc_final: 0.7490 (m-40) REVERT: k 68 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7663 (ttm170) REVERT: k 92 ARG cc_start: 0.8060 (ptt90) cc_final: 0.6960 (ptt180) REVERT: k 105 ARG cc_start: 0.7016 (tmm160) cc_final: 0.6561 (tpt-90) REVERT: k 113 THR cc_start: 0.7720 (m) cc_final: 0.7226 (p) REVERT: l 93 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7212 (ptp-170) REVERT: l 107 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7815 (mmpt) REVERT: m 26 LYS cc_start: 0.7635 (tttp) cc_final: 0.7346 (tptp) REVERT: m 38 ILE cc_start: 0.7689 (mm) cc_final: 0.7443 (mp) REVERT: m 76 ILE cc_start: 0.7669 (mt) cc_final: 0.7458 (mt) REVERT: m 77 LYS cc_start: 0.7700 (tttm) cc_final: 0.6965 (tptt) REVERT: m 80 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7828 (mtp) REVERT: m 112 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6406 (mtt90) REVERT: n 15 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7162 (tt) REVERT: n 62 ASN cc_start: 0.8492 (t0) cc_final: 0.8083 (t0) REVERT: n 75 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8058 (ttm170) REVERT: o 71 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6975 (ptp90) REVERT: p 18 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7617 (mt0) REVERT: p 31 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7039 (mtm-85) REVERT: q 20 ILE cc_start: 0.7861 (tt) cc_final: 0.7639 (pt) REVERT: q 24 ILE cc_start: 0.8518 (mt) cc_final: 0.8225 (mp) REVERT: r 29 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8233 (mtmt) REVERT: r 47 ARG cc_start: 0.7672 (mmt-90) cc_final: 0.6504 (mtm180) REVERT: s 5 LYS cc_start: 0.4791 (OUTLIER) cc_final: 0.3880 (pptt) REVERT: s 19 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7215 (mt-10) REVERT: s 42 ASN cc_start: 0.7739 (p0) cc_final: 0.7509 (t0) REVERT: s 43 MET cc_start: 0.8437 (mtp) cc_final: 0.8107 (mtp) REVERT: t 47 GLN cc_start: 0.6982 (tt0) cc_final: 0.6488 (tm-30) REVERT: u 9 GLU cc_start: 0.3839 (OUTLIER) cc_final: 0.2723 (mp0) REVERT: u 19 LYS cc_start: 0.5854 (tttt) cc_final: 0.4863 (tptt) REVERT: z 6 GLU cc_start: 0.6706 (mm-30) cc_final: 0.5860 (tm-30) REVERT: z 9 LYS cc_start: 0.6254 (mttt) cc_final: 0.5992 (mtpp) REVERT: z 11 HIS cc_start: 0.7506 (t70) cc_final: 0.7049 (t70) REVERT: z 54 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6266 (pm20) REVERT: z 68 GLU cc_start: 0.7200 (tt0) cc_final: 0.6250 (tp30) REVERT: z 99 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5652 (m-30) REVERT: z 112 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7550 (mmm) REVERT: z 204 ARG cc_start: 0.4183 (OUTLIER) cc_final: 0.3492 (mmp80) REVERT: z 216 ASP cc_start: 0.6863 (t0) cc_final: 0.6127 (p0) REVERT: z 241 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7191 (mm-30) REVERT: z 243 GLU cc_start: 0.7986 (tt0) cc_final: 0.7343 (tt0) REVERT: z 266 ASP cc_start: 0.6002 (m-30) cc_final: 0.4616 (p0) REVERT: z 267 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6307 (mt-10) REVERT: z 282 LYS cc_start: 0.7666 (mttt) cc_final: 0.6886 (mptt) REVERT: z 285 GLU cc_start: 0.7159 (pt0) cc_final: 0.6094 (pt0) REVERT: z 294 LYS cc_start: 0.6819 (ttpp) cc_final: 0.6344 (tmtt) REVERT: z 305 GLU cc_start: 0.6309 (mt-10) cc_final: 0.5947 (tm-30) REVERT: z 338 THR cc_start: 0.8280 (m) cc_final: 0.8029 (m) REVERT: z 358 MET cc_start: 0.5364 (pmm) cc_final: 0.4592 (pmm) REVERT: z 381 ARG cc_start: 0.4144 (ptm160) cc_final: 0.3612 (ppt170) REVERT: z 390 LYS cc_start: 0.7050 (ttmt) cc_final: 0.6702 (tppt) outliers start: 369 outliers final: 135 residues processed: 1533 average time/residue: 2.3102 time to fit residues: 5076.5062 Evaluate side-chains 1347 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1154 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 LYS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 ARG Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 28 SER Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 23 ILE Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 134 LEU Chi-restraints excluded: chain b residue 207 ARG Chi-restraints excluded: chain b residue 210 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 30 LYS Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 30 LYS Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain k residue 23 HIS Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 114 SER Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 80 MET Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 112 ARG Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 39 GLN Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 31 ARG Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 99 ASP Chi-restraints excluded: chain z residue 112 MET Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 204 ARG Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 254 THR Chi-restraints excluded: chain z residue 264 LEU Chi-restraints excluded: chain z residue 302 THR Chi-restraints excluded: chain z residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 548 optimal weight: 10.0000 chunk 306 optimal weight: 0.6980 chunk 821 optimal weight: 7.9990 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 988 optimal weight: 0.8980 chunk 1068 optimal weight: 8.9990 chunk 880 optimal weight: 5.9990 chunk 980 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 chunk 793 optimal weight: 8.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN C 199 HIS E 195 GLN F 62 GLN G 103 ASN H 43 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN J 76 HIS K 89 ASN N 62 ASN ** O 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS U 26 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN W 8 ASN Y 20 ASN Y 45 GLN 0 4 GLN 0 5 ASN 4 33 HIS 5 4 ASN c 138 GLN d 88 ASN e 60 GLN e 77 ASN f 81 ASN g 141 HIS g 147 ASN l 5 GLN p 40 ASN s 51 HIS t 2 ASN z 135 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 165478 Z= 0.302 Angle : 0.749 18.424 247206 Z= 0.402 Chirality : 0.040 0.382 31414 Planarity : 0.008 0.136 13504 Dihedral : 24.123 178.969 81873 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.23 % Favored : 91.03 % Rotamer: Outliers : 8.23 % Allowed : 21.72 % Favored : 70.05 % 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: -2.08 (0.10), residues: 6219 helix: 0.05 (0.12), residues: 1939 sheet: -1.87 (0.14), residues: 1197 loop : -2.12 (0.10), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP f 42 HIS 0.063 0.002 HIS k 23 PHE 0.023 0.002 PHE e 47 TYR 0.024 0.002 TYR R 2 ARG 0.013 0.001 ARG d 80 *********************** 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 1655 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 1230 time to evaluate : 6.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 LYS cc_start: 0.7857 (mttt) cc_final: 0.7080 (mmtt) REVERT: C 27 LYS cc_start: 0.7961 (mttt) cc_final: 0.7106 (mmtm) REVERT: C 110 LYS cc_start: 0.7699 (mttt) cc_final: 0.7364 (mtpp) REVERT: C 113 ASP cc_start: 0.7273 (m-30) cc_final: 0.6806 (m-30) REVERT: C 114 GLN cc_start: 0.7387 (tt0) cc_final: 0.7086 (mt0) REVERT: C 119 VAL cc_start: 0.8361 (t) cc_final: 0.8115 (m) REVERT: C 131 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8144 (mtm) REVERT: C 152 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.6513 (mp10) REVERT: C 166 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8011 (ttp80) REVERT: C 179 GLU cc_start: 0.7682 (tt0) cc_final: 0.7467 (tt0) REVERT: C 180 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8266 (mmt) REVERT: C 182 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7449 (mtpp) REVERT: C 186 ASP cc_start: 0.7739 (m-30) cc_final: 0.7467 (t0) REVERT: C 202 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7682 (ttm-80) REVERT: C 260 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8614 (ttmm) REVERT: C 269 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7617 (mtp-110) REVERT: D 105 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7357 (mmpt) REVERT: D 168 GLU cc_start: 0.7552 (tt0) cc_final: 0.7203 (tt0) REVERT: D 169 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7683 (ttp80) REVERT: D 183 GLU cc_start: 0.7841 (tt0) cc_final: 0.7324 (pt0) REVERT: E 27 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7976 (mt) REVERT: E 88 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7000 (mtt-85) REVERT: F 25 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6628 (mpm) REVERT: F 47 LYS cc_start: 0.7037 (ptmt) cc_final: 0.5872 (tmtm) REVERT: F 48 LEU cc_start: 0.7497 (mm) cc_final: 0.6750 (tm) REVERT: F 51 ASN cc_start: 0.7126 (m-40) cc_final: 0.6316 (m110) REVERT: F 67 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8198 (p) REVERT: F 91 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.6376 (ptm160) REVERT: F 97 GLU cc_start: 0.6790 (tp30) cc_final: 0.6141 (tp30) REVERT: F 111 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6508 (mmm-85) REVERT: F 129 MET cc_start: 0.7367 (ttt) cc_final: 0.6994 (tmm) REVERT: F 142 TYR cc_start: 0.6508 (t80) cc_final: 0.5947 (t80) REVERT: F 177 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5267 (mtm180) REVERT: G 5 LYS cc_start: 0.5883 (mtmm) cc_final: 0.5131 (pttp) REVERT: G 11 PRO cc_start: 0.6942 (Cg_exo) cc_final: 0.6725 (Cg_endo) REVERT: G 82 PHE cc_start: 0.7207 (m-80) cc_final: 0.6802 (m-80) REVERT: H 45 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: I 135 MET cc_start: 0.0540 (mtp) cc_final: -0.0206 (tmt) REVERT: K 45 GLU cc_start: 0.7769 (tt0) cc_final: 0.7423 (tt0) REVERT: K 53 LYS cc_start: 0.7708 (pttp) cc_final: 0.7057 (mmtt) REVERT: K 78 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7356 (mtp180) REVERT: K 100 PHE cc_start: 0.8358 (m-10) cc_final: 0.7962 (m-80) REVERT: K 113 MET cc_start: 0.6639 (mmm) cc_final: 0.6303 (mpt) REVERT: L 60 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7488 (ptt90) REVERT: L 80 SER cc_start: 0.8205 (t) cc_final: 0.7520 (p) REVERT: M 6 ARG cc_start: 0.7703 (ttt90) cc_final: 0.7047 (ttp-110) REVERT: M 20 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.6924 (pp) REVERT: M 47 GLU cc_start: 0.7577 (tp30) cc_final: 0.7206 (tp30) REVERT: M 51 ARG cc_start: 0.7332 (mtt90) cc_final: 0.7051 (mtp85) REVERT: M 75 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: M 81 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8271 (mtt-85) REVERT: M 127 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7236 (tptm) REVERT: M 133 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7769 (tttp) REVERT: N 18 GLN cc_start: 0.8301 (tt0) cc_final: 0.7831 (tt0) REVERT: N 43 GLU cc_start: 0.8735 (tp30) cc_final: 0.8304 (tp30) REVERT: N 74 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: N 114 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: O 3 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6670 (mtpt) REVERT: O 16 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7099 (mmm-85) REVERT: O 115 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6745 (mp) REVERT: P 29 VAL cc_start: 0.8724 (t) cc_final: 0.8391 (p) REVERT: P 38 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7581 (mtp-110) REVERT: P 70 GLU cc_start: 0.7349 (tt0) cc_final: 0.7061 (mm-30) REVERT: P 100 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: P 112 ARG cc_start: 0.5752 (mtp85) cc_final: 0.5224 (mtm-85) REVERT: Q 86 SER cc_start: 0.7183 (OUTLIER) cc_final: 0.6929 (p) REVERT: Q 106 THR cc_start: 0.7611 (m) cc_final: 0.7409 (p) REVERT: Q 110 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6945 (mm-30) REVERT: R 18 GLN cc_start: 0.7522 (pt0) cc_final: 0.7094 (pt0) REVERT: R 60 LYS cc_start: 0.8575 (tppp) cc_final: 0.8052 (mptt) REVERT: R 95 ASP cc_start: 0.7474 (m-30) cc_final: 0.6919 (m-30) REVERT: S 3 THR cc_start: 0.8893 (m) cc_final: 0.8662 (m) REVERT: S 4 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8136 (tt) REVERT: S 92 ARG cc_start: 0.6396 (ptp90) cc_final: 0.6154 (ptm160) REVERT: T 66 LYS cc_start: 0.7284 (mtpt) cc_final: 0.7068 (mtmm) REVERT: U 21 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7731 (mtm110) REVERT: U 25 LYS cc_start: 0.7154 (mmmt) cc_final: 0.6470 (mtpm) REVERT: U 46 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7490 (ptpp) REVERT: U 59 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7674 (tp30) REVERT: U 78 LYS cc_start: 0.6991 (pttp) cc_final: 0.6321 (ptpp) REVERT: V 7 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7489 (tm-30) REVERT: V 17 SER cc_start: 0.8734 (t) cc_final: 0.8437 (m) REVERT: V 21 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6167 (mtp180) REVERT: V 62 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7491 (t) REVERT: V 71 LYS cc_start: 0.7801 (mtpp) cc_final: 0.7526 (mptm) REVERT: V 87 GLN cc_start: 0.8244 (mt0) cc_final: 0.8020 (mt0) REVERT: W 7 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7576 (mmm-85) REVERT: W 64 LYS cc_start: 0.7994 (tptm) cc_final: 0.7710 (tptm) REVERT: W 74 LYS cc_start: 0.7964 (mttt) cc_final: 0.7496 (mmmt) REVERT: W 79 GLU cc_start: 0.6749 (pm20) cc_final: 0.6533 (pm20) REVERT: X 36 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8180 (mtp85) REVERT: X 44 ARG cc_start: 0.7299 (ptt-90) cc_final: 0.7085 (ptt-90) REVERT: X 49 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6981 (ttt-90) REVERT: Y 17 GLU cc_start: 0.8413 (tp30) cc_final: 0.8127 (tp30) REVERT: Y 19 LEU cc_start: 0.7476 (mt) cc_final: 0.7189 (mt) REVERT: Y 21 LEU cc_start: 0.6756 (mt) cc_final: 0.6478 (mt) REVERT: Y 36 GLN cc_start: 0.6715 (mt0) cc_final: 0.5930 (mm-40) REVERT: 0 28 SER cc_start: 0.8626 (t) cc_final: 0.8213 (t) REVERT: 0 36 LYS cc_start: 0.7754 (mttt) cc_final: 0.7456 (mttt) REVERT: 0 49 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6972 (mmm160) REVERT: 1 49 LYS cc_start: 0.7695 (mttt) cc_final: 0.6837 (mmtm) REVERT: 2 25 LYS cc_start: 0.8441 (tppt) cc_final: 0.8190 (ttmp) REVERT: 2 41 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7242 (ttt-90) REVERT: 3 14 LYS cc_start: 0.8125 (mptt) cc_final: 0.7898 (mptt) REVERT: 4 37 GLN cc_start: 0.8034 (tt0) cc_final: 0.7691 (tm-30) REVERT: 5 34 THR cc_start: -0.0534 (OUTLIER) cc_final: -0.0770 (m) REVERT: 5 38 MET cc_start: 0.1084 (mtt) cc_final: 0.0845 (mtp) REVERT: 5 60 LEU cc_start: 0.0014 (OUTLIER) cc_final: -0.0221 (mp) REVERT: 6 11 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: 6 32 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5938 (mt) REVERT: b 8 MET cc_start: 0.5006 (pp-130) cc_final: 0.4365 (ppp) REVERT: b 21 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.4998 (p90) REVERT: b 27 LYS cc_start: 0.7354 (tttt) cc_final: 0.7146 (ttmt) REVERT: b 40 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7161 (tp) REVERT: b 41 ASN cc_start: 0.4908 (t0) cc_final: 0.4064 (m-40) REVERT: b 42 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7048 (tm) REVERT: b 108 GLN cc_start: 0.7606 (pt0) cc_final: 0.7311 (mm-40) REVERT: b 115 ASP cc_start: 0.6772 (t0) cc_final: 0.6371 (m-30) REVERT: b 116 LEU cc_start: 0.7185 (tt) cc_final: 0.6967 (tp) REVERT: b 193 ASP cc_start: 0.7485 (m-30) cc_final: 0.7263 (m-30) REVERT: c 17 TRP cc_start: 0.8341 (m-90) cc_final: 0.7689 (m-90) REVERT: c 71 ARG cc_start: 0.6359 (mtt90) cc_final: 0.5912 (mtm-85) REVERT: c 126 ARG cc_start: 0.7947 (mmt-90) cc_final: 0.7215 (mmm160) REVERT: c 134 LYS cc_start: 0.7096 (mttt) cc_final: 0.6766 (mtmt) REVERT: c 139 ASN cc_start: 0.7642 (t0) cc_final: 0.7383 (m110) REVERT: c 167 TYR cc_start: 0.7642 (m-80) cc_final: 0.7398 (m-80) REVERT: d 66 VAL cc_start: 0.8383 (t) cc_final: 0.8074 (m) REVERT: d 69 ARG cc_start: 0.7481 (tpp80) cc_final: 0.6942 (ttt180) REVERT: d 77 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7349 (tp30) REVERT: d 102 TYR cc_start: 0.7490 (t80) cc_final: 0.6879 (t80) REVERT: d 137 SER cc_start: 0.7799 (t) cc_final: 0.7287 (p) REVERT: d 142 VAL cc_start: 0.7291 (OUTLIER) cc_final: 0.7014 (t) REVERT: d 177 MET cc_start: 0.7019 (mmp) cc_final: 0.6101 (mpp) REVERT: d 178 GLU cc_start: 0.7236 (tt0) cc_final: 0.6786 (tp30) REVERT: d 181 PHE cc_start: 0.6687 (t80) cc_final: 0.6420 (t80) REVERT: d 182 LYS cc_start: 0.7001 (ttmt) cc_final: 0.6695 (mtmt) REVERT: d 184 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6716 (mtpt) REVERT: d 201 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6859 (mt-10) REVERT: e 12 GLU cc_start: 0.6530 (pt0) cc_final: 0.6193 (pm20) REVERT: e 99 SER cc_start: 0.7445 (t) cc_final: 0.7084 (p) REVERT: f 5 GLU cc_start: 0.7482 (tt0) cc_final: 0.7205 (tt0) REVERT: f 40 GLU cc_start: 0.6644 (tt0) cc_final: 0.5681 (mt-10) REVERT: f 90 MET cc_start: 0.8300 (mpp) cc_final: 0.8027 (mpp) REVERT: g 55 LYS cc_start: 0.6688 (ttmt) cc_final: 0.6375 (ttmp) REVERT: g 77 ARG cc_start: 0.4495 (ttt-90) cc_final: 0.2577 (ptt180) REVERT: g 89 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: g 100 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7467 (mtm) REVERT: g 125 ASP cc_start: 0.8308 (m-30) cc_final: 0.8099 (m-30) REVERT: g 145 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: h 3 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: h 30 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7089 (mtpp) REVERT: h 49 LYS cc_start: 0.8172 (mttp) cc_final: 0.7617 (mppt) REVERT: h 91 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7890 (mp) REVERT: h 93 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6084 (mmtp) REVERT: h 116 ARG cc_start: 0.7322 (mmm160) cc_final: 0.6897 (mtt90) REVERT: i 32 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6073 (mpp80) REVERT: i 45 MET cc_start: 0.5927 (pp-130) cc_final: 0.5625 (pp-130) REVERT: i 63 TYR cc_start: 0.7965 (t80) cc_final: 0.7618 (t80) REVERT: i 109 GLN cc_start: 0.8347 (mp10) cc_final: 0.8109 (mm-40) REVERT: j 10 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7565 (pp) REVERT: j 45 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6925 (tmt-80) REVERT: j 63 ASP cc_start: 0.8380 (m-30) cc_final: 0.8063 (m-30) REVERT: j 68 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7222 (mtt-85) REVERT: j 88 MET cc_start: 0.6681 (mmm) cc_final: 0.6473 (ttp) REVERT: k 17 ASP cc_start: 0.6979 (p0) cc_final: 0.6345 (m-30) REVERT: k 92 ARG cc_start: 0.8101 (ptt90) cc_final: 0.7538 (ptt180) REVERT: k 105 ARG cc_start: 0.6923 (tmm160) cc_final: 0.6564 (tpt-90) REVERT: k 108 ASN cc_start: 0.8461 (p0) cc_final: 0.7926 (p0) REVERT: k 113 THR cc_start: 0.7566 (m) cc_final: 0.7164 (p) REVERT: k 118 ASN cc_start: 0.7152 (t0) cc_final: 0.6742 (t0) REVERT: l 53 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6506 (mmp-170) REVERT: l 93 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7118 (ptp-170) REVERT: l 107 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7860 (mmpt) REVERT: m 26 LYS cc_start: 0.7760 (tttp) cc_final: 0.7492 (tptp) REVERT: m 38 ILE cc_start: 0.7712 (mm) cc_final: 0.7415 (mp) REVERT: m 77 LYS cc_start: 0.7707 (tttm) cc_final: 0.7187 (tptt) REVERT: m 80 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: m 92 ARG cc_start: 0.7539 (mmt180) cc_final: 0.7338 (mmt180) REVERT: n 3 GLN cc_start: 0.7494 (mm110) cc_final: 0.7202 (mm-40) REVERT: n 62 ASN cc_start: 0.8352 (t0) cc_final: 0.8147 (t0) REVERT: n 75 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8277 (mtm180) REVERT: n 90 ARG cc_start: 0.8538 (ttt90) cc_final: 0.8126 (ttp-170) REVERT: o 71 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6989 (ptp90) REVERT: p 1 MET cc_start: 0.6886 (ptp) cc_final: 0.6487 (ptt) REVERT: p 66 THR cc_start: 0.7988 (m) cc_final: 0.7780 (m) REVERT: q 24 ILE cc_start: 0.8542 (mt) cc_final: 0.8249 (mp) REVERT: q 80 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7612 (mptt) REVERT: r 29 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8393 (mtmt) REVERT: s 5 LYS cc_start: 0.4343 (OUTLIER) cc_final: 0.3585 (tmmt) REVERT: s 19 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7229 (mt-10) REVERT: s 31 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7126 (ttm-80) REVERT: s 36 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7697 (ptp-170) REVERT: s 42 ASN cc_start: 0.7942 (p0) cc_final: 0.7652 (t0) REVERT: s 43 MET cc_start: 0.8381 (mtp) cc_final: 0.8068 (mtp) REVERT: t 33 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (mttt) REVERT: t 47 GLN cc_start: 0.6961 (tt0) cc_final: 0.6478 (tm-30) REVERT: u 9 GLU cc_start: 0.3555 (OUTLIER) cc_final: 0.3022 (mp0) REVERT: u 19 LYS cc_start: 0.6056 (tttt) cc_final: 0.4793 (tptt) REVERT: z 9 LYS cc_start: 0.5863 (mttt) cc_final: 0.5575 (mtpp) REVERT: z 11 HIS cc_start: 0.7538 (t70) cc_final: 0.7013 (t70) REVERT: z 24 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7745 (ttmm) REVERT: z 54 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5905 (pm20) REVERT: z 68 GLU cc_start: 0.7228 (tt0) cc_final: 0.6303 (tp30) REVERT: z 151 MET cc_start: 0.6404 (tmm) cc_final: 0.5791 (mmp) REVERT: z 171 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6011 (mpt-90) REVERT: z 237 LYS cc_start: 0.7007 (mtmt) cc_final: 0.6672 (mtpp) REVERT: z 241 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7338 (mm-30) REVERT: z 243 GLU cc_start: 0.7981 (tt0) cc_final: 0.7306 (tt0) REVERT: z 266 ASP cc_start: 0.6151 (m-30) cc_final: 0.5097 (t70) REVERT: z 267 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6053 (pt0) REVERT: z 294 LYS cc_start: 0.7025 (ttpp) cc_final: 0.6604 (tmtt) REVERT: z 299 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.5951 (mtmm) REVERT: z 305 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5827 (tm-30) REVERT: z 368 MET cc_start: 0.4992 (ttp) cc_final: 0.4445 (ttp) REVERT: z 381 ARG cc_start: 0.4117 (ptm160) cc_final: 0.3750 (ppt170) outliers start: 425 outliers final: 180 residues processed: 1476 average time/residue: 2.2411 time to fit residues: 4778.3605 Evaluate side-chains 1363 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1120 time to evaluate : 6.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 LYS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 3 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 49 ARG Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 30 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 207 ARG Chi-restraints excluded: chain b residue 210 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 30 LYS Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 100 ASN Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 80 MET Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 115 ILE Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 39 GLN Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 81 ILE Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 24 LYS Chi-restraints excluded: chain z residue 50 ASP Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 150 GLU Chi-restraints excluded: chain z residue 171 ARG Chi-restraints excluded: chain z residue 188 ILE Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 264 LEU Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 299 LYS Chi-restraints excluded: chain z residue 302 THR Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 369 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 977 optimal weight: 8.9990 chunk 743 optimal weight: 30.0000 chunk 513 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 471 optimal weight: 1.9990 chunk 664 optimal weight: 20.0000 chunk 992 optimal weight: 10.0000 chunk 1050 optimal weight: 8.9990 chunk 518 optimal weight: 4.9990 chunk 940 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 GLN E 41 GLN E 165 HIS E 195 GLN F 36 ASN G 21 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 3 GLN M 60 GLN M 88 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 31 GLN T 15 HIS W 8 ASN Z 33 HIS 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 33 HIS 6 65 ASN c 138 GLN e 72 ASN e 77 ASN f 58 HIS f 68 GLN f 81 ASN g 67 ASN g 147 ASN h 37 ASN k 23 HIS ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 ASN o 34 GLN p 63 GLN z 11 HIS z 329 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.185 165478 Z= 0.493 Angle : 0.883 17.388 247206 Z= 0.460 Chirality : 0.048 0.406 31414 Planarity : 0.008 0.143 13504 Dihedral : 24.216 179.065 81871 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.76 % Favored : 90.59 % Rotamer: Outliers : 9.93 % Allowed : 23.21 % Favored : 66.86 % 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: -2.15 (0.10), residues: 6219 helix: -0.20 (0.11), residues: 1939 sheet: -1.76 (0.14), residues: 1222 loop : -2.10 (0.10), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP f 42 HIS 0.011 0.002 HIS C 24 PHE 0.037 0.003 PHE r 9 TYR 0.021 0.003 TYR p 17 ARG 0.012 0.001 ARG e 68 *********************** 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 1697 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 513 poor density : 1184 time to evaluate : 6.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8101 (mttt) cc_final: 0.7204 (mmtm) REVERT: C 110 LYS cc_start: 0.7666 (mttt) cc_final: 0.7293 (mtpp) REVERT: C 113 ASP cc_start: 0.7444 (m-30) cc_final: 0.7032 (m-30) REVERT: C 114 GLN cc_start: 0.7552 (tt0) cc_final: 0.7146 (mt0) REVERT: C 152 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: C 162 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: C 166 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7997 (ttp80) REVERT: C 179 GLU cc_start: 0.7950 (tt0) cc_final: 0.7551 (tt0) REVERT: C 180 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8441 (mmt) REVERT: C 198 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: C 235 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7735 (mm-30) REVERT: C 260 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8607 (ttmm) REVERT: C 266 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 269 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7777 (mtp-110) REVERT: D 99 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7931 (mt-10) REVERT: D 105 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7404 (mmpt) REVERT: D 168 GLU cc_start: 0.7688 (tt0) cc_final: 0.7227 (tm-30) REVERT: D 169 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7610 (ttp80) REVERT: D 183 GLU cc_start: 0.7750 (tt0) cc_final: 0.7542 (tt0) REVERT: E 27 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8192 (mt) REVERT: E 88 ARG cc_start: 0.7447 (mmm160) cc_final: 0.6959 (mtt-85) REVERT: F 25 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6619 (mpm) REVERT: F 26 GLN cc_start: 0.8102 (mt0) cc_final: 0.7866 (mt0) REVERT: F 31 GLU cc_start: 0.7650 (tt0) cc_final: 0.7374 (mp0) REVERT: F 51 ASN cc_start: 0.7084 (m-40) cc_final: 0.6375 (m110) REVERT: F 67 THR cc_start: 0.8463 (p) cc_final: 0.8089 (p) REVERT: F 91 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6316 (ptm160) REVERT: F 133 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7416 (pt0) REVERT: F 142 TYR cc_start: 0.6842 (t80) cc_final: 0.6156 (t80) REVERT: F 177 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5415 (mtm180) REVERT: G 5 LYS cc_start: 0.5836 (mtmm) cc_final: 0.4998 (pttp) REVERT: G 82 PHE cc_start: 0.7133 (m-80) cc_final: 0.6867 (m-80) REVERT: G 129 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: G 150 TYR cc_start: 0.7434 (m-80) cc_final: 0.7215 (m-80) REVERT: H 45 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6166 (pp20) REVERT: I 135 MET cc_start: 0.0543 (mtp) cc_final: -0.0013 (tpt) REVERT: J 31 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: J 99 ARG cc_start: 0.7664 (mmm160) cc_final: 0.7086 (mmm160) REVERT: K 45 GLU cc_start: 0.7930 (tt0) cc_final: 0.7609 (tt0) REVERT: K 53 LYS cc_start: 0.7817 (pttp) cc_final: 0.7163 (mmtt) REVERT: K 113 MET cc_start: 0.6601 (mmm) cc_final: 0.6345 (mpt) REVERT: L 41 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8083 (mpt180) REVERT: L 60 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7535 (ptt90) REVERT: L 80 SER cc_start: 0.8164 (t) cc_final: 0.7599 (p) REVERT: M 6 ARG cc_start: 0.7736 (ttt90) cc_final: 0.7063 (ttp-110) REVERT: M 20 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7267 (pp) REVERT: M 47 GLU cc_start: 0.7538 (tp30) cc_final: 0.7192 (tp30) REVERT: M 51 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7137 (mtp85) REVERT: M 73 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (mm) REVERT: M 75 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: M 81 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8366 (mtt-85) REVERT: M 127 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7393 (tptm) REVERT: M 133 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7842 (tttp) REVERT: M 136 MET cc_start: 0.5876 (tmm) cc_final: 0.5676 (tmm) REVERT: N 18 GLN cc_start: 0.8353 (tt0) cc_final: 0.7934 (tt0) REVERT: N 43 GLU cc_start: 0.8869 (tp30) cc_final: 0.8264 (tp30) REVERT: N 74 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: N 103 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.6731 (ttm-80) REVERT: N 114 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: O 108 ASP cc_start: 0.6767 (m-30) cc_final: 0.6488 (m-30) REVERT: O 115 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6594 (mp) REVERT: P 9 GLN cc_start: 0.7427 (tt0) cc_final: 0.7163 (mp-120) REVERT: P 29 VAL cc_start: 0.8746 (t) cc_final: 0.8358 (p) REVERT: P 38 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7613 (mtm-85) REVERT: P 70 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: P 100 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: P 112 ARG cc_start: 0.5809 (mtp85) cc_final: 0.5314 (mtm-85) REVERT: Q 106 THR cc_start: 0.7605 (m) cc_final: 0.7351 (p) REVERT: Q 110 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7001 (mm-30) REVERT: R 18 GLN cc_start: 0.7248 (pt0) cc_final: 0.6855 (pt0) REVERT: R 78 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.8222 (ttm-80) REVERT: S 19 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8262 (mp) REVERT: S 92 ARG cc_start: 0.6413 (ptp90) cc_final: 0.6100 (ptm160) REVERT: T 66 LYS cc_start: 0.7477 (mtpt) cc_final: 0.7181 (mtmm) REVERT: U 46 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7601 (ptpp) REVERT: U 59 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7595 (tp30) REVERT: U 78 LYS cc_start: 0.6953 (pttp) cc_final: 0.6353 (ptpp) REVERT: V 7 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7186 (tm-30) REVERT: V 21 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7608 (ttp-170) REVERT: W 7 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7528 (mmm-85) REVERT: W 35 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7588 (mtp85) REVERT: W 36 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: W 64 LYS cc_start: 0.8034 (tptm) cc_final: 0.7780 (tptm) REVERT: W 74 LYS cc_start: 0.7952 (mttt) cc_final: 0.7490 (mmmt) REVERT: W 79 GLU cc_start: 0.7021 (pm20) cc_final: 0.6771 (pm20) REVERT: X 36 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8278 (mtp85) REVERT: X 49 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7045 (ttt-90) REVERT: Y 17 GLU cc_start: 0.8311 (tp30) cc_final: 0.8028 (tp30) REVERT: Y 21 LEU cc_start: 0.7213 (mt) cc_final: 0.6956 (mt) REVERT: Y 31 GLN cc_start: 0.7084 (tt0) cc_final: 0.6867 (tt0) REVERT: Y 36 GLN cc_start: 0.6835 (mt0) cc_final: 0.5989 (mm-40) REVERT: 0 28 SER cc_start: 0.8603 (t) cc_final: 0.8127 (t) REVERT: 0 30 ASP cc_start: 0.7483 (t70) cc_final: 0.7148 (t0) REVERT: 0 36 LYS cc_start: 0.7899 (mttt) cc_final: 0.7552 (mtpt) REVERT: 0 49 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7085 (mmm160) REVERT: 1 39 ASP cc_start: 0.8412 (t70) cc_final: 0.8009 (t0) REVERT: 2 14 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8419 (mmm160) REVERT: 2 41 ARG cc_start: 0.8029 (mmt180) cc_final: 0.7380 (ttt-90) REVERT: 3 38 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7909 (tttt) REVERT: 5 38 MET cc_start: 0.0814 (mtt) cc_final: 0.0498 (mtp) REVERT: 6 32 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5988 (mt) REVERT: b 8 MET cc_start: 0.5028 (pp-130) cc_final: 0.4389 (ppp) REVERT: b 21 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5031 (p90) REVERT: b 46 VAL cc_start: 0.6377 (OUTLIER) cc_final: 0.6169 (m) REVERT: b 108 GLN cc_start: 0.7560 (pt0) cc_final: 0.7305 (mm-40) REVERT: b 115 ASP cc_start: 0.6800 (t0) cc_final: 0.6448 (m-30) REVERT: b 116 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6896 (tp) REVERT: b 125 PHE cc_start: 0.5228 (p90) cc_final: 0.4786 (m-10) REVERT: b 158 ASP cc_start: 0.7573 (t0) cc_final: 0.7362 (m-30) REVERT: c 71 ARG cc_start: 0.6231 (mtt90) cc_final: 0.5943 (mtm-85) REVERT: c 126 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7240 (mmm160) REVERT: c 134 LYS cc_start: 0.6924 (mttt) cc_final: 0.6588 (mttt) REVERT: c 167 TYR cc_start: 0.7792 (m-80) cc_final: 0.7538 (m-80) REVERT: d 66 VAL cc_start: 0.8431 (t) cc_final: 0.8154 (m) REVERT: d 69 ARG cc_start: 0.7654 (tpp80) cc_final: 0.7112 (ttt180) REVERT: d 77 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7298 (tp30) REVERT: d 102 TYR cc_start: 0.7609 (t80) cc_final: 0.7082 (t80) REVERT: d 137 SER cc_start: 0.7596 (t) cc_final: 0.6956 (p) REVERT: d 170 LEU cc_start: 0.7872 (pt) cc_final: 0.7594 (pt) REVERT: d 176 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6492 (pmtt) REVERT: d 177 MET cc_start: 0.7121 (mmp) cc_final: 0.6365 (mpp) REVERT: d 178 GLU cc_start: 0.7154 (tt0) cc_final: 0.6090 (pp20) REVERT: d 181 PHE cc_start: 0.6769 (t80) cc_final: 0.6553 (t80) REVERT: d 182 LYS cc_start: 0.7190 (ttmt) cc_final: 0.6949 (mttt) REVERT: d 184 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6614 (mtpt) REVERT: d 201 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6682 (mt-10) REVERT: e 99 SER cc_start: 0.7288 (t) cc_final: 0.7082 (p) REVERT: f 4 TYR cc_start: 0.7937 (m-80) cc_final: 0.7723 (m-80) REVERT: g 14 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6725 (p0) REVERT: g 74 VAL cc_start: 0.8208 (m) cc_final: 0.7786 (t) REVERT: g 77 ARG cc_start: 0.4669 (ttt-90) cc_final: 0.2525 (ptt180) REVERT: g 78 ARG cc_start: 0.0858 (OUTLIER) cc_final: 0.0321 (mtp-110) REVERT: g 89 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: g 109 LYS cc_start: 0.6915 (ptpt) cc_final: 0.6715 (ptpt) REVERT: g 125 ASP cc_start: 0.8312 (m-30) cc_final: 0.8055 (m-30) REVERT: h 91 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7856 (mp) REVERT: h 93 LYS cc_start: 0.7292 (ptpt) cc_final: 0.6037 (mmtp) REVERT: h 116 ARG cc_start: 0.7223 (mmm160) cc_final: 0.6750 (mtt90) REVERT: i 18 VAL cc_start: 0.8489 (t) cc_final: 0.8101 (m) REVERT: i 34 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6703 (pt) REVERT: i 35 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: