Starting phenix.real_space_refine on Sat Mar 2 23:52:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5we4_8814/03_2024/5we4_8814_updated.pdb" } resolution = 3.1 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 4805 5.49 5 Mg 1618 5.21 5 S 171 5.16 5 C 76938 2.51 5 N 28331 2.21 5 O 43203 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 ARG 174": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C ARG 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 79": "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 152": "OD1" <-> "OD2" Residue "F ASP 162": "OD1" <-> "OD2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ASP 136": "OD1" <-> "OD2" 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 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 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 81": "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 ARG 33": "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 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q GLU 88": "OE1" <-> "OE2" 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 ASP 62": "OD1" <-> "OD2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "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 69": "NH1" <-> "NH2" 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 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 ARG 73": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "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 "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 GLU 165": "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 GLU 16": "OE1" <-> "OE2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f ASP 72": "OD1" <-> "OD2" Residue "g ARG 2": "NH1" <-> "NH2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g GLU 128": "OE1" <-> "OE2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ARG 113": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "i PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "k ARG 12": "NH1" <-> "NH2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k GLU 82": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "l 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 "l ARG 109": "NH1" <-> "NH2" 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 GLU 15": "OE1" <-> "OE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "s ARG 31": "NH1" <-> "NH2" Residue "s GLU 72": "OE1" <-> "OE2" Residue "t ARG 9": "NH1" <-> "NH2" 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 ARG 123": "NH1" <-> "NH2" Residue "z ASP 141": "OD1" <-> "OD2" 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 GLU 203": "OE1" <-> "OE2" Residue "z ARG 223": "NH1" <-> "NH2" Residue "z ARG 233": "NH1" <-> "NH2" Residue "z GLU 240": "OE1" <-> "OE2" Residue "z GLU 249": "OE1" <-> "OE2" Residue "z ARG 269": "NH1" <-> "NH2" Residue "z ARG 279": "NH1" <-> "NH2" Residue "z GLU 285": "OE1" <-> "OE2" Residue "z ARG 288": "NH1" <-> "NH2" Residue "z ARG 318": "NH1" <-> "NH2" Residue "z ASP 336": "OD1" <-> "OD2" 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 155067 Number of models: 1 Model: "" Number of chains: 117 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': 6, 'rna2p_pur': 253, 'rna2p_pyr': 126, 'rna3p': 18, 'rna3p_pur': 1414, 'rna3p_pyr': 1082} Link IDs: {'rna2p': 385, 'rna3p': 2514} 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': 114, 'rna2p_pyr': 70, 'rna3p': 10, 'rna3p_pur': 755, 'rna3p_pyr': 590} 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': 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: "w" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "x" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 3, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "y" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1632 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 4 Chain: "z" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3036 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain: "A" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 1182 Unusual residues: {' K': 1, ' MG': 1181} Classifications: {'undetermined': 1182} Link IDs: {None: 1181} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Unusual residues: {' MG': 31} Classifications: {'undetermined': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 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: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: 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: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 373 Unusual residues: {' MG': 373} Classifications: {'undetermined': 373} Link IDs: {None: 372} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 17 Unusual residues: {' MG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "z" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "A" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 751 Classifications: {'water': 751} Link IDs: {None: 750} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 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: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" 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: 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: "y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 56.66, per 1000 atoms: 0.37 Number of scatterers: 155067 At special positions: 0 Unit cell: (277.34, 270.48, 240.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 171 16.00 P 4805 15.00 Mg 1618 11.99 O 43203 8.00 N 28331 7.00 C 76938 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: 62.18 Conformation dependent library (CDL) restraints added in 8.2 seconds 12438 Ramachandran restraints generated. 6219 Oldfield, 0 Emsley, 6219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11606 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 194 helices and 72 sheets defined 38.6% alpha, 18.5% beta 1423 base pairs and 2418 stacking pairs defined. Time for finding SS restraints: 79.96 Creating SS restraints... Processing helix chain 'C' and resid 9 through 16 removed outlier: 7.804A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.684A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.112A 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: 3.993A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.746A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.121A 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: 5.969A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.955A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.332A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.614A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.139A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.481A 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: 3.547A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.677A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.295A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.991A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.589A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.654A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 4.887A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.160A 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: 3.756A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.534A pdb=" N ASP F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.000A 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: 4.663A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.667A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 4.707A 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: 3.920A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.277A 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: 3.719A pdb=" N LYS G 5 " --> pdb=" O SER G 1 " (cutoff:3.500A) removed outlier: 4.213A 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: 4.267A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 4.520A 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: 3.568A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.679A 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: 5.396A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 5.181A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.777A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.036A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.591A 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: 5.243A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 49 removed outlier: 4.599A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.709A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 3.824A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.786A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.654A 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: 4.421A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.832A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.460A 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: 5.742A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.745A 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: 3.597A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.635A 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: 3.927A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.816A 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: 3.797A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 5.754A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.527A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.808A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 37 through 57 removed outlier: 3.570A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.594A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 5.137A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.417A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.697A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.337A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.600A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.607A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.659A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 13 removed outlier: 3.546A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.657A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 109 removed outlier: 3.588A pdb=" N ARG P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 104 through 109' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.501A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.622A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.587A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.049A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.845A 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: 4.020A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.698A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.510A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR S 37 " --> pdb=" O LEU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.734A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 11 removed outlier: 6.647A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.442A 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: 3.539A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.876A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.032A 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: 3.547A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.904A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.560A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.647A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 removed outlier: 3.582A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 8 removed outlier: 3.852A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.840A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 4.381A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 4.956A 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: 4.301A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.566A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.684A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.153A 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: 4.723A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '4' and resid 30 through 35 removed outlier: 4.135A pdb=" N LYS 4 34 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 30 through 35' Processing helix chain '5' and resid 3 through 21 removed outlier: 3.508A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.618A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR 5 39 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 70 removed outlier: 4.147A 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: 4.297A pdb=" N VAL 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.811A pdb=" N GLU 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE 5 106 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 114 removed outlier: 6.561A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 53 removed outlier: 4.318A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.133A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.280A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.546A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.576A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.920A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.507A pdb=" N VAL b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 153 removed outlier: 3.660A pdb=" N LYS b 151 " --> pdb=" O GLY b 148 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 removed outlier: 3.792A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.699A pdb=" N ALA c 47 " --> pdb=" O THR c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.957A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.736A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.558A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.713A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET c 141 " --> pdb=" O VAL c 137 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.944A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.552A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.595A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.726A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.760A 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: 4.172A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 3.584A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.987A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.237A 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: 4.477A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.531A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.275A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.593A 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 removed outlier: 3.500A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.571A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 removed outlier: 3.679A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 3.549A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 3.550A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 5.995A pdb=" N ALA g 23 " --> pdb=" O SER g 19 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 3.536A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 removed outlier: 4.193A pdb=" N ALA g 60 " --> pdb=" O SER g 56 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.007A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 6.032A 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: 3.913A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.708A 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: 3.568A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 removed outlier: 4.167A pdb=" N GLY i 39 " --> pdb=" O GLU i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 53 removed outlier: 4.637A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.616A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.008A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 101 removed outlier: 3.545A pdb=" N SER i 95 " --> pdb=" O GLU i 91 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 3.620A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.749A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.730A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.241A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.795A 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: 3.623A pdb=" N ALA k 65 " --> pdb=" O ALA k 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.743A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.041A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.903A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.191A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.558A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 