i 99 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7215 (mptt) REVERT: i 109 GLN cc_start: 0.8108 (mp10) cc_final: 0.7749 (mm-40) REVERT: i 112 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7673 (ptt90) REVERT: j 10 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7405 (pp) REVERT: j 37 ARG cc_start: 0.5435 (mtp85) cc_final: 0.5109 (mtp85) REVERT: j 45 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6788 (tmt-80) REVERT: j 68 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7180 (mtt-85) REVERT: j 88 MET cc_start: 0.6557 (mmm) cc_final: 0.6294 (ttp) REVERT: k 84 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7833 (mtt) REVERT: k 92 ARG cc_start: 0.8273 (ptt90) cc_final: 0.7870 (ptt90) REVERT: k 105 ARG cc_start: 0.6980 (tmm160) cc_final: 0.6674 (tpt-90) REVERT: k 118 ASN cc_start: 0.7287 (t0) cc_final: 0.6817 (t0) REVERT: l 87 LYS cc_start: 0.8335 (tmtt) cc_final: 0.8097 (tptp) REVERT: l 93 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7209 (ptp-170) REVERT: l 107 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7881 (mmpt) REVERT: m 26 LYS cc_start: 0.7866 (tttp) cc_final: 0.7587 (tptp) REVERT: m 38 ILE cc_start: 0.7639 (mm) cc_final: 0.7327 (mp) REVERT: m 46 GLU cc_start: 0.8130 (tt0) cc_final: 0.7658 (mm-30) REVERT: m 63 VAL cc_start: 0.8099 (t) cc_final: 0.7825 (p) REVERT: m 99 GLN cc_start: 0.8485 (mt0) cc_final: 0.7691 (mt0) REVERT: n 3 GLN cc_start: 0.7717 (mm110) cc_final: 0.7308 (mm-40) REVERT: n 23 ARG cc_start: 0.6097 (ttm110) cc_final: 0.5683 (ttm170) REVERT: n 62 ASN cc_start: 0.8556 (t0) cc_final: 0.8160 (t0) REVERT: n 75 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8186 (ttm170) REVERT: o 71 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6557 (ptt-90) REVERT: o 76 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6403 (ptp-170) REVERT: q 8 GLN cc_start: 0.7311 (tt0) cc_final: 0.6573 (mm-40) REVERT: q 24 ILE cc_start: 0.8560 (mt) cc_final: 0.8268 (mp) REVERT: q 80 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7778 (mptt) REVERT: r 24 ASP cc_start: 0.7579 (p0) cc_final: 0.7245 (OUTLIER) REVERT: r 29 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8512 (mtmt) REVERT: r 42 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6848 (tmm-80) REVERT: r 47 ARG cc_start: 0.7635 (mmt180) cc_final: 0.6815 (mmt90) REVERT: s 15 LEU cc_start: 0.6717 (tp) cc_final: 0.6502 (tp) REVERT: s 19 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7308 (mt-10) REVERT: s 37 SER cc_start: 0.8381 (p) cc_final: 0.7923 (m) REVERT: s 42 ASN cc_start: 0.7851 (p0) cc_final: 0.7466 (t0) REVERT: s 43 MET cc_start: 0.8414 (mtp) cc_final: 0.8088 (mtp) REVERT: t 47 GLN cc_start: 0.6870 (tt0) cc_final: 0.6540 (tm-30) REVERT: u 4 LYS cc_start: 0.7414 (mttt) cc_final: 0.6852 (mppt) REVERT: u 19 LYS cc_start: 0.6171 (tttt) cc_final: 0.5026 (tptt) REVERT: u 32 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7266 (ttt90) REVERT: u 34 ARG cc_start: 0.7925 (tpt170) cc_final: 0.7495 (tpt90) REVERT: u 43 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6826 (pt0) REVERT: u 44 ARG cc_start: 0.6903 (mtt180) cc_final: 0.6413 (mtt90) REVERT: z 3 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6787 (mp0) REVERT: z 53 PRO cc_start: 0.6067 (Cg_exo) cc_final: 0.5805 (Cg_endo) REVERT: z 54 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5593 (pm20) REVERT: z 68 GLU cc_start: 0.7179 (tt0) cc_final: 0.6251 (tp30) REVERT: z 69 TYR cc_start: 0.7250 (p90) cc_final: 0.6990 (p90) REVERT: z 143 GLU cc_start: 0.7902 (tp30) cc_final: 0.7588 (tp30) REVERT: z 151 MET cc_start: 0.6344 (tmm) cc_final: 0.5803 (mmp) REVERT: z 228 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8358 (t) REVERT: z 232 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7503 (tm-30) REVERT: z 237 LYS cc_start: 0.7189 (mtmt) cc_final: 0.6803 (mtpp) REVERT: z 241 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7607 (mm-30) REVERT: z 243 GLU cc_start: 0.7943 (tt0) cc_final: 0.7284 (tt0) REVERT: z 267 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6668 (pt0) REVERT: z 279 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6711 (ttp-170) REVERT: z 282 LYS cc_start: 0.7719 (mttt) cc_final: 0.6873 (mptt) REVERT: z 305 GLU cc_start: 0.5964 (mt-10) cc_final: 0.5612 (tm-30) REVERT: z 381 ARG cc_start: 0.4747 (ptm160) cc_final: 0.4159 (ppt170) outliers start: 513 outliers final: 244 residues processed: 1492 average time/residue: 2.2554 time to fit residues: 4871.1913 Evaluate side-chains 1425 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1118 time to evaluate : 6.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 LYS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 49 ARG Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 30 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 3 residue 38 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 30 GLU Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 207 ARG Chi-restraints excluded: chain b residue 210 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 176 LYS Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain g residue 113 LYS Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 112 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 115 ILE Chi-restraints excluded: chain n residue 40 ASP Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 74 LEU Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 38 LYS Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 42 ARG Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 84 LYS Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 150 GLU Chi-restraints excluded: chain z residue 206 ILE Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 228 THR Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 251 GLN Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 302 THR Chi-restraints excluded: chain z residue 320 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 875 optimal weight: 4.9990 chunk 596 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 782 optimal weight: 7.9990 chunk 433 optimal weight: 0.7980 chunk 896 optimal weight: 3.9990 chunk 726 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 536 optimal weight: 2.9990 chunk 943 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN D 49 GLN E 165 HIS E 195 GLN F 36 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN O 19 GLN R 11 GLN S 61 ASN V 49 ASN 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 ASN e 121 ASN f 63 ASN f 81 ASN g 147 ASN h 37 ASN h 75 GLN j 35 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN p 63 GLN z 90 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 165478 Z= 0.260 Angle : 0.724 16.882 247206 Z= 0.389 Chirality : 0.039 0.412 31414 Planarity : 0.007 0.132 13504 Dihedral : 24.084 178.510 81866 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.01 % Favored : 91.38 % Rotamer: Outliers : 7.96 % Allowed : 26.81 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.10), residues: 6219 helix: 0.17 (0.12), residues: 1948 sheet: -1.55 (0.14), residues: 1179 loop : -1.94 (0.10), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 247 HIS 0.010 0.001 HIS C 24 PHE 0.027 0.002 PHE b 31 TYR 0.023 0.002 TYR i 6 ARG 0.009 0.001 ARG n 23 *********************** 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 1583 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 1172 time to evaluate : 6.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8138 (tttp) REVERT: C 6 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7139 (mtmt) REVERT: C 27 LYS cc_start: 0.8113 (mttt) cc_final: 0.7236 (mmtm) REVERT: C 110 LYS cc_start: 0.7685 (mttt) cc_final: 0.7265 (mtpp) REVERT: C 113 ASP cc_start: 0.7431 (m-30) cc_final: 0.6914 (m-30) REVERT: C 114 GLN cc_start: 0.7528 (tt0) cc_final: 0.7143 (mt0) REVERT: C 131 MET cc_start: 0.8696 (mtm) cc_final: 0.8131 (mtm) REVERT: C 166 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7937 (ttp80) REVERT: C 179 GLU cc_start: 0.7731 (tt0) cc_final: 0.7445 (tt0) REVERT: C 186 ASP cc_start: 0.7611 (t0) cc_final: 0.7322 (m-30) REVERT: C 198 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: C 202 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7848 (ptp-110) REVERT: C 260 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: C 269 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7636 (mtp-110) REVERT: D 168 GLU cc_start: 0.7524 (tt0) cc_final: 0.7154 (tt0) REVERT: D 169 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7665 (ttp80) REVERT: D 183 GLU cc_start: 0.7738 (tt0) cc_final: 0.7512 (tt0) REVERT: E 27 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7998 (mt) REVERT: E 88 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6933 (mtt-85) REVERT: F 2 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7131 (ttmt) REVERT: F 21 TYR cc_start: 0.7728 (m-80) cc_final: 0.7396 (m-80) REVERT: F 25 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6572 (mpm) REVERT: F 26 GLN cc_start: 0.7997 (mt0) cc_final: 0.7651 (mt0) REVERT: F 51 ASN cc_start: 0.6912 (m-40) cc_final: 0.6316 (m110) REVERT: F 67 THR cc_start: 0.8557 (p) cc_final: 0.8247 (p) REVERT: F 91 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6217 (ptm160) REVERT: F 133 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7280 (pt0) REVERT: F 142 TYR cc_start: 0.6878 (t80) cc_final: 0.6116 (t80) REVERT: F 162 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6617 (p0) REVERT: F 163 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7432 (tm-30) REVERT: F 177 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5219 (mtm180) REVERT: G 5 LYS cc_start: 0.5830 (mtmm) cc_final: 0.5071 (pttt) REVERT: G 132 LEU cc_start: 0.8608 (pt) cc_final: 0.8003 (mp) REVERT: G 150 TYR cc_start: 0.7355 (m-80) cc_final: 0.7101 (m-80) REVERT: H 37 VAL cc_start: 0.6474 (OUTLIER) cc_final: 0.6236 (p) REVERT: H 45 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6148 (pp20) REVERT: I 135 MET cc_start: 0.0461 (mtp) cc_final: -0.0087 (tpt) REVERT: J 28 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8617 (tp) REVERT: J 57 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8112 (pp) REVERT: J 85 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7766 (mttm) REVERT: J 99 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7119 (mmm160) REVERT: K 45 GLU cc_start: 0.7983 (tt0) cc_final: 0.7588 (tt0) REVERT: K 53 LYS cc_start: 0.7858 (pttp) cc_final: 0.7209 (mmtt) REVERT: K 100 PHE cc_start: 0.8238 (m-80) cc_final: 0.7847 (m-80) REVERT: K 113 MET cc_start: 0.6662 (mmm) cc_final: 0.6418 (mpt) REVERT: L 60 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7460 (ptt90) REVERT: L 80 SER cc_start: 0.8149 (t) cc_final: 0.7728 (p) REVERT: L 81 ASP cc_start: 0.7653 (m-30) cc_final: 0.7344 (m-30) REVERT: M 6 ARG cc_start: 0.7727 (ttt90) cc_final: 0.7068 (ttp-110) REVERT: M 20 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7259 (pp) REVERT: M 47 GLU cc_start: 0.7564 (tp30) cc_final: 0.7185 (tp30) REVERT: M 51 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7121 (mtp85) REVERT: M 75 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: M 81 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8314 (mtt-85) REVERT: M 127 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7245 (tptm) REVERT: M 133 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7785 (tttp) REVERT: N 18 GLN cc_start: 0.8293 (tt0) cc_final: 0.7891 (tt0) REVERT: N 74 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7131 (tp30) REVERT: O 16 ARG cc_start: 0.8041 (mpt180) cc_final: 0.7003 (mmm-85) REVERT: O 115 LEU cc_start: 0.7186 (tp) cc_final: 0.6756 (mp) REVERT: P 9 GLN cc_start: 0.7412 (tt0) cc_final: 0.7103 (mp-120) REVERT: P 29 VAL cc_start: 0.8806 (t) cc_final: 0.8406 (p) REVERT: P 70 GLU cc_start: 0.7468 (tt0) cc_final: 0.6840 (mm-30) REVERT: P 100 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7496 (mtp180) REVERT: P 112 ARG cc_start: 0.5501 (mtp85) cc_final: 0.5189 (mtm-85) REVERT: R 18 GLN cc_start: 0.7169 (pt0) cc_final: 0.6794 (pt0) REVERT: R 46 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: S 4 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8128 (tt) REVERT: S 19 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8346 (mp) REVERT: S 92 ARG cc_start: 0.6204 (ptp90) cc_final: 0.5990 (ptm160) REVERT: T 66 LYS cc_start: 0.7337 (mtpt) cc_final: 0.7134 (mtmm) REVERT: T 77 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7248 (mtt90) REVERT: U 6 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5312 (tmm-80) REVERT: U 8 ASP cc_start: 0.6476 (m-30) cc_final: 0.6236 (m-30) REVERT: U 17 ASP cc_start: 0.7526 (m-30) cc_final: 0.7047 (t0) REVERT: U 46 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7611 (ptpp) REVERT: U 59 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7572 (tp30) REVERT: U 78 LYS cc_start: 0.7016 (pttp) cc_final: 0.6368 (ptpp) REVERT: V 7 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7182 (tm-30) REVERT: V 21 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6297 (mtp180) REVERT: V 49 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7283 (m110) REVERT: V 51 GLN cc_start: 0.6593 (pp30) cc_final: 0.6027 (tm130) REVERT: V 71 LYS cc_start: 0.7929 (mptt) cc_final: 0.7707 (mptm) REVERT: W 7 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7605 (mmm-85) REVERT: W 35 ARG cc_start: 0.7767 (mtt-85) cc_final: 0.7233 (mtp85) REVERT: W 64 LYS cc_start: 0.7965 (tptm) cc_final: 0.7755 (tptm) REVERT: W 74 LYS cc_start: 0.7951 (mttt) cc_final: 0.7379 (mmtt) REVERT: W 79 GLU cc_start: 0.6712 (pm20) cc_final: 0.6420 (pm20) REVERT: X 36 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8208 (mtp85) REVERT: X 44 ARG cc_start: 0.7146 (ptt-90) cc_final: 0.6946 (ptt90) REVERT: Y 5 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6267 (mt-10) REVERT: Y 17 GLU cc_start: 0.8309 (tp30) cc_final: 0.8026 (tp30) REVERT: Y 19 LEU cc_start: 0.7372 (mt) cc_final: 0.7072 (mt) REVERT: Y 21 LEU cc_start: 0.6845 (mt) cc_final: 0.6600 (mt) REVERT: Y 36 GLN cc_start: 0.6887 (mt0) cc_final: 0.6012 (mm-40) REVERT: 0 28 SER cc_start: 0.8528 (t) cc_final: 0.8090 (t) REVERT: 0 30 ASP cc_start: 0.7655 (t70) cc_final: 0.7263 (t0) REVERT: 0 36 LYS cc_start: 0.7822 (mttt) cc_final: 0.7483 (mtpt) REVERT: 0 49 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6865 (mmm160) REVERT: 1 39 ASP cc_start: 0.8288 (t70) cc_final: 0.7924 (t0) REVERT: 2 41 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7305 (ptm-80) REVERT: 3 38 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7903 (tttt) REVERT: 4 17 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8195 (p) REVERT: 5 38 MET cc_start: 0.1100 (mtt) cc_final: 0.0822 (mtp) REVERT: 6 9 TYR cc_start: 0.6985 (t80) cc_final: 0.5834 (t80) REVERT: 6 20 ASN cc_start: 0.6561 (t0) cc_final: 0.5948 (p0) REVERT: 6 32 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5918 (mt) REVERT: b 8 MET cc_start: 0.4935 (pp-130) cc_final: 0.4298 (ppp) REVERT: b 21 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.5248 (p90) REVERT: b 23 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7699 (t0) REVERT: b 80 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6987 (tppt) REVERT: b 108 GLN cc_start: 0.7580 (pt0) cc_final: 0.7349 (mm-40) REVERT: b 115 ASP cc_start: 0.6750 (t0) cc_final: 0.6389 (m-30) REVERT: b 125 PHE cc_start: 0.5256 (p90) cc_final: 0.4910 (m-10) REVERT: b 158 ASP cc_start: 0.7763 (t0) cc_final: 0.7505 (m-30) REVERT: b 183 PHE cc_start: 0.6172 (p90) cc_final: 0.5149 (p90) REVERT: b 196 ASP cc_start: 0.7413 (m-30) cc_final: 0.6730 (p0) REVERT: b 202 ASN cc_start: 0.7487 (p0) cc_final: 0.6665 (t0) REVERT: c 71 ARG cc_start: 0.6282 (mtt90) cc_final: 0.5900 (mtm-85) REVERT: c 126 ARG cc_start: 0.7923 (mmt-90) cc_final: 0.7212 (mmm160) REVERT: c 134 LYS cc_start: 0.6838 (mttt) cc_final: 0.6512 (mmtt) REVERT: c 139 ASN cc_start: 0.7258 (m-40) cc_final: 0.6828 (m110) REVERT: d 66 VAL cc_start: 0.8444 (t) cc_final: 0.8182 (m) REVERT: d 69 ARG cc_start: 0.7519 (tpp80) cc_final: 0.7054 (ttt180) REVERT: d 77 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7305 (tp30) REVERT: d 102 TYR cc_start: 0.7530 (t80) cc_final: 0.6990 (t80) REVERT: d 153 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.4897 (ptm160) REVERT: d 165 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: d 170 LEU cc_start: 0.7873 (pt) cc_final: 0.7613 (pt) REVERT: d 176 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6260 (pmtt) REVERT: d 177 MET cc_start: 0.7120 (mmp) cc_final: 0.6363 (mpp) REVERT: d 178 GLU cc_start: 0.7198 (tt0) cc_final: 0.6098 (pp20) REVERT: d 181 PHE cc_start: 0.6670 (t80) cc_final: 0.6342 (t80) REVERT: d 182 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6898 (mttt) REVERT: d 184 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6662 (mtpt) REVERT: d 201 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6662 (mt-10) REVERT: e 99 SER cc_start: 0.7155 (t) cc_final: 0.6825 (p) REVERT: g 39 GLU cc_start: 0.7470 (pt0) cc_final: 0.7029 (pp20) REVERT: g 74 VAL cc_start: 0.8311 (m) cc_final: 0.7976 (t) REVERT: g 77 ARG cc_start: 0.4512 (ttt-90) cc_final: 0.2815 (ptt180) REVERT: g 78 ARG cc_start: 0.0865 (OUTLIER) cc_final: -0.0093 (mmp80) REVERT: g 89 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: g 125 ASP cc_start: 0.8265 (m-30) cc_final: 0.8004 (m-30) REVERT: h 91 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7801 (mp) REVERT: h 93 LYS cc_start: 0.7207 (ptpt) cc_final: 0.5905 (mmtp) REVERT: h 104 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8447 (t) REVERT: h 116 ARG cc_start: 0.7231 (mmm160) cc_final: 0.6676 (mtt90) REVERT: i 4 GLN cc_start: 0.6408 (tt0) cc_final: 0.5817 (pm20) REVERT: i 6 TYR cc_start: 0.6651 (t80) cc_final: 0.6391 (t80) REVERT: i 18 VAL cc_start: 0.8365 (t) cc_final: 0.8051 (m) REVERT: i 34 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6707 (pt) REVERT: i 35 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: i 64 ILE cc_start: 0.8335 (mt) cc_final: 0.8090 (pt) REVERT: i 87 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6446 (ptm) REVERT: i 99 LYS cc_start: 0.7719 (ttpt) cc_final: 0.7242 (mmtm) REVERT: i 109 GLN cc_start: 0.8284 (mp10) cc_final: 0.8019 (mm-40) REVERT: j 10 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7435 (pp) REVERT: j 37 ARG cc_start: 0.5385 (mtp85) cc_final: 0.5069 (mtp85) REVERT: j 45 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7007 (tmt-80) REVERT: j 68 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7044 (mtt-85) REVERT: j 88 MET cc_start: 0.6486 (mmm) cc_final: 0.6283 (ttp) REVERT: k 17 ASP cc_start: 0.6876 (p0) cc_final: 0.6018 (m-30) REVERT: k 36 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7284 (tpt170) REVERT: k 84 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7569 (mtp) REVERT: k 92 ARG cc_start: 0.8301 (ptt90) cc_final: 0.7878 (ptt90) REVERT: k 105 ARG cc_start: 0.6846 (tmm160) cc_final: 0.6603 (tpt-90) REVERT: l 53 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6506 (tpt170) REVERT: l 87 LYS cc_start: 0.8268 (tmtt) cc_final: 0.8000 (tptp) REVERT: l 89 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7763 (mt) REVERT: l 93 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7108 (ptp-170) REVERT: l 107 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7830 (mmpt) REVERT: m 26 LYS cc_start: 0.7837 (tttp) cc_final: 0.7494 (tptp) REVERT: m 46 GLU cc_start: 0.8148 (tt0) cc_final: 0.7714 (mm-30) REVERT: m 77 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7057 (tptt) REVERT: m 92 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7341 (mmt180) REVERT: m 99 GLN cc_start: 0.8530 (mt0) cc_final: 0.7783 (mt0) REVERT: n 3 GLN cc_start: 0.7629 (mm110) cc_final: 0.7295 (mm-40) REVERT: n 62 ASN cc_start: 0.8419 (t0) cc_final: 0.8063 (t0) REVERT: n 75 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8366 (mtm180) REVERT: o 71 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7013 (ptp90) REVERT: p 59 HIS cc_start: 0.6936 (t-90) cc_final: 0.6285 (t70) REVERT: p 63 GLN cc_start: 0.6431 (mt0) cc_final: 0.6200 (mt0) REVERT: q 24 ILE cc_start: 0.8584 (mt) cc_final: 0.8361 (mp) REVERT: q 26 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.7156 (ttp80) REVERT: q 62 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: q 80 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7529 (mptt) REVERT: r 11 ARG cc_start: 0.3660 (ptp90) cc_final: 0.3098 (tpm170) REVERT: r 29 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8493 (mtmt) REVERT: r 42 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6814 (tmm-80) REVERT: r 47 ARG cc_start: 0.7623 (mmt180) cc_final: 0.6047 (mtt-85) REVERT: s 15 LEU cc_start: 0.6837 (tp) cc_final: 0.6584 (tp) REVERT: s 19 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7306 (mt-10) REVERT: s 37 SER cc_start: 0.8365 (p) cc_final: 0.8060 (m) REVERT: s 42 ASN cc_start: 0.7866 (p0) cc_final: 0.7445 (t0) REVERT: s 43 MET cc_start: 0.8276 (mtp) cc_final: 0.7912 (mtm) REVERT: t 47 GLN cc_start: 0.6956 (tt0) cc_final: 0.6476 (tm-30) REVERT: u 19 LYS cc_start: 0.6166 (tttt) cc_final: 0.4899 (tptt) REVERT: u 32 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7084 (ttt90) REVERT: u 34 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7302 (tpt90) REVERT: z 3 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6834 (mp0) REVERT: z 24 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7790 (mtmm) REVERT: z 26 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7777 (p) REVERT: z 53 PRO cc_start: 0.5948 (Cg_exo) cc_final: 0.5698 (Cg_endo) REVERT: z 54 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5768 (pm20) REVERT: z 69 TYR cc_start: 0.7221 (p90) cc_final: 0.6996 (p90) REVERT: z 91 MET cc_start: 0.7921 (tmt) cc_final: 0.7650 (tmt) REVERT: z 99 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.6115 (m-30) REVERT: z 143 GLU cc_start: 0.7924 (tp30) cc_final: 0.7605 (tp30) REVERT: z 148 LEU cc_start: 0.5539 (tp) cc_final: 0.5135 (pp) REVERT: z 150 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5383 (tt0) REVERT: z 151 MET cc_start: 0.6412 (tmm) cc_final: 0.5795 (mmp) REVERT: z 236 ILE cc_start: 0.7459 (mt) cc_final: 0.7248 (mt) REVERT: z 237 LYS cc_start: 0.7174 (mtmt) cc_final: 0.6866 (mtpp) REVERT: z 241 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7258 (mm-30) REVERT: z 243 GLU cc_start: 0.7982 (tt0) cc_final: 0.7344 (tt0) REVERT: z 267 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6536 (pt0) REVERT: z 282 LYS cc_start: 0.7598 (mttt) cc_final: 0.6796 (mptt) REVERT: z 305 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5560 (tm-30) REVERT: z 358 MET cc_start: 0.4872 (OUTLIER) cc_final: 0.4536 (ptp) REVERT: z 381 ARG cc_start: 0.5114 (ptm160) cc_final: 0.4516 (ppt170) outliers start: 411 outliers final: 208 residues processed: 1408 average time/residue: 2.2759 time to fit residues: 4603.0877 Evaluate side-chains 1398 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1122 time to evaluate : 6.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 30 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 3 residue 38 LYS Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 45 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 207 ARG Chi-restraints excluded: chain b residue 210 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 128 MET Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 165 GLU Chi-restraints excluded: chain d residue 176 LYS Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 86 ARG 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 89 GLU Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 87 MET Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 115 ILE Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 42 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain z residue 24 LYS Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 54 GLU Chi-restraints excluded: chain z residue 99 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 150 GLU Chi-restraints excluded: chain z residue 165 ASP Chi-restraints excluded: chain z residue 178 LEU Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 251 GLN Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 358 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 353 optimal weight: 0.8980 chunk 946 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 616 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 1051 optimal weight: 0.8980 chunk 873 optimal weight: 7.9990 chunk 486 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 552 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS E 195 GLN G 127 GLN G 138 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN M 88 ASN P 40 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS U 98 ASN 0 4 GLN 0 5 ASN 0 41 HIS ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 102 ASN b 176 ASN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN g 67 ASN h 37 ASN h 75 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN k 39 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN p 40 ASN t 60 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 165478 Z= 0.148 Angle : 0.656 16.662 247206 Z= 0.357 Chirality : 0.034 0.510 31414 Planarity : 0.007 0.125 13504 Dihedral : 23.918 179.747 81862 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.20 % Favored : 92.20 % Rotamer: Outliers : 6.47 % Allowed : 28.94 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.10), residues: 6219 helix: 0.63 (0.12), residues: 1933 sheet: -1.37 (0.14), residues: 1178 loop : -1.79 (0.10), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.009 0.001 HIS E 165 PHE 0.024 0.001 PHE b 31 TYR 0.027 0.001 TYR 6 9 ARG 0.012 0.001 ARG u 33 *********************** 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 1513 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1179 time to evaluate : 6.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8020 (tppt) REVERT: C 27 LYS cc_start: 0.7964 (mttt) cc_final: 0.6942 (mmtm) REVERT: C 110 LYS cc_start: 0.7766 (mttt) cc_final: 0.7325 (mtpp) REVERT: C 113 ASP cc_start: 0.7515 (m-30) cc_final: 0.6889 (m-30) REVERT: C 114 GLN cc_start: 0.7448 (tt0) cc_final: 0.7103 (mt0) REVERT: C 159 THR cc_start: 0.9176 (m) cc_final: 0.8913 (p) REVERT: C 179 GLU cc_start: 0.7575 (tt0) cc_final: 0.7353 (tt0) REVERT: C 184 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: C 186 ASP cc_start: 0.7689 (t0) cc_final: 0.7353 (m-30) REVERT: C 198 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: C 202 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7632 (ptp-110) REVERT: C 260 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8434 (ttmm) REVERT: C 269 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7618 (mtp-110) REVERT: D 168 GLU cc_start: 0.7477 (tt0) cc_final: 0.7139 (tt0) REVERT: D 169 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7513 (ttp80) REVERT: D 186 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7655 (mp) REVERT: E 27 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7858 (mt) REVERT: E 88 ARG cc_start: 0.7315 (mmm160) cc_final: 0.6834 (mtt-85) REVERT: F 25 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6540 (mpm) REVERT: F 26 GLN cc_start: 0.8102 (mt0) cc_final: 0.7766 (mt0) REVERT: F 31 GLU cc_start: 0.7558 (mp0) cc_final: 0.7205 (mm-30) REVERT: F 51 ASN cc_start: 0.6972 (m-40) cc_final: 0.6428 (m110) REVERT: F 67 THR cc_start: 0.8681 (p) cc_final: 0.8429 (p) REVERT: F 71 LYS cc_start: 0.7328 (mtmt) cc_final: 0.7127 (ptmt) REVERT: F 129 MET cc_start: 0.7514 (ttt) cc_final: 0.7277 (ttp) REVERT: F 132 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7409 (mmm-85) REVERT: F 133 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7268 (pt0) REVERT: G 5 LYS cc_start: 0.5459 (mtmm) cc_final: 0.5043 (ptpp) REVERT: G 98 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7505 (tppp) REVERT: H 33 GLN cc_start: 0.7061 (mt0) cc_final: 0.6802 (mt0) REVERT: I 116 MET cc_start: -0.1036 (ttm) cc_final: -0.1282 (ttm) REVERT: I 135 MET cc_start: 0.0198 (mtp) cc_final: -0.0207 (tpt) REVERT: J 1 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6723 (pp-130) REVERT: K 45 GLU cc_start: 0.7877 (tt0) cc_final: 0.7525 (tt0) REVERT: K 53 LYS cc_start: 0.7860 (pttp) cc_final: 0.7168 (mmtt) REVERT: K 100 PHE cc_start: 0.8302 (m-80) cc_final: 0.7813 (m-80) REVERT: K 108 ARG cc_start: 0.6973 (ttm110) cc_final: 0.6704 (mtm110) REVERT: L 80 SER cc_start: 0.7989 (t) cc_final: 0.7532 (p) REVERT: L 81 ASP cc_start: 0.7739 (m-30) cc_final: 0.7439 (m-30) REVERT: M 6 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7187 (ttp-110) REVERT: M 20 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7056 (pp) REVERT: M 47 GLU cc_start: 0.7547 (tp30) cc_final: 0.7040 (tp30) REVERT: M 55 ARG cc_start: 0.6702 (ptp-110) cc_final: 0.6358 (ttp-110) REVERT: M 75 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: M 81 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8214 (mtt-85) REVERT: M 127 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7274 (tptm) REVERT: M 133 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7765 (tttp) REVERT: N 18 GLN cc_start: 0.8270 (tt0) cc_final: 0.7932 (tt0) REVERT: N 74 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: N 114 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: O 16 ARG cc_start: 0.7992 (mpt180) cc_final: 0.7045 (mmm-85) REVERT: O 115 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6685 (mp) REVERT: P 23 ASP cc_start: 0.7414 (m-30) cc_final: 0.7201 (m-30) REVERT: P 29 VAL cc_start: 0.8853 (t) cc_final: 0.8485 (p) REVERT: P 70 GLU cc_start: 0.7306 (tt0) cc_final: 0.6720 (mm-30) REVERT: P 100 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7490 (mtp180) REVERT: P 112 ARG cc_start: 0.5225 (mtp85) cc_final: 0.4778 (mtm-85) REVERT: Q 86 SER cc_start: 0.7271 (OUTLIER) cc_final: 0.6946 (p) REVERT: R 46 GLU cc_start: 0.7243 (mp0) cc_final: 0.6989 (pm20) REVERT: S 3 THR cc_start: 0.8847 (m) cc_final: 0.8465 (m) REVERT: S 92 ARG cc_start: 0.6259 (ptp90) cc_final: 0.5910 (ptm160) REVERT: U 46 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7633 (ptpp) REVERT: U 59 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7734 (tp30) REVERT: U 78 LYS cc_start: 0.7112 (pttp) cc_final: 0.6510 (ptpp) REVERT: U 98 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7516 (OUTLIER) REVERT: U 99 SER cc_start: 0.7507 (m) cc_final: 0.7185 (p) REVERT: V 7 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7417 (tm-30) REVERT: V 21 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6041 (mtp180) REVERT: V 51 GLN cc_start: 0.6649 (pp30) cc_final: 0.6179 (pm20) REVERT: V 71 LYS cc_start: 0.7860 (mptt) cc_final: 0.7614 (mptm) REVERT: W 64 LYS cc_start: 0.8024 (tptm) cc_final: 0.7768 (tptm) REVERT: W 74 LYS cc_start: 0.7909 (mttt) cc_final: 0.7373 (mmtt) REVERT: Y 5 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6187 (mt-10) REVERT: Y 17 GLU cc_start: 0.8264 (tp30) cc_final: 0.8019 (tp30) REVERT: Y 19 LEU cc_start: 0.7554 (mt) cc_final: 0.7178 (mt) REVERT: Y 21 LEU cc_start: 0.6688 (mt) cc_final: 0.6429 (mt) REVERT: Y 36 GLN cc_start: 0.6688 (mt0) cc_final: 0.5876 (mm-40) REVERT: 0 28 SER cc_start: 0.8488 (t) cc_final: 0.8059 (t) REVERT: 0 36 LYS cc_start: 0.7691 (mttt) cc_final: 0.7366 (mttt) REVERT: 2 41 ARG cc_start: 0.7804 (mmt180) cc_final: 0.7263 (ptm-80) REVERT: 3 38 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7820 (tttm) REVERT: 4 37 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7458 (tm-30) REVERT: 5 1 MET cc_start: 0.1660 (OUTLIER) cc_final: 0.0186 (pp-130) REVERT: 5 38 MET cc_start: 0.1090 (mtt) cc_final: 0.0820 (mtp) REVERT: 6 20 ASN cc_start: 0.6159 (t0) cc_final: 0.5752 (p0) REVERT: b 8 MET cc_start: 0.4964 (pp-130) cc_final: 0.4397 (ppp) REVERT: b 21 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.5429 (p90) REVERT: b 23 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7579 (t0) REVERT: b 115 ASP cc_start: 0.6803 (t0) cc_final: 0.6451 (m-30) REVERT: b 116 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7127 (tp) REVERT: b 125 PHE cc_start: 0.5335 (p90) cc_final: 0.4689 (m-10) REVERT: b 136 ARG cc_start: 0.6527 (ttm170) cc_final: 0.5787 (ttm110) REVERT: b 158 ASP cc_start: 0.7667 (t0) cc_final: 0.7412 (m-30) REVERT: b 183 PHE cc_start: 0.5783 (p90) cc_final: 0.4883 (p90) REVERT: b 196 ASP cc_start: 0.7487 (m-30) cc_final: 0.6764 (p0) REVERT: c 71 ARG cc_start: 0.6348 (mtt90) cc_final: 0.5976 (mtm-85) REVERT: c 99 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.4677 (tm-30) REVERT: c 126 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7213 (mmm160) REVERT: c 134 LYS cc_start: 0.6836 (mttt) cc_final: 0.6412 (mmtt) REVERT: c 139 ASN cc_start: 0.7361 (m-40) cc_final: 0.6983 (m110) REVERT: d 66 VAL cc_start: 0.8303 (t) cc_final: 0.8065 (m) REVERT: d 69 ARG cc_start: 0.7439 (tpp80) cc_final: 0.6991 (ttt180) REVERT: d 71 PHE cc_start: 0.8857 (t80) cc_final: 0.8636 (t80) REVERT: d 76 LYS cc_start: 0.8322 (mttm) cc_final: 0.8016 (mttm) REVERT: d 77 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7282 (tp30) REVERT: d 102 TYR cc_start: 0.7487 (t80) cc_final: 0.6918 (t80) REVERT: d 114 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7692 (ttt180) REVERT: d 127 ARG cc_start: 0.6188 (mtp85) cc_final: 0.5566 (mtp-110) REVERT: d 153 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.4955 (ptm160) REVERT: d 165 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: d 177 MET cc_start: 0.7185 (mmp) cc_final: 0.6368 (mpp) REVERT: d 178 GLU cc_start: 0.7032 (tt0) cc_final: 0.6043 (pp20) REVERT: d 181 PHE cc_start: 0.6606 (t80) cc_final: 0.6380 (t80) REVERT: d 182 LYS cc_start: 0.7092 (ttmt) cc_final: 0.6831 (mttt) REVERT: d 184 LYS cc_start: 0.6977 (tttp) cc_final: 0.6690 (mtpt) REVERT: d 201 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6565 (mt-10) REVERT: e 13 LYS cc_start: 0.7997 (ptmt) cc_final: 0.7226 (ptpt) REVERT: g 74 VAL cc_start: 0.8338 (m) cc_final: 0.8051 (t) REVERT: g 77 ARG cc_start: 0.4415 (ttt-90) cc_final: 0.2875 (ptt180) REVERT: g 78 ARG cc_start: 0.0943 (OUTLIER) cc_final: 0.0063 (mmp80) REVERT: g 95 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6731 (mtp180) REVERT: g 125 ASP cc_start: 0.8148 (m-30) cc_final: 0.7851 (m-30) REVERT: h 93 LYS cc_start: 0.7101 (ptpt) cc_final: 0.5835 (mmtp) REVERT: h 104 SER cc_start: 0.8838 (m) cc_final: 0.8517 (t) REVERT: h 116 ARG cc_start: 0.7237 (mmm160) cc_final: 0.6820 (mtt-85) REVERT: i 4 GLN cc_start: 0.6377 (tt0) cc_final: 0.5658 (pm20) REVERT: i 32 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5979 (mtp85) REVERT: i 34 LEU cc_start: 0.7277 (tm) cc_final: 0.6719 (pt) REVERT: i 46 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7209 (t) REVERT: i 87 MET cc_start: 0.6703 (ptp) cc_final: 0.6309 (ptm) REVERT: i 99 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7398 (mmtm) REVERT: i 109 GLN cc_start: 0.8281 (mp10) cc_final: 0.8078 (mm-40) REVERT: j 37 ARG cc_start: 0.5191 (mtp85) cc_final: 0.4963 (mtp85) REVERT: j 62 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6945 (mtt180) REVERT: j 68 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6959 (mtt-85) REVERT: j 88 MET cc_start: 0.6482 (mmm) cc_final: 0.6249 (ttp) REVERT: k 17 ASP cc_start: 0.6871 (p0) cc_final: 0.6122 (m-30) REVERT: k 26 PHE cc_start: 0.8348 (m-80) cc_final: 0.7716 (m-80) REVERT: k 36 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.7321 (tpt170) REVERT: k 84 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7556 (mtm) REVERT: k 92 ARG cc_start: 0.8369 (ptt90) cc_final: 0.7975 (ptt-90) REVERT: k 105 ARG cc_start: 0.6799 (tmm160) cc_final: 0.6575 (tpt-90) REVERT: k 108 ASN cc_start: 0.8337 (p0) cc_final: 0.7785 (p0) REVERT: k 110 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7737 (t) REVERT: l 53 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6496 (tpt170) REVERT: l 87 LYS cc_start: 0.8240 (tmtt) cc_final: 0.8002 (tptp) REVERT: l 89 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7711 (mt) REVERT: l 107 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7832 (mmpt) REVERT: m 26 LYS cc_start: 0.7815 (tttp) cc_final: 0.7447 (tptp) REVERT: m 46 GLU cc_start: 0.8108 (tt0) cc_final: 0.7606 (mm-30) REVERT: m 77 LYS cc_start: 0.8060 (ttpp) cc_final: 0.6994 (tptt) REVERT: m 79 LEU cc_start: 0.7962 (mt) cc_final: 0.7720 (mp) REVERT: m 80 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: m 92 ARG cc_start: 0.7702 (mmt180) cc_final: 0.7417 (mmt180) REVERT: m 99 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: n 3 GLN cc_start: 0.7516 (mm110) cc_final: 0.7278 (mm-40) REVERT: n 39 GLU cc_start: 0.8260 (tt0) cc_final: 0.7990 (tt0) REVERT: n 62 ASN cc_start: 0.8243 (t0) cc_final: 0.7980 (t0) REVERT: n 67 THR cc_start: 0.8732 (p) cc_final: 0.8484 (m) REVERT: o 71 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6997 (ptp90) REVERT: p 1 MET cc_start: 0.6827 (ptp) cc_final: 0.6609 (ptt) REVERT: p 59 HIS cc_start: 0.7318 (t-90) cc_final: 0.6647 (t70) REVERT: q 24 ILE cc_start: 0.8531 (mt) cc_final: 0.8324 (mp) REVERT: q 26 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.7078 (ttp80) REVERT: r 11 ARG cc_start: 0.3461 (ptp90) cc_final: 0.3168 (tpp-160) REVERT: r 29 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8468 (mtmt) REVERT: r 47 ARG cc_start: 0.7616 (mmt180) cc_final: 0.6079 (mtt-85) REVERT: s 42 ASN cc_start: 0.7888 (p0) cc_final: 0.7401 (t0) REVERT: t 17 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7745 (ttp80) REVERT: t 47 GLN cc_start: 0.6966 (tt0) cc_final: 0.6330 (tm-30) REVERT: u 19 LYS cc_start: 0.6044 (tttt) cc_final: 0.4835 (tptt) REVERT: u 32 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7049 (ttt90) REVERT: z 3 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6880 (mp0) REVERT: z 24 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7643 (mtmm) REVERT: z 26 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7739 (p) REVERT: z 91 MET cc_start: 0.7928 (tmt) cc_final: 0.7591 (tmt) REVERT: z 143 GLU cc_start: 0.7981 (tp30) cc_final: 0.7656 (tp30) REVERT: z 148 LEU cc_start: 0.5574 (tp) cc_final: 0.5091 (pp) REVERT: z 150 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.5377 (tt0) REVERT: z 151 MET cc_start: 0.6468 (tmm) cc_final: 0.5820 (mmp) REVERT: z 232 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7510 (tm-30) REVERT: z 237 LYS cc_start: 0.7041 (mtmt) cc_final: 0.6679 (mtpp) REVERT: z 241 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7182 (mm-30) REVERT: z 243 GLU cc_start: 0.8047 (tt0) cc_final: 0.7413 (tt0) REVERT: z 266 ASP cc_start: 0.6272 (m-30) cc_final: 0.5153 (t70) REVERT: z 267 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6285 (pt0) REVERT: z 282 LYS cc_start: 0.7574 (mttt) cc_final: 0.6874 (mptt) REVERT: z 294 LYS cc_start: 0.7060 (ttpp) cc_final: 0.6626 (tmtt) REVERT: z 305 GLU cc_start: 0.5816 (mt-10) cc_final: 0.5450 (tm-30) REVERT: z 358 MET cc_start: 0.4906 (OUTLIER) cc_final: 0.4585 (ptp) REVERT: z 381 ARG cc_start: 0.5233 (ptm160) cc_final: 0.4616 (ppt170) outliers start: 334 outliers final: 142 residues processed: 1369 average time/residue: 2.2476 time to fit residues: 4454.6918 Evaluate side-chains 1300 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1114 time to evaluate : 6.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 3 residue 38 LYS Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 36 LYS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 165 GLU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 80 MET Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain z residue 24 LYS Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 71 THR Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 150 GLU Chi-restraints excluded: chain z residue 165 ASP Chi-restraints excluded: chain z residue 188 ILE Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 253 SER Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 354 ASP Chi-restraints excluded: chain z residue 358 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 1013 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 599 optimal weight: 0.0070 chunk 768 optimal weight: 10.0000 chunk 595 optimal weight: 0.5980 chunk 885 optimal weight: 0.7980 chunk 587 optimal weight: 3.9990 chunk 1047 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 20.0000 chunk 483 optimal weight: 0.0470 overall best weight: 1.0898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 HIS E 195 GLN F 36 ASN G 138 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN M 88 ASN P 40 GLN R 6 GLN S 31 GLN ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN b 176 ASN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN g 51 GLN g 67 ASN g 129 ASN h 37 ASN h 75 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 HIS o 27 GLN o 34 GLN s 68 HIS t 12 GLN t 20 ASN ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 165478 Z= 0.145 Angle : 0.639 16.633 247206 Z= 0.348 Chirality : 0.033 0.519 31414 Planarity : 0.006 0.126 13504 Dihedral : 23.818 179.976 81840 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.40 % Favored : 92.09 % Rotamer: Outliers : 5.50 % Allowed : 30.72 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.10), residues: 6219 helix: 0.79 (0.12), residues: 1938 sheet: -1.25 (0.14), residues: 1183 loop : -1.68 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP f 42 HIS 0.011 0.001 HIS E 165 PHE 0.024 0.001 PHE b 29 TYR 0.027 0.001 TYR F 21 ARG 0.013 0.000 ARG u 33 *********************** 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 1449 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1165 time to evaluate : 6.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8072 (tptm) REVERT: C 27 LYS cc_start: 0.7963 (mttt) cc_final: 0.6957 (mmtm) REVERT: C 110 LYS cc_start: 0.7780 (mttt) cc_final: 0.7309 (mtpp) REVERT: C 113 ASP cc_start: 0.7503 (m-30) cc_final: 0.6916 (m-30) REVERT: C 114 GLN cc_start: 0.7496 (tt0) cc_final: 0.7069 (mt0) REVERT: C 159 THR cc_start: 0.9198 (m) cc_final: 0.8961 (p) REVERT: C 198 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: C 202 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7588 (ptp-110) REVERT: C 260 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8369 (ttmm) REVERT: C 269 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7594 (mtp-110) REVERT: D 168 GLU cc_start: 0.7487 (tt0) cc_final: 0.7206 (tt0) REVERT: D 169 ARG cc_start: 0.7782 (ttt-90) cc_final: 0.7454 (ttp80) REVERT: D 186 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7640 (mp) REVERT: E 27 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7801 (mt) REVERT: E 88 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6846 (mtt-85) REVERT: F 25 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6441 (mpm) REVERT: F 51 ASN cc_start: 0.6994 (m-40) cc_final: 0.6432 (m110) REVERT: F 67 THR cc_start: 0.8675 (p) cc_final: 0.8439 (p) REVERT: F 71 LYS cc_start: 0.7340 (mtmt) cc_final: 0.7132 (ptmt) REVERT: F 104 THR cc_start: 0.7550 (m) cc_final: 0.7277 (m) REVERT: F 129 MET cc_start: 0.7547 (ttt) cc_final: 0.7297 (ttp) REVERT: F 133 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7242 (pt0) REVERT: F 177 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5374 (mtm180) REVERT: G 5 LYS cc_start: 0.5476 (mtmm) cc_final: 0.5055 (ptpp) REVERT: G 98 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7505 (tppp) REVERT: G 129 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: G 152 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7496 (ptp-170) REVERT: H 5 LEU cc_start: 0.5658 (mt) cc_final: 0.5452 (mt) REVERT: H 33 GLN cc_start: 0.7070 (mt0) cc_final: 0.6782 (mt0) REVERT: I 116 MET cc_start: -0.1027 (ttm) cc_final: -0.1337 (ttm) REVERT: I 135 MET cc_start: 0.0243 (mtp) cc_final: -0.0162 (tpt) REVERT: K 45 GLU cc_start: 0.7951 (tt0) cc_final: 0.7593 (tt0) REVERT: K 53 LYS cc_start: 0.7868 (pttp) cc_final: 0.7164 (mmtt) REVERT: K 100 PHE cc_start: 0.8325 (m-80) cc_final: 0.7787 (m-80) REVERT: K 113 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6183 (ppp) REVERT: L 80 SER cc_start: 0.7993 (t) cc_final: 0.7559 (p) REVERT: L 81 ASP cc_start: 0.7767 (m-30) cc_final: 0.7510 (m-30) REVERT: L 126 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7922 (ttp-110) REVERT: M 6 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7184 (ttp-110) REVERT: M 20 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.6942 (pp) REVERT: M 47 GLU cc_start: 0.7622 (tp30) cc_final: 0.7090 (tp30) REVERT: M 55 ARG cc_start: 0.6676 (ptp-110) cc_final: 0.6423 (ttp-110) REVERT: M 75 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7571 (tp30) REVERT: M 81 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8201 (mtt-85) REVERT: M 105 MET cc_start: 0.8191 (ttp) cc_final: 0.7987 (ttp) REVERT: M 127 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7271 (tptm) REVERT: M 133 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7753 (tttp) REVERT: N 18 GLN cc_start: 0.8283 (tt0) cc_final: 0.7839 (tt0) REVERT: N 74 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: N 114 GLU cc_start: 0.8178 (pt0) cc_final: 0.7693 (pt0) REVERT: O 16 ARG cc_start: 0.7993 (mpt180) cc_final: 0.7068 (mmm-85) REVERT: O 115 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6657 (mp) REVERT: P 29 VAL cc_start: 0.8835 (t) cc_final: 0.8394 (p) REVERT: P 70 GLU cc_start: 0.7269 (tt0) cc_final: 0.6727 (mm-30) REVERT: P 100 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7488 (mtp180) REVERT: P 112 ARG cc_start: 0.5233 (mtp85) cc_final: 0.4783 (mtm-85) REVERT: Q 86 SER cc_start: 0.7292 (OUTLIER) cc_final: 0.6957 (p) REVERT: R 46 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: S 3 THR cc_start: 0.8884 (m) cc_final: 0.8579 (m) REVERT: S 37 THR cc_start: 0.8411 (m) cc_final: 0.7992 (p) REVERT: S 92 ARG cc_start: 0.6271 (ptp90) cc_final: 0.5939 (ptm160) REVERT: U 46 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7627 (ptpp) REVERT: U 59 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7614 (tp30) REVERT: U 78 LYS cc_start: 0.7150 (pttp) cc_final: 0.6507 (ptpp) REVERT: V 7 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7332 (tm-30) REVERT: V 21 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6041 (mtp180) REVERT: V 49 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7289 (m110) REVERT: V 51 GLN cc_start: 0.6483 (pp30) cc_final: 0.6009 (tm130) REVERT: V 71 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7618 (mptm) REVERT: W 64 LYS cc_start: 0.8042 (tptm) cc_final: 0.7822 (tptm) REVERT: W 74 LYS cc_start: 0.7895 (mttt) cc_final: 0.7371 (mmtt) REVERT: Y 5 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6274 (mt-10) REVERT: Y 17 GLU cc_start: 0.8311 (tp30) cc_final: 0.8038 (tp30) REVERT: Y 19 LEU cc_start: 0.7561 (mt) cc_final: 0.7192 (mt) REVERT: Y 21 LEU cc_start: 0.6595 (mt) cc_final: 0.6327 (mt) REVERT: Y 36 GLN cc_start: 0.6762 (mt0) cc_final: 0.5948 (mm-40) REVERT: 0 28 SER cc_start: 0.8571 (t) cc_final: 0.8123 (t) REVERT: 0 36 LYS cc_start: 0.7723 (mttt) cc_final: 0.7429 (mmmt) REVERT: 2 41 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7230 (ttt-90) REVERT: 3 38 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7829 (tttm) REVERT: 4 37 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7443 (tm-30) REVERT: 5 1 MET cc_start: 0.1841 (OUTLIER) cc_final: 0.0118 (pp-130) REVERT: 5 38 MET cc_start: 0.1005 (mtt) cc_final: 0.0752 (mtp) REVERT: 6 20 ASN cc_start: 0.6053 (t0) cc_final: 0.5665 (p0) REVERT: b 8 MET cc_start: 0.5082 (pp-130) cc_final: 0.4504 (ppp) REVERT: b 21 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.5516 (p90) REVERT: b 80 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7020 (tppt) REVERT: b 107 ARG cc_start: 0.7073 (ttp-170) cc_final: 0.6816 (mtm180) REVERT: b 115 ASP cc_start: 0.6819 (t0) cc_final: 0.6500 (m-30) REVERT: b 116 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7071 (tp) REVERT: b 125 PHE cc_start: 0.5332 (p90) cc_final: 0.4957 (m-10) REVERT: b 158 ASP cc_start: 0.7679 (t0) cc_final: 0.7429 (m-30) REVERT: b 183 PHE cc_start: 0.5791 (p90) cc_final: 0.4930 (p90) REVERT: b 196 ASP cc_start: 0.7395 (m-30) cc_final: 0.6596 (p0) REVERT: b 202 ASN cc_start: 0.7026 (p0) cc_final: 0.6024 (t0) REVERT: c 57 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: c 71 ARG cc_start: 0.6457 (mtt90) cc_final: 0.6078 (mtm-85) REVERT: c 126 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7257 (mmm160) REVERT: c 139 ASN cc_start: 0.7423 (m-40) cc_final: 0.7054 (m110) REVERT: d 7 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7049 (mttt) REVERT: d 66 VAL cc_start: 0.8291 (t) cc_final: 0.8028 (m) REVERT: d 69 ARG cc_start: 0.7342 (tpp80) cc_final: 0.6903 (ttt180) REVERT: d 76 LYS cc_start: 0.8317 (mttm) cc_final: 0.8006 (mttm) REVERT: d 77 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7231 (tp30) REVERT: d 102 TYR cc_start: 0.7452 (t80) cc_final: 0.6883 (t80) REVERT: d 109 THR cc_start: 0.8508 (m) cc_final: 0.8240 (p) REVERT: d 114 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7712 (ttt180) REVERT: d 127 ARG cc_start: 0.6252 (mtp85) cc_final: 0.5607 (mtp-110) REVERT: d 165 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: d 176 LYS cc_start: 0.6671 (pmtt) cc_final: 0.6199 (pmtt) REVERT: d 177 MET cc_start: 0.7154 (mmp) cc_final: 0.6292 (mpp) REVERT: d 178 GLU cc_start: 0.6979 (tt0) cc_final: 0.6077 (pp20) REVERT: d 181 PHE cc_start: 0.6603 (t80) cc_final: 0.6348 (t80) REVERT: d 182 LYS cc_start: 0.7011 (ttmt) cc_final: 0.6747 (mttt) REVERT: d 184 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6741 (mtpt) REVERT: d 187 ARG cc_start: 0.6228 (tmt-80) cc_final: 0.5956 (tpt90) REVERT: d 201 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6490 (mt-10) REVERT: e 121 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7613 (m110) REVERT: e 162 GLU cc_start: 0.7800 (tt0) cc_final: 0.7517 (tt0) REVERT: g 74 VAL cc_start: 0.8417 (m) cc_final: 0.8118 (t) REVERT: g 78 ARG cc_start: 0.0930 (OUTLIER) cc_final: -0.0099 (mmp80) REVERT: g 100 MET cc_start: 0.8118 (ptp) cc_final: 0.7895 (ptp) REVERT: g 113 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5789 (mmmt) REVERT: g 125 ASP cc_start: 0.8035 (m-30) cc_final: 0.7717 (m-30) REVERT: h 93 LYS cc_start: 0.7106 (ptpt) cc_final: 0.5835 (mmtp) REVERT: h 104 SER cc_start: 0.8667 (m) cc_final: 0.8451 (t) REVERT: h 116 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6714 (mtt-85) REVERT: i 4 GLN cc_start: 0.6571 (tt0) cc_final: 0.5800 (pm20) REVERT: i 32 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6137 (mtp85) REVERT: i 35 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: i 46 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7157 (t) REVERT: i 87 MET cc_start: 0.6612 (ptp) cc_final: 0.6176 (ptm) REVERT: j 37 ARG cc_start: 0.5118 (mtp85) cc_final: 0.4883 (mtp85) REVERT: j 62 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6910 (mtt180) REVERT: j 68 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6925 (mtt-85) REVERT: j 88 MET cc_start: 0.6473 (mmm) cc_final: 0.6223 (ttp) REVERT: k 17 ASP cc_start: 0.6851 (p0) cc_final: 0.6068 (m-30) REVERT: k 26 PHE cc_start: 0.8301 (m-80) cc_final: 0.7710 (m-80) REVERT: k 84 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (mtm) REVERT: k 92 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: k 105 ARG cc_start: 0.6799 (tmm160) cc_final: 0.6544 (tpt-90) REVERT: k 108 ASN cc_start: 0.8359 (p0) cc_final: 0.7871 (p0) REVERT: l 53 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6599 (tpt170) REVERT: l 55 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7215 (ptm160) REVERT: l 107 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7870 (mmpt) REVERT: m 26 LYS cc_start: 0.7781 (tttp) cc_final: 0.7409 (tptp) REVERT: m 46 GLU cc_start: 0.8082 (tt0) cc_final: 0.7664 (mm-30) REVERT: m 77 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7004 (tptt) REVERT: m 79 LEU cc_start: 0.7968 (mt) cc_final: 0.7745 (mp) REVERT: m 80 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8146 (mpp) REVERT: m 92 ARG cc_start: 0.7704 (mmt180) cc_final: 0.7429 (mmt180) REVERT: m 99 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: n 3 GLN cc_start: 0.7523 (mm110) cc_final: 0.7300 (mm-40) REVERT: n 39 GLU cc_start: 0.8238 (tt0) cc_final: 0.7976 (tt0) REVERT: n 62 ASN cc_start: 0.8224 (t0) cc_final: 0.7943 (t0) REVERT: n 67 THR cc_start: 0.8724 (p) cc_final: 0.8506 (m) REVERT: n 97 LYS cc_start: 0.8431 (pttt) cc_final: 0.8114 (pttp) REVERT: o 71 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6943 (ptp90) REVERT: p 1 MET cc_start: 0.6803 (ptp) cc_final: 0.6584 (ptt) REVERT: p 35 ARG cc_start: 0.8152 (ptm-80) cc_final: 0.7736 (ttt-90) REVERT: p 61 VAL cc_start: 0.8238 (t) cc_final: 0.7976 (m) REVERT: p 63 GLN cc_start: 0.6585 (mt0) cc_final: 0.6377 (mt0) REVERT: q 24 ILE cc_start: 0.8538 (mt) cc_final: 0.8326 (mp) REVERT: r 11 ARG cc_start: 0.3422 (ptp90) cc_final: 0.2925 (tpp-160) REVERT: r 29 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (mtmt) REVERT: r 47 ARG cc_start: 0.7503 (mmt180) cc_final: 0.6359 (ttp-170) REVERT: s 42 ASN cc_start: 0.7893 (p0) cc_final: 0.7420 (t0) REVERT: t 47 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: t 60 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7534 (mp10) REVERT: u 19 LYS cc_start: 0.5963 (tttt) cc_final: 0.4754 (tptt) REVERT: u 32 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7041 (ttt90) REVERT: z 3 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6918 (mp0) REVERT: z 26 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7740 (p) REVERT: z 68 GLU cc_start: 0.7207 (tt0) cc_final: 0.6455 (tp30) REVERT: z 91 MET cc_start: 0.7924 (tmt) cc_final: 0.7529 (tmt) REVERT: z 143 GLU cc_start: 0.7999 (tp30) cc_final: 0.7668 (tp30) REVERT: z 148 LEU cc_start: 0.5727 (tp) cc_final: 0.5242 (pp) REVERT: z 151 MET cc_start: 0.6459 (tmm) cc_final: 0.5822 (mmp) REVERT: z 194 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6763 (t80) REVERT: z 216 ASP cc_start: 0.6393 (t0) cc_final: 0.6186 (p0) REVERT: z 237 LYS cc_start: 0.7023 (mtmt) cc_final: 0.6654 (mtpp) REVERT: z 241 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7219 (mm-30) REVERT: z 243 GLU cc_start: 0.8066 (tt0) cc_final: 0.7453 (tt0) REVERT: z 259 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5845 (mt-10) REVERT: z 266 ASP cc_start: 0.6302 (m-30) cc_final: 0.5171 (t70) REVERT: z 267 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6224 (pt0) REVERT: z 282 LYS cc_start: 0.7530 (mttt) cc_final: 0.6860 (mptt) REVERT: z 294 LYS cc_start: 0.7113 (ttpp) cc_final: 0.6722 (tmtt) REVERT: z 298 ILE cc_start: 0.7687 (mm) cc_final: 0.7368 (mt) REVERT: z 305 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5596 (tm-30) REVERT: z 327 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6152 (mtm-85) REVERT: z 358 MET cc_start: 0.4778 (OUTLIER) cc_final: 0.4446 (ptp) REVERT: z 381 ARG cc_start: 0.5308 (ptm160) cc_final: 0.4616 (ppt170) outliers start: 284 outliers final: 140 residues processed: 1324 average time/residue: 2.2449 time to fit residues: 4324.9711 Evaluate side-chains 1292 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1102 time to evaluate : 6.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 3 residue 38 LYS Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 88 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 165 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 113 LYS Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 80 MET Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 47 GLN Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 71 THR Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 165 ASP Chi-restraints excluded: chain z residue 188 ILE Chi-restraints excluded: chain z residue 194 PHE Chi-restraints excluded: chain z residue 206 ILE Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 253 SER Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 358 MET 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: 30.0000 chunk 625 optimal weight: 50.0000 chunk 315 optimal weight: 0.2980 chunk 205 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 666 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 517 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 823 optimal weight: 5.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 127 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN L 104 GLN M 88 ASN N 73 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 31 GLN S 61 ASN U 98 ASN Z 19 HIS ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 102 ASN ** b 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 ASN d 58 GLN e 134 ASN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN g 67 ASN g 129 ASN h 37 ASN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN o 27 GLN o 34 GLN t 12 GLN t 19 HIS ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 165478 Z= 0.416 Angle : 0.806 17.875 247206 Z= 0.423 Chirality : 0.043 0.380 31414 Planarity : 0.008 0.140 13504 Dihedral : 23.954 177.883 81839 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.81 % Favored : 90.62 % Rotamer: Outliers : 6.58 % Allowed : 30.02 % Favored : 63.40 % 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: -1.59 (0.10), residues: 6219 helix: 0.21 (0.12), residues: 1981 sheet: -1.26 (0.14), residues: 1175 loop : -1.82 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 169 HIS 0.009 0.002 HIS E 165 PHE 0.029 0.002 PHE b 89 TYR 0.026 0.002 TYR i 6 ARG 0.014 0.001 ARG u 33 *********************** 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 1475 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1135 time to evaluate : 6.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7370 (mtmt) REVERT: C 27 LYS cc_start: 0.8104 (mttt) cc_final: 0.7198 (mmtm) REVERT: C 110 LYS cc_start: 0.7627 (mttt) cc_final: 0.7157 (mtpp) REVERT: C 113 ASP cc_start: 0.7426 (m-30) cc_final: 0.7025 (m-30) REVERT: C 114 GLN cc_start: 0.7490 (tt0) cc_final: 0.6966 (mt0) REVERT: C 131 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: C 179 GLU cc_start: 0.7835 (tt0) cc_final: 0.7511 (tt0) REVERT: C 198 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: C 202 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7973 (ptp-110) REVERT: C 260 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8634 (ttmm) REVERT: C 269 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7608 (mtp-110) REVERT: D 112 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8062 (t) REVERT: D 168 GLU cc_start: 0.7558 (tt0) cc_final: 0.7163 (tt0) REVERT: D 169 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7741 (ttp80) REVERT: D 183 GLU cc_start: 0.7723 (tt0) cc_final: 0.7482 (tt0) REVERT: E 27 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8113 (mt) REVERT: E 88 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6843 (mtt-85) REVERT: F 25 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6537 (mpm) REVERT: F 51 ASN cc_start: 0.6986 (m-40) cc_final: 0.6431 (m110) REVERT: F 67 THR cc_start: 0.8541 (p) cc_final: 0.8227 (p) REVERT: F 129 MET cc_start: 0.7518 (ttt) cc_final: 0.7289 (ttp) REVERT: F 132 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7461 (mmm-85) REVERT: F 162 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6500 (p0) REVERT: F 177 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5364 (mtm180) REVERT: G 5 LYS cc_start: 0.5755 (mtmm) cc_final: 0.4903 (pttp) REVERT: H 5 LEU cc_start: 0.5552 (mt) cc_final: 0.5339 (mt) REVERT: I 35 MET cc_start: 0.0475 (OUTLIER) cc_final: 0.0009 (pmm) REVERT: I 116 MET cc_start: -0.0920 (ttm) cc_final: -0.1169 (ttm) REVERT: I 135 MET cc_start: 0.1381 (mtp) cc_final: 0.0142 (tmt) REVERT: J 99 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7176 (mmm160) REVERT: K 20 MET cc_start: 0.8429 (ttp) cc_final: 0.8185 (ttm) REVERT: K 45 GLU cc_start: 0.7952 (tt0) cc_final: 0.7641 (tt0) REVERT: K 53 LYS cc_start: 0.7890 (pttp) cc_final: 0.7284 (mmtt) REVERT: K 113 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.6282 (ppp) REVERT: L 60 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7429 (ptt90) REVERT: L 80 SER cc_start: 0.8216 (t) cc_final: 0.7820 (p) REVERT: M 20 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7217 (pp) REVERT: M 47 GLU cc_start: 0.7686 (tp30) cc_final: 0.7218 (tp30) REVERT: M 75 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: M 81 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8360 (mtt-85) REVERT: M 127 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7284 (tptm) REVERT: M 133 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7871 (tttp) REVERT: N 18 GLN cc_start: 0.8388 (tt0) cc_final: 0.7967 (tt0) REVERT: N 74 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: N 114 GLU cc_start: 0.7992 (pt0) cc_final: 0.7651 (pt0) REVERT: O 16 ARG cc_start: 0.8076 (mpt180) cc_final: 0.7076 (mmm-85) REVERT: O 46 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: O 115 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6645 (mp) REVERT: P 9 GLN cc_start: 0.7539 (tt0) cc_final: 0.7247 (mp-120) REVERT: P 29 VAL cc_start: 0.8766 (t) cc_final: 0.8345 (p) REVERT: P 100 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: P 112 ARG cc_start: 0.5551 (mtp85) cc_final: 0.4942 (mtm-85) REVERT: Q 106 THR cc_start: 0.7670 (m) cc_final: 0.7226 (p) REVERT: Q 110 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6762 (mm-30) REVERT: R 46 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: R 78 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8200 (ttm-80) REVERT: S 92 ARG cc_start: 0.6606 (ptp90) cc_final: 0.6200 (ptm160) REVERT: T 26 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6954 (mmpt) REVERT: T 77 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7442 (mtt90) REVERT: U 6 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5360 (tmm-80) REVERT: U 46 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7566 (ptpp) REVERT: U 59 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7587 (tp30) REVERT: U 78 LYS cc_start: 0.7082 (pttp) cc_final: 0.6453 (ptpp) REVERT: V 7 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7365 (tm-30) REVERT: V 21 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6233 (mtp180) REVERT: V 49 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.7098 (m110) REVERT: V 51 GLN cc_start: 0.6770 (pp30) cc_final: 0.6233 (tm130) REVERT: V 71 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7726 (mptm) REVERT: W 7 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7565 (mmm-85) REVERT: W 64 LYS cc_start: 0.7969 (tptm) cc_final: 0.7758 (tptm) REVERT: W 74 LYS cc_start: 0.7939 (mttt) cc_final: 0.7333 (mmtt) REVERT: Y 5 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6663 (mt-10) REVERT: Y 17 GLU cc_start: 0.8278 (tp30) cc_final: 0.7979 (tp30) REVERT: Y 21 LEU cc_start: 0.7173 (mt) cc_final: 0.6909 (mt) REVERT: Y 36 GLN cc_start: 0.6878 (mt0) cc_final: 0.5954 (mm-40) REVERT: 0 28 SER cc_start: 0.8679 (t) cc_final: 0.8177 (t) REVERT: 0 36 LYS cc_start: 0.7942 (mttt) cc_final: 0.7658 (mptt) REVERT: 1 39 ASP cc_start: 0.8183 (t70) cc_final: 0.7815 (t0) REVERT: 1 50 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6110 (tm-30) REVERT: 2 22 MET cc_start: 0.8183 (mmt) cc_final: 0.7613 (mmt) REVERT: 2 41 ARG cc_start: 0.7992 (mmt180) cc_final: 0.7465 (ptm-80) REVERT: 3 38 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7943 (tttt) REVERT: 5 38 MET cc_start: 0.0781 (mtt) cc_final: 0.0557 (mtm) REVERT: 6 20 ASN cc_start: 0.6365 (t0) cc_final: 0.5845 (p0) REVERT: 6 63 ARG cc_start: 0.5263 (mtt-85) cc_final: 0.4438 (mmm-85) REVERT: b 8 MET cc_start: 0.5465 (pp-130) cc_final: 0.4946 (ppp) REVERT: b 21 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5221 (p90) REVERT: b 23 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7731 (t0) REVERT: b 80 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7063 (tppt) REVERT: b 88 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: b 107 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.6949 (mtm180) REVERT: b 115 ASP cc_start: 0.6852 (t0) cc_final: 0.6519 (m-30) REVERT: b 116 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7077 (tp) REVERT: b 125 PHE cc_start: 0.5320 (p90) cc_final: 0.4996 (m-10) REVERT: b 158 ASP cc_start: 0.7711 (t0) cc_final: 0.7446 (m-30) REVERT: b 196 ASP cc_start: 0.7527 (m-30) cc_final: 0.6688 (p0) REVERT: b 202 ASN cc_start: 0.7610 (p0) cc_final: 0.6876 (t0) REVERT: c 71 ARG cc_start: 0.6299 (mtt90) cc_final: 0.5921 (mtm-85) REVERT: c 106 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6965 (ptp90) REVERT: c 126 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7302 (mmm160) REVERT: c 139 ASN cc_start: 0.7366 (m-40) cc_final: 0.7001 (m110) REVERT: d 66 VAL cc_start: 0.8346 (t) cc_final: 0.8048 (m) REVERT: d 69 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7069 (ttt180) REVERT: d 76 LYS cc_start: 0.8356 (mttm) cc_final: 0.8070 (mttm) REVERT: d 77 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7394 (tp30) REVERT: d 102 TYR cc_start: 0.7630 (t80) cc_final: 0.7130 (t80) REVERT: d 127 ARG cc_start: 0.6206 (mtp85) cc_final: 0.5549 (mtp-110) REVERT: d 153 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.4958 (ptm160) REVERT: d 176 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6378 (pmtt) REVERT: d 177 MET cc_start: 0.7148 (mmp) cc_final: 0.6377 (mpp) REVERT: d 178 GLU cc_start: 0.6946 (tt0) cc_final: 0.6049 (pp20) REVERT: d 181 PHE cc_start: 0.6691 (t80) cc_final: 0.6394 (t80) REVERT: d 182 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6859 (mttt) REVERT: d 184 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6671 (mtpt) REVERT: d 201 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6627 (mt-10) REVERT: e 68 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7744 (mtm-85) REVERT: e 121 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7553 (m110) REVERT: e 162 GLU cc_start: 0.7701 (tt0) cc_final: 0.7448 (tt0) REVERT: g 74 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8058 (t) REVERT: g 78 ARG cc_start: 0.0885 (OUTLIER) cc_final: 0.0017 (mmp80) REVERT: g 100 MET cc_start: 0.8256 (ptp) cc_final: 0.7978 (ptp) REVERT: g 125 ASP cc_start: 0.8134 (m-30) cc_final: 0.7823 (m-30) REVERT: h 4 ASP cc_start: 0.7863 (t70) cc_final: 0.7644 (t70) REVERT: h 57 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7878 (tp30) REVERT: h 93 LYS cc_start: 0.7124 (ptpt) cc_final: 0.5779 (mmtp) REVERT: h 104 SER cc_start: 0.8772 (m) cc_final: 0.8502 (t) REVERT: h 116 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6830 (mtp180) REVERT: i 4 GLN cc_start: 0.6387 (tt0) cc_final: 0.5966 (pm20) REVERT: i 21 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.5969 (ptpt) REVERT: i 32 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.6023 (mtp85) REVERT: i 34 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6685 (pt) REVERT: i 35 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: i 87 MET cc_start: 0.6570 (ptp) cc_final: 0.6171 (ptm) REVERT: i 99 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7225 (mmtm) REVERT: i 109 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7781 (mm-40) REVERT: j 37 ARG cc_start: 0.5253 (mtp85) cc_final: 0.5051 (mtp85) REVERT: j 68 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7108 (mtt-85) REVERT: j 88 MET cc_start: 0.6446 (mmm) cc_final: 0.6168 (ttp) REVERT: k 17 ASP cc_start: 0.6933 (p0) cc_final: 0.6656 (p0) REVERT: k 26 PHE cc_start: 0.8358 (m-80) cc_final: 0.7639 (m-80) REVERT: k 84 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7619 (mtp) REVERT: k 105 ARG cc_start: 0.6853 (tmm160) cc_final: 0.6542 (tpt-90) REVERT: k 110 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7531 (t) REVERT: l 107 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7902 (mmpt) REVERT: m 26 LYS cc_start: 0.7945 (tttp) cc_final: 0.7559 (tptp) REVERT: m 63 VAL cc_start: 0.8142 (t) cc_final: 0.7890 (p) REVERT: m 77 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7150 (tptt) REVERT: m 78 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6868 (ttt90) REVERT: m 99 GLN cc_start: 0.8584 (mt0) cc_final: 0.7871 (mt0) REVERT: n 3 GLN cc_start: 0.7659 (mm110) cc_final: 0.7352 (mm-40) REVERT: n 23 ARG cc_start: 0.6141 (ttm-80) cc_final: 0.5537 (ttm170) REVERT: n 62 ASN cc_start: 0.8497 (t0) cc_final: 0.8079 (t0) REVERT: o 71 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6591 (ptt-90) REVERT: p 1 MET cc_start: 0.6655 (ptp) cc_final: 0.6388 (ptt) REVERT: p 61 VAL cc_start: 0.8272 (t) cc_final: 0.8029 (m) REVERT: q 24 ILE cc_start: 0.8580 (mt) cc_final: 0.8357 (mp) REVERT: q 62 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: r 11 ARG cc_start: 0.3628 (ptp90) cc_final: 0.2764 (tpp-160) REVERT: r 24 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7119 (t0) REVERT: r 29 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8504 (mtmt) REVERT: r 47 ARG cc_start: 0.7601 (mmt180) cc_final: 0.6350 (ttp-170) REVERT: s 42 ASN cc_start: 0.7855 (p0) cc_final: 0.7497 (t0) REVERT: t 47 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: t 60 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7609 (mm-40) REVERT: u 4 LYS cc_start: 0.7150 (mttt) cc_final: 0.6795 (mtpt) REVERT: u 19 LYS cc_start: 0.6103 (tttt) cc_final: 0.4909 (tptt) REVERT: u 32 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7035 (ttt90) REVERT: z 3 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6752 (mp0) REVERT: z 7 ARG cc_start: 0.6128 (mmm-85) cc_final: 0.5783 (tpp80) REVERT: z 26 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7908 (p) REVERT: z 68 GLU cc_start: 0.7234 (tt0) cc_final: 0.6393 (tp30) REVERT: z 143 GLU cc_start: 0.7904 (tp30) cc_final: 0.7580 (tp30) REVERT: z 148 LEU cc_start: 0.5703 (tp) cc_final: 0.5344 (pp) REVERT: z 151 MET cc_start: 0.6315 (tmm) cc_final: 0.5703 (mmp) REVERT: z 194 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6706 (t80) REVERT: z 232 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7447 (tm-30) REVERT: z 237 LYS cc_start: 0.7050 (mtmt) cc_final: 0.6557 (mtpp) REVERT: z 243 GLU cc_start: 0.8022 (tt0) cc_final: 0.7393 (tt0) REVERT: z 282 LYS cc_start: 0.7554 (mttt) cc_final: 0.6914 (mptt) REVERT: z 305 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5562 (tm-30) REVERT: z 356 ILE cc_start: 0.6234 (pt) cc_final: 0.5879 (tt) REVERT: z 358 MET cc_start: 0.4821 (OUTLIER) cc_final: 0.4561 (ptp) outliers start: 340 outliers final: 186 residues processed: 1336 average time/residue: 2.2954 time to fit residues: 4418.7607 Evaluate side-chains 1338 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1094 time to evaluate : 6.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 26 LYS Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain Z residue 30 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 3 residue 38 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 88 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 106 ARG Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 176 LYS Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 113 LYS Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 21 LYS Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 78 ARG Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 24 ASP Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 47 GLN Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ARG Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 71 THR Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 165 ASP Chi-restraints excluded: chain z residue 194 PHE Chi-restraints excluded: chain z residue 206 ILE Chi-restraints excluded: chain z residue 208 LYS Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 253 SER Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 354 ASP Chi-restraints excluded: chain z residue 358 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 953 optimal weight: 1.9990 chunk 1003 optimal weight: 0.9990 chunk 915 optimal weight: 10.0000 chunk 976 optimal weight: 2.9990 chunk 587 optimal weight: 3.9990 chunk 425 optimal weight: 9.9990 chunk 766 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 882 optimal weight: 0.0980 chunk 923 optimal weight: 0.8980 chunk 972 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 26 GLN F 36 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN M 88 ASN P 40 GLN S 61 ASN Y 31 GLN 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN b 176 ASN d 58 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN g 147 ASN h 37 ASN h 75 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN o 34 GLN ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.115 165478 Z= 0.152 Angle : 0.667 16.864 247206 Z= 0.361 Chirality : 0.034 0.656 31414 Planarity : 0.007 0.126 13504 Dihedral : 23.843 178.212 81839 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.59 % Favored : 91.89 % Rotamer: Outliers : 4.74 % Allowed : 32.29 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.10), residues: 6219 helix: 0.65 (0.12), residues: 1951 sheet: -1.13 (0.15), residues: 1179 loop : -1.72 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP d 169 HIS 0.009 0.001 HIS E 165 PHE 0.020 0.001 PHE e 94 TYR 0.018 0.001 TYR i 6 ARG 0.015 0.001 ARG u 33 *********************** 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 1362 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1117 time to evaluate : 6.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8063 (tptm) REVERT: C 27 LYS cc_start: 0.8083 (mttt) cc_final: 0.7117 (mmtm) REVERT: C 110 LYS cc_start: 0.7751 (mttt) cc_final: 0.7349 (mtpp) REVERT: C 113 ASP cc_start: 0.7421 (m-30) cc_final: 0.6892 (m-30) REVERT: C 114 GLN cc_start: 0.7581 (tt0) cc_final: 0.7158 (mt0) REVERT: C 198 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: C 202 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7715 (ptp-110) REVERT: C 260 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: C 269 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7582 (mtp-110) REVERT: D 168 GLU cc_start: 0.7537 (tt0) cc_final: 0.7165 (tt0) REVERT: D 169 ARG cc_start: 0.7861 (ttt-90) cc_final: 0.7527 (ttp80) REVERT: D 183 GLU cc_start: 0.7749 (tt0) cc_final: 0.7495 (tt0) REVERT: E 27 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7940 (mt) REVERT: E 88 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6797 (mtt-85) REVERT: F 25 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6401 (mpm) REVERT: F 51 ASN cc_start: 0.6965 (m-40) cc_final: 0.6489 (m110) REVERT: F 67 THR cc_start: 0.8639 (p) cc_final: 0.8387 (p) REVERT: F 129 MET cc_start: 0.7555 (ttt) cc_final: 0.7307 (ttp) REVERT: F 177 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5297 (mtm180) REVERT: G 5 LYS cc_start: 0.5655 (mtmm) cc_final: 0.5127 (ptpp) REVERT: G 98 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7502 (tppp) REVERT: H 5 LEU cc_start: 0.5763 (mt) cc_final: 0.5563 (mt) REVERT: H 33 GLN cc_start: 0.6980 (mt0) cc_final: 0.6706 (mt0) REVERT: I 116 MET cc_start: -0.0967 (ttm) cc_final: -0.1286 (ttm) REVERT: I 135 MET cc_start: 0.0748 (mtp) cc_final: 0.0135 (tmt) REVERT: J 99 ARG cc_start: 0.7637 (mmm160) cc_final: 0.6930 (mmm160) REVERT: K 31 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7487 (mtm-85) REVERT: K 45 GLU cc_start: 0.7998 (tt0) cc_final: 0.7628 (tt0) REVERT: K 53 LYS cc_start: 0.7915 (pttp) cc_final: 0.7323 (mmtt) REVERT: K 100 PHE cc_start: 0.8324 (m-80) cc_final: 0.7886 (m-80) REVERT: K 113 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6301 (ppp) REVERT: L 80 SER cc_start: 0.7896 (t) cc_final: 0.7504 (p) REVERT: L 81 ASP cc_start: 0.7728 (m-30) cc_final: 0.7487 (m-30) REVERT: M 20 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7066 (pp) REVERT: M 47 GLU cc_start: 0.7602 (tp30) cc_final: 0.7064 (tp30) REVERT: M 55 ARG cc_start: 0.6695 (ptp-110) cc_final: 0.6387 (ttp-110) REVERT: M 75 GLU cc_start: 0.7970 (tp30) cc_final: 0.7628 (tp30) REVERT: M 81 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8228 (mtt-85) REVERT: M 127 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7261 (tptm) REVERT: M 133 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7833 (tttp) REVERT: N 18 GLN cc_start: 0.8286 (tt0) cc_final: 0.7862 (tt0) REVERT: N 74 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: N 114 GLU cc_start: 0.8215 (pt0) cc_final: 0.7838 (pt0) REVERT: O 16 ARG cc_start: 0.8019 (mpt180) cc_final: 0.7055 (mmm-85) REVERT: O 46 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: O 115 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6593 (mp) REVERT: P 9 GLN cc_start: 0.7473 (tt0) cc_final: 0.7255 (mp-120) REVERT: P 29 VAL cc_start: 0.8820 (t) cc_final: 0.8414 (p) REVERT: P 70 GLU cc_start: 0.7500 (tt0) cc_final: 0.6680 (mm-30) REVERT: P 96 LEU cc_start: 0.8710 (mt) cc_final: 0.8493 (mt) REVERT: P 100 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: P 112 ARG cc_start: 0.5247 (mtp85) cc_final: 0.4786 (mtm-85) REVERT: Q 106 THR cc_start: 0.7479 (m) cc_final: 0.7001 (p) REVERT: Q 110 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6714 (mm-30) REVERT: R 18 GLN cc_start: 0.6958 (pt0) cc_final: 0.6615 (pt0) REVERT: R 46 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: S 37 THR cc_start: 0.8507 (m) cc_final: 0.8078 (p) REVERT: S 92 ARG cc_start: 0.6277 (ptp90) cc_final: 0.5990 (ptm160) REVERT: U 46 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7610 (ptpp) REVERT: U 59 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7684 (tp30) REVERT: U 78 LYS cc_start: 0.7158 (pttp) cc_final: 0.6509 (ptpp) REVERT: V 7 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7271 (tt0) REVERT: V 21 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6098 (mtp180) REVERT: V 50 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7813 (mtt) REVERT: V 51 GLN cc_start: 0.6686 (pp30) cc_final: 0.6140 (tm130) REVERT: V 71 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7697 (mptm) REVERT: W 7 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7560 (mmm-85) REVERT: W 74 LYS cc_start: 0.7904 (mttt) cc_final: 0.7364 (mmtt) REVERT: Y 5 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6616 (mt-10) REVERT: Y 17 GLU cc_start: 0.8326 (tp30) cc_final: 0.8076 (tp30) REVERT: Y 19 LEU cc_start: 0.7565 (mt) cc_final: 0.7231 (mt) REVERT: Y 21 LEU cc_start: 0.6792 (mt) cc_final: 0.6560 (mt) REVERT: Y 36 GLN cc_start: 0.6877 (mt0) cc_final: 0.6005 (mm-40) REVERT: 0 28 SER cc_start: 0.8703 (t) cc_final: 0.8297 (t) REVERT: 0 36 LYS cc_start: 0.7857 (mttt) cc_final: 0.7542 (mmtp) REVERT: 1 29 LYS cc_start: 0.7230 (mmmt) cc_final: 0.6699 (mmmt) REVERT: 1 50 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6154 (tm-30) REVERT: 2 41 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7260 (ptt180) REVERT: 5 38 MET cc_start: 0.0994 (mtt) cc_final: 0.0748 (mtm) REVERT: 6 20 ASN cc_start: 0.6154 (t0) cc_final: 0.5704 (p0) REVERT: b 8 MET cc_start: 0.5480 (pp-130) cc_final: 0.5007 (ppp) REVERT: b 21 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.5399 (p90) REVERT: b 46 VAL cc_start: 0.6372 (OUTLIER) cc_final: 0.6137 (m) REVERT: b 80 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7032 (tppt) REVERT: b 107 ARG cc_start: 0.7204 (ttp-170) cc_final: 0.6889 (mtm180) REVERT: b 115 ASP cc_start: 0.6812 (t0) cc_final: 0.6497 (m-30) REVERT: b 125 PHE cc_start: 0.5312 (p90) cc_final: 0.5021 (m-10) REVERT: b 158 ASP cc_start: 0.7706 (t0) cc_final: 0.7434 (m-30) REVERT: b 196 ASP cc_start: 0.7559 (m-30) cc_final: 0.6740 (p0) REVERT: b 202 ASN cc_start: 0.7297 (p0) cc_final: 0.6344 (t0) REVERT: b 212 TYR cc_start: 0.6776 (m-80) cc_final: 0.6516 (m-80) REVERT: c 41 TYR cc_start: 0.7728 (t80) cc_final: 0.7517 (t80) REVERT: c 57 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: c 71 ARG cc_start: 0.6332 (mtt90) cc_final: 0.5981 (mtm-85) REVERT: c 78 LYS cc_start: 0.7335 (ttmm) cc_final: 0.6975 (mmmt) REVERT: c 126 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7211 (mmm160) REVERT: c 139 ASN cc_start: 0.7349 (m-40) cc_final: 0.6996 (m110) REVERT: d 7 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7092 (mttt) REVERT: d 66 VAL cc_start: 0.8317 (t) cc_final: 0.8011 (m) REVERT: d 69 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7058 (ttt180) REVERT: d 71 PHE cc_start: 0.8901 (t80) cc_final: 0.8685 (t80) REVERT: d 76 LYS cc_start: 0.8401 (mttm) cc_final: 0.8117 (mttm) REVERT: d 77 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7273 (tp30) REVERT: d 102 TYR cc_start: 0.7502 (t80) cc_final: 0.6927 (t80) REVERT: d 127 ARG cc_start: 0.6174 (mtp85) cc_final: 0.5536 (mtp-110) REVERT: d 153 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.4923 (ptm160) REVERT: d 176 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6258 (pmtt) REVERT: d 177 MET cc_start: 0.7179 (mmp) cc_final: 0.6341 (mpp) REVERT: d 178 GLU cc_start: 0.6819 (tt0) cc_final: 0.6030 (pp20) REVERT: d 181 PHE cc_start: 0.6562 (t80) cc_final: 0.6357 (t80) REVERT: d 182 LYS cc_start: 0.7224 (ttmt) cc_final: 0.6825 (mttt) REVERT: d 184 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6901 (mtpt) REVERT: d 201 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6505 (mt-10) REVERT: e 162 GLU cc_start: 0.7711 (tt0) cc_final: 0.7180 (pt0) REVERT: g 74 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8113 (t) REVERT: g 78 ARG cc_start: 0.0790 (OUTLIER) cc_final: -0.0029 (mmp80) REVERT: g 100 MET cc_start: 0.8048 (ptp) cc_final: 0.7783 (ptp) REVERT: g 125 ASP cc_start: 0.7994 (m-30) cc_final: 0.7662 (m-30) REVERT: h 57 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7881 (tp30) REVERT: h 93 LYS cc_start: 0.7114 (ptpt) cc_final: 0.5568 (mmtp) REVERT: h 104 SER cc_start: 0.8715 (m) cc_final: 0.8487 (t) REVERT: h 116 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6713 (mtt-85) REVERT: i 4 GLN cc_start: 0.6457 (tt0) cc_final: 0.6036 (pm20) REVERT: i 32 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.6099 (mtp85) REVERT: i 35 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: i 99 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7454 (mmtm) REVERT: i 109 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7701 (mm-40) REVERT: j 68 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6973 (mtt-85) REVERT: j 88 MET cc_start: 0.6364 (mmm) cc_final: 0.6035 (ttp) REVERT: k 17 ASP cc_start: 0.6950 (p0) cc_final: 0.6087 (m-30) REVERT: k 26 PHE cc_start: 0.8252 (m-80) cc_final: 0.7962 (m-80) REVERT: k 92 ARG cc_start: 0.8245 (ptt90) cc_final: 0.7902 (ptt180) REVERT: k 105 ARG cc_start: 0.6798 (tmm160) cc_final: 0.6530 (tpt-90) REVERT: k 108 ASN cc_start: 0.8320 (p0) cc_final: 0.7839 (p0) REVERT: k 113 THR cc_start: 0.7346 (m) cc_final: 0.7124 (p) REVERT: l 53 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6581 (tpt170) REVERT: l 107 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7912 (mmpt) REVERT: m 26 LYS cc_start: 0.7874 (tttp) cc_final: 0.7457 (tptp) REVERT: m 77 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7020 (tptt) REVERT: m 78 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6842 (ttt90) REVERT: m 79 LEU cc_start: 0.7922 (mt) cc_final: 0.7696 (mp) REVERT: m 92 ARG cc_start: 0.7650 (mmt180) cc_final: 0.7360 (mmt180) REVERT: m 99 GLN cc_start: 0.8348 (mt0) cc_final: 0.7618 (mt0) REVERT: n 3 GLN cc_start: 0.7587 (mm110) cc_final: 0.7353 (mm-40) REVERT: n 23 ARG cc_start: 0.6221 (ttm-80) cc_final: 0.5622 (ttm170) REVERT: n 62 ASN cc_start: 0.8296 (t0) cc_final: 0.7962 (t0) REVERT: n 97 LYS cc_start: 0.8478 (pttt) cc_final: 0.8152 (pttp) REVERT: o 71 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6985 (ptp90) REVERT: p 1 MET cc_start: 0.6700 (ptp) cc_final: 0.6463 (ptt) REVERT: p 61 VAL cc_start: 0.8309 (t) cc_final: 0.8078 (m) REVERT: q 16 MET cc_start: 0.6073 (ttm) cc_final: 0.5826 (ttp) REVERT: r 11 ARG cc_start: 0.3475 (ptp90) cc_final: 0.2771 (tpp-160) REVERT: r 29 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8496 (mtmt) REVERT: r 47 ARG cc_start: 0.7493 (mmt180) cc_final: 0.6330 (ttp-170) REVERT: s 37 SER cc_start: 0.8076 (p) cc_final: 0.7726 (m) REVERT: s 42 ASN cc_start: 0.7765 (p0) cc_final: 0.7506 (t0) REVERT: t 47 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6440 (tm-30) REVERT: t 60 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7392 (mp10) REVERT: u 4 LYS cc_start: 0.7124 (mttt) cc_final: 0.6903 (mtpt) REVERT: u 19 LYS cc_start: 0.6015 (tttt) cc_final: 0.5250 (tptt) REVERT: z 3 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6816 (mp0) REVERT: z 26 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7789 (p) REVERT: z 68 GLU cc_start: 0.7234 (tt0) cc_final: 0.6516 (tp30) REVERT: z 143 GLU cc_start: 0.7896 (tp30) cc_final: 0.7542 (tm-30) REVERT: z 148 LEU cc_start: 0.5828 (tp) cc_final: 0.5469 (pp) REVERT: z 151 MET cc_start: 0.6562 (tmm) cc_final: 0.5889 (mmp) REVERT: z 194 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6851 (t80) REVERT: z 216 ASP cc_start: 0.6406 (t0) cc_final: 0.6130 (p0) REVERT: z 237 LYS cc_start: 0.6963 (mtmt) cc_final: 0.6513 (mtpp) REVERT: z 241 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7304 (mm-30) REVERT: z 243 GLU cc_start: 0.8069 (tt0) cc_final: 0.7425 (tt0) REVERT: z 259 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5952 (mt-10) REVERT: z 282 LYS cc_start: 0.7518 (mttt) cc_final: 0.6878 (mptt) REVERT: z 298 ILE cc_start: 0.7720 (mm) cc_final: 0.7331 (mt) REVERT: z 305 GLU cc_start: 0.5876 (mt-10) cc_final: 0.5568 (tm-30) REVERT: z 349 MET cc_start: 0.4716 (ttp) cc_final: 0.3956 (ttm) REVERT: z 358 MET cc_start: 0.4919 (OUTLIER) cc_final: 0.4661 (ptp) REVERT: z 381 ARG cc_start: 0.5136 (ptm160) cc_final: 0.4888 (ptm160) outliers start: 245 outliers final: 145 residues processed: 1258 average time/residue: 2.2476 time to fit residues: 4102.0503 Evaluate side-chains 1267 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1085 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 88 GLN Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 176 LYS Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 78 ARG Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 47 GLN Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 71 THR Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 165 ASP Chi-restraints excluded: chain z residue 194 PHE Chi-restraints excluded: chain z residue 206 ILE Chi-restraints excluded: chain z residue 208 LYS Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 251 GLN Chi-restraints excluded: chain z residue 253 SER Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 358 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 641 optimal weight: 2.9990 chunk 1032 optimal weight: 10.0000 chunk 630 optimal weight: 5.9990 chunk 489 optimal weight: 0.8980 chunk 717 optimal weight: 10.0000 chunk 1082 optimal weight: 4.9990 chunk 996 optimal weight: 6.9990 chunk 862 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 36 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN M 88 ASN N 73 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN ** b 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 ASN d 58 GLN e 121 ASN f 81 ASN g 67 ASN g 147 ASN h 37 ASN h 75 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN o 34 GLN t 12 GLN t 19 HIS ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 165478 Z= 0.331 Angle : 0.745 17.052 247206 Z= 0.394 Chirality : 0.039 0.491 31414 Planarity : 0.007 0.135 13504 Dihedral : 23.865 178.541 81839 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.60 % Favored : 90.83 % Rotamer: Outliers : 4.70 % Allowed : 32.54 % Favored : 62.76 % 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: -1.41 (0.10), residues: 6219 helix: 0.41 (0.12), residues: 1961 sheet: -1.14 (0.15), residues: 1176 loop : -1.75 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP d 169 HIS 0.009 0.001 HIS E 165 PHE 0.044 0.002 PHE b 89 TYR 0.024 0.002 TYR i 6 ARG 0.014 0.001 ARG Y 29 ********************** 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 1321 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1078 time to evaluate : 6.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8029 (tptm) REVERT: C 27 LYS cc_start: 0.8132 (mttt) cc_final: 0.7275 (mmtm) REVERT: C 110 LYS cc_start: 0.7647 (mttt) cc_final: 0.7441 (mtpp) REVERT: C 114 GLN cc_start: 0.7478 (tt0) cc_final: 0.6959 (mt0) REVERT: C 179 GLU cc_start: 0.7647 (tt0) cc_final: 0.7423 (tt0) REVERT: C 191 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8540 (mt) REVERT: C 198 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: C 202 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7968 (ptp-110) REVERT: C 260 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8611 (ttmm) REVERT: C 269 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7598 (mtp-110) REVERT: D 168 GLU cc_start: 0.7538 (tt0) cc_final: 0.7147 (tt0) REVERT: D 183 GLU cc_start: 0.7773 (tt0) cc_final: 0.7526 (tt0) REVERT: E 27 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8020 (mt) REVERT: E 88 ARG cc_start: 0.7300 (mmm160) cc_final: 0.6823 (mtt-85) REVERT: F 25 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6267 (mpm) REVERT: F 26 GLN cc_start: 0.8026 (mt0) cc_final: 0.7802 (mt0) REVERT: F 51 ASN cc_start: 0.6944 (m-40) cc_final: 0.6435 (m110) REVERT: F 67 THR cc_start: 0.8610 (p) cc_final: 0.8332 (p) REVERT: F 129 MET cc_start: 0.7570 (ttt) cc_final: 0.7323 (ttp) REVERT: F 177 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5290 (mtm180) REVERT: G 5 LYS cc_start: 0.5751 (mtmm) cc_final: 0.4946 (pttp) REVERT: I 35 MET cc_start: 0.0641 (OUTLIER) cc_final: 0.0190 (pmm) REVERT: I 116 MET cc_start: -0.0961 (ttm) cc_final: -0.1245 (ttm) REVERT: I 135 MET cc_start: 0.1300 (mtp) cc_final: 0.0339 (tmt) REVERT: J 99 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7180 (mmm160) REVERT: K 45 GLU cc_start: 0.7960 (tt0) cc_final: 0.7559 (tt0) REVERT: K 53 LYS cc_start: 0.7886 (pttp) cc_final: 0.7325 (mmtt) REVERT: K 113 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6221 (ppp) REVERT: L 60 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7410 (ptt90) REVERT: L 80 SER cc_start: 0.8122 (t) cc_final: 0.7752 (p) REVERT: L 81 ASP cc_start: 0.7790 (m-30) cc_final: 0.7545 (m-30) REVERT: L 141 LYS cc_start: 0.8058 (mttt) cc_final: 0.7721 (pptt) REVERT: M 20 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7180 (pp) REVERT: M 47 GLU cc_start: 0.7630 (tp30) cc_final: 0.7103 (tp30) REVERT: M 53 MET cc_start: 0.6836 (mtm) cc_final: 0.6086 (ptp) REVERT: M 75 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: M 81 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: M 127 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7255 (tptm) REVERT: M 133 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7855 (tttp) REVERT: N 18 GLN cc_start: 0.8370 (tt0) cc_final: 0.7919 (tt0) REVERT: N 74 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: N 114 GLU cc_start: 0.7987 (pt0) cc_final: 0.7635 (pt0) REVERT: O 16 ARG cc_start: 0.8082 (mpt180) cc_final: 0.7082 (mmm-85) REVERT: O 46 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: O 115 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6626 (mp) REVERT: P 9 GLN cc_start: 0.7554 (tt0) cc_final: 0.7236 (mp-120) REVERT: P 29 VAL cc_start: 0.8739 (t) cc_final: 0.8360 (p) REVERT: P 100 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: P 112 ARG cc_start: 0.5467 (mtp85) cc_final: 0.4932 (mtm-85) REVERT: Q 106 THR cc_start: 0.7558 (m) cc_final: 0.7253 (p) REVERT: R 46 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: R 78 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8171 (ttm-80) REVERT: S 4 ILE cc_start: 0.8436 (mp) cc_final: 0.8170 (tt) REVERT: S 92 ARG cc_start: 0.6499 (ptp90) cc_final: 0.6127 (ptm160) REVERT: U 46 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7566 (ptpp) REVERT: U 59 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7593 (tp30) REVERT: U 78 LYS cc_start: 0.7152 (pttp) cc_final: 0.6539 (ptpp) REVERT: V 7 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7304 (tm-30) REVERT: V 21 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6159 (mtp180) REVERT: V 49 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7139 (m110) REVERT: V 50 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.8008 (mtt) REVERT: V 51 GLN cc_start: 0.6698 (pp30) cc_final: 0.6163 (tm130) REVERT: V 71 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7711 (mptm) REVERT: W 7 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7547 (mmm-85) REVERT: W 64 LYS cc_start: 0.7953 (tptm) cc_final: 0.7739 (tptm) REVERT: W 74 LYS cc_start: 0.7917 (mttt) cc_final: 0.7314 (mmtt) REVERT: Y 5 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6704 (mt-10) REVERT: Y 19 LEU cc_start: 0.7355 (mt) cc_final: 0.7038 (mt) REVERT: Y 30 MET cc_start: 0.7122 (tpp) cc_final: 0.6821 (mmm) REVERT: Y 36 GLN cc_start: 0.6865 (mt0) cc_final: 0.5940 (mm-40) REVERT: 0 28 SER cc_start: 0.8717 (t) cc_final: 0.8223 (t) REVERT: 0 36 LYS cc_start: 0.7926 (mttt) cc_final: 0.7553 (mmtp) REVERT: 0 54 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7284 (mt) REVERT: 1 29 LYS cc_start: 0.7301 (mmmt) cc_final: 0.7078 (mptm) REVERT: 1 39 ASP cc_start: 0.8130 (t70) cc_final: 0.7779 (t0) REVERT: 1 50 GLU cc_start: 0.6515 (tm-30) cc_final: 0.6172 (tm-30) REVERT: 2 22 MET cc_start: 0.8218 (mmt) cc_final: 0.7698 (mmt) REVERT: 2 41 ARG cc_start: 0.7964 (mmt180) cc_final: 0.7689 (mtm110) REVERT: 4 37 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7542 (tm-30) REVERT: 5 38 MET cc_start: 0.0967 (mtt) cc_final: 0.0750 (mtm) REVERT: 5 52 MET cc_start: 0.1055 (ttp) cc_final: 0.0615 (ttp) REVERT: 6 20 ASN cc_start: 0.6374 (t0) cc_final: 0.6050 (t0) REVERT: b 8 MET cc_start: 0.5723 (pp-130) cc_final: 0.5255 (ppp) REVERT: b 21 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.5257 (p90) REVERT: b 80 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7069 (tppt) REVERT: b 107 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7007 (mtm180) REVERT: b 115 ASP cc_start: 0.6819 (t0) cc_final: 0.6498 (m-30) REVERT: b 116 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7001 (tp) REVERT: b 125 PHE cc_start: 0.5322 (p90) cc_final: 0.5019 (m-10) REVERT: b 158 ASP cc_start: 0.7723 (t0) cc_final: 0.7425 (m-30) REVERT: b 196 ASP cc_start: 0.7478 (m-30) cc_final: 0.6653 (p0) REVERT: b 202 ASN cc_start: 0.7527 (p0) cc_final: 0.6669 (t0) REVERT: c 41 TYR cc_start: 0.7744 (t80) cc_final: 0.7535 (t80) REVERT: c 57 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: c 78 LYS cc_start: 0.7189 (ttmm) cc_final: 0.6860 (mmmt) REVERT: c 126 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7231 (mmm160) REVERT: c 139 ASN cc_start: 0.7349 (m-40) cc_final: 0.6996 (m110) REVERT: d 7 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7267 (mttt) REVERT: d 66 VAL cc_start: 0.8358 (t) cc_final: 0.8055 (m) REVERT: d 69 ARG cc_start: 0.7532 (tpp80) cc_final: 0.7053 (ttt180) REVERT: d 76 LYS cc_start: 0.8386 (mttm) cc_final: 0.8090 (mttm) REVERT: d 77 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7398 (tp30) REVERT: d 102 TYR cc_start: 0.7638 (t80) cc_final: 0.7164 (t80) REVERT: d 127 ARG cc_start: 0.6181 (mtp85) cc_final: 0.5521 (mtp-110) REVERT: d 153 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.4929 (ptm160) REVERT: d 176 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6353 (pmtt) REVERT: d 177 MET cc_start: 0.7129 (mmp) cc_final: 0.6381 (mpp) REVERT: d 178 GLU cc_start: 0.6840 (tt0) cc_final: 0.6002 (pp20) REVERT: d 181 PHE cc_start: 0.6701 (t80) cc_final: 0.6376 (t80) REVERT: d 182 LYS cc_start: 0.7158 (ttmt) cc_final: 0.6861 (mttt) REVERT: d 184 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6812 (mtpt) REVERT: d 201 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6559 (mt-10) REVERT: e 162 GLU cc_start: 0.7641 (tt0) cc_final: 0.7409 (tt0) REVERT: g 74 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8142 (t) REVERT: g 78 ARG cc_start: 0.0854 (OUTLIER) cc_final: 0.0016 (mmp80) REVERT: g 100 MET cc_start: 0.8167 (ptp) cc_final: 0.7887 (ptp) REVERT: g 113 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5977 (mmmt) REVERT: g 125 ASP cc_start: 0.8071 (m-30) cc_final: 0.7749 (m-30) REVERT: h 57 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7838 (tp30) REVERT: h 93 LYS cc_start: 0.7083 (ptpt) cc_final: 0.5716 (mmtp) REVERT: h 104 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8475 (t) REVERT: h 110 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6723 (pmm) REVERT: h 116 ARG cc_start: 0.7130 (mmm160) cc_final: 0.6672 (mtt-85) REVERT: i 32 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.6092 (mtp85) REVERT: i 35 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: i 99 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7436 (mmtm) REVERT: i 109 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7820 (mm-40) REVERT: j 68 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7069 (mtt-85) REVERT: j 88 MET cc_start: 0.6293 (mmm) cc_final: 0.5957 (ttp) REVERT: k 26 PHE cc_start: 0.8310 (m-80) cc_final: 0.8101 (m-80) REVERT: k 84 MET cc_start: 0.7950 (mtt) cc_final: 0.7649 (mtp) REVERT: k 92 ARG cc_start: 0.8227 (ptt90) cc_final: 0.7856 (ptt180) REVERT: k 105 ARG cc_start: 0.6840 (tmm160) cc_final: 0.6537 (tpt-90) REVERT: k 110 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7566 (t) REVERT: l 107 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7856 (mmpt) REVERT: m 26 LYS cc_start: 0.7922 (tttp) cc_final: 0.7522 (tptm) REVERT: m 77 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7038 (tptt) REVERT: m 78 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6876 (ttt90) REVERT: m 79 LEU cc_start: 0.7929 (mt) cc_final: 0.7690 (mp) REVERT: m 92 ARG cc_start: 0.7681 (mmt180) cc_final: 0.7373 (mmt180) REVERT: m 99 GLN cc_start: 0.8593 (mt0) cc_final: 0.7835 (mt0) REVERT: n 3 GLN cc_start: 0.7635 (mm110) cc_final: 0.7329 (mm-40) REVERT: n 23 ARG cc_start: 0.6234 (ttm-80) cc_final: 0.5629 (ttm170) REVERT: n 62 ASN cc_start: 0.8472 (t0) cc_final: 0.8068 (t0) REVERT: n 97 LYS cc_start: 0.8553 (pttt) cc_final: 0.8245 (pttp) REVERT: o 71 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6676 (ptt-90) REVERT: p 61 VAL cc_start: 0.8253 (t) cc_final: 0.7999 (m) REVERT: q 12 VAL cc_start: 0.7999 (t) cc_final: 0.7689 (m) REVERT: r 11 ARG cc_start: 0.3496 (ptp90) cc_final: 0.2632 (tpp-160) REVERT: r 24 ASP cc_start: 0.7576 (p0) cc_final: 0.7040 (t0) REVERT: r 29 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8517 (mtmt) REVERT: r 47 ARG cc_start: 0.7688 (mmt180) cc_final: 0.6502 (ttp-170) REVERT: s 42 ASN cc_start: 0.7845 (p0) cc_final: 0.7488 (t0) REVERT: t 47 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: t 60 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7674 (mm-40) REVERT: u 4 LYS cc_start: 0.7089 (mttt) cc_final: 0.6711 (mtpt) REVERT: u 19 LYS cc_start: 0.6067 (tttt) cc_final: 0.5409 (tptt) REVERT: z 3 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6704 (mp0) REVERT: z 26 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7831 (p) REVERT: z 68 GLU cc_start: 0.7206 (tt0) cc_final: 0.6424 (tp30) REVERT: z 143 GLU cc_start: 0.7858 (tp30) cc_final: 0.7503 (tm-30) REVERT: z 148 LEU cc_start: 0.5742 (tp) cc_final: 0.5476 (pp) REVERT: z 151 MET cc_start: 0.6358 (tmm) cc_final: 0.5778 (mmp) REVERT: z 194 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6886 (t80) REVERT: z 232 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7474 (tm-30) REVERT: z 237 LYS cc_start: 0.6924 (mtmt) cc_final: 0.6472 (mtpp) REVERT: z 241 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7329 (mm-30) REVERT: z 243 GLU cc_start: 0.8039 (tt0) cc_final: 0.7444 (tt0) REVERT: z 259 GLU cc_start: 0.6499 (mt-10) cc_final: 0.5972 (mt-10) REVERT: z 282 LYS cc_start: 0.7566 (mttt) cc_final: 0.6953 (mptt) REVERT: z 305 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5577 (tm-30) REVERT: z 349 MET cc_start: 0.5438 (ttp) cc_final: 0.5116 (ttm) REVERT: z 356 ILE cc_start: 0.6281 (pt) cc_final: 0.5980 (tt) REVERT: z 358 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.4717 (ptp) outliers start: 243 outliers final: 164 residues processed: 1224 average time/residue: 2.2696 time to fit residues: 4025.0048 Evaluate side-chains 1280 residues out of total 5164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1070 time to evaluate : 6.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 81 ARG Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 12 GLN Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 50 MET Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 88 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 176 LYS Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 113 LYS Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 20 GLN Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 109 ILE Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 53 ARG Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 110 LYS Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 74 MET Chi-restraints excluded: chain m residue 78 ARG Chi-restraints excluded: chain m residue 96 VAL Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 29 LYS Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 47 GLN Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 47 ASP Chi-restraints excluded: chain z residue 71 THR Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 165 ASP Chi-restraints excluded: chain z residue 194 PHE Chi-restraints excluded: chain z residue 206 ILE Chi-restraints excluded: chain z residue 208 LYS Chi-restraints excluded: chain z residue 217 VAL Chi-restraints excluded: chain z residue 231 VAL Chi-restraints excluded: chain z residue 245 VAL Chi-restraints excluded: chain z residue 251 GLN Chi-restraints excluded: chain z residue 253 SER Chi-restraints excluded: chain z residue 290 GLN Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 358 MET Chi-restraints excluded: chain z residue 387 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: 10.0000 chunk 264 optimal weight: 9.9990 chunk 795 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 863 optimal weight: 8.9990 chunk 361 optimal weight: 0.0000 chunk 886 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS E 195 GLN F 36 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN M 88 ASN N 73 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN ** b 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 ASN ** d 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN g 67 ASN h 37 ASN h 75 GLN ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN t 19 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115356 restraints weight = 245854.649| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.92 r_work: 0.3375 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.233 165478 Z= 0.423 Angle : 0.788 59.129 247206 Z= 0.425 Chirality : 0.043 0.672 31414 Planarity : 0.008 0.160 13504 Dihedral : 23.864 178.517 81839 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.68 % Favored : 90.77 % Rotamer: Outliers : 4.96 % Allowed : 32.56 % Favored : 62.49 % 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: -1.44 (0.10), residues: 6219 helix: 0.36 (0.12), residues: 1961 sheet: -1.14 (0.15), residues: 1167 loop : -1.76 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP d 169 HIS 0.008 0.001 HIS C 24 PHE 0.036 0.002 PHE b 89 TYR 0.021 0.002 TYR i 6 ARG 0.014 0.001 ARG b 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 61694.59 seconds wall clock time: 1065 minutes 37.42 seconds (63937.42 seconds total)