5.060A 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: 3.578A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.564A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.619A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 31 removed outlier: 4.220A pdb=" N ILE n 29 " --> pdb=" O ALA n 24 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER n 31 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.500A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 3.589A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.713A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.618A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.769A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.574A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.371A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.331A 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: 3.535A pdb=" N SER s 24 " --> pdb=" O LYS s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.486A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 39 removed outlier: 4.989A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 64 removed outlier: 3.516A pdb=" N ALA t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.663A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 85 removed outlier: 4.275A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 3.788A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 34 removed outlier: 4.958A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 61 Proline residue: u 40 - end of helix removed outlier: 3.698A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'z' and resid 23 through 39 removed outlier: 3.538A pdb=" N THR z 28 " --> pdb=" O LYS z 24 " (cutoff:3.500A) Processing helix chain 'z' and resid 45 through 51 removed outlier: 4.472A pdb=" N ILE z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP z 50 " --> pdb=" O PHE z 46 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN z 51 " --> pdb=" O ASN z 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 45 through 51' Processing helix chain 'z' and resid 52 through 59 removed outlier: 4.171A pdb=" N LYS z 56 " --> pdb=" O ALA z 52 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG z 58 " --> pdb=" O GLU z 54 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY z 59 " --> pdb=" O GLU z 55 " (cutoff:3.500A) Processing helix chain 'z' and resid 87 through 99 removed outlier: 3.792A pdb=" N THR z 93 " --> pdb=" O LYS z 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY z 94 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.578A pdb=" N ARG z 116 " --> pdb=" O MET z 112 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN z 124 " --> pdb=" O LEU z 120 " (cutoff:3.500A) Processing helix chain 'z' and resid 136 through 141 removed outlier: 5.976A pdb=" N VAL z 140 " --> pdb=" O LYS z 136 " (cutoff:3.500A) removed outlier: 4.447A 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: 4.126A pdb=" N LEU z 146 " --> pdb=" O ASP z 142 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU z 147 " --> pdb=" O GLU z 143 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL z 149 " --> pdb=" O LEU z 145 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU z 150 " --> pdb=" O LEU z 146 " (cutoff:3.500A) removed outlier: 3.531A 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: 3.621A pdb=" N ALA z 177 " --> pdb=" O SER z 173 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU z 179 " --> pdb=" O LEU z 175 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY z 180 " --> pdb=" O LYS z 176 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 198 removed outlier: 3.589A pdb=" N ILE z 188 " --> pdb=" O TRP z 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU z 191 " --> pdb=" O LYS z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 282 through 287 removed outlier: 3.667A pdb=" N ILE z 286 " --> pdb=" O LYS z 282 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU z 287 " --> pdb=" O ARG z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain 'C' and resid 72 through 77 removed outlier: 4.307A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.636A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.745A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.463A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.887A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.989A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.055A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.525A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 64 through 68 removed outlier: 5.571A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 11, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 12, first strand: chain 'G' and resid 93 through 97 Processing sheet with id= 13, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.970A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 16 through 20 removed outlier: 5.584A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA H 39 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.348A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 78 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.206A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.151A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.365A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.765A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.273A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 33 through 36 removed outlier: 5.331A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.525A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.456A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.627A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.713A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 32 through 36 removed outlier: 5.125A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.129A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.731A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S' and resid 80 through 88 removed outlier: 3.682A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.393A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'U' and resid 41 through 44 Processing sheet with id= 33, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.569A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.613A pdb=" N ILE V 4 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'W' and resid 25 through 28 removed outlier: 4.614A pdb=" N GLU W 25 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE W 78 " --> pdb=" O GLY W 44 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 46 through 50 removed outlier: 7.150A pdb=" N ASN W 46 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.533A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 39, first strand: chain 'Z' and resid 33 through 38 removed outlier: 4.256A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN Z 8 " --> pdb=" O HIS Z 33 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '0' and resid 27 through 30 removed outlier: 6.362A pdb=" N SER 0 28 " --> pdb=" O LYS 0 36 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS 0 36 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP 0 30 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '1' and resid 19 through 24 removed outlier: 3.553A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '3' and resid 21 through 24 removed outlier: 5.615A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 44, first strand: chain '5' and resid 24 through 28 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain '6' and resid 21 through 25 Processing sheet with id= 46, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.641A pdb=" N PHE b 29 " --> pdb=" O ASN b 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN b 41 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 66 through 70 removed outlier: 3.857A pdb=" N PHE b 183 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL b 162 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA b 184 " --> pdb=" O PHE b 197 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.614A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE c 63 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.593A pdb=" N VAL c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 139 through 143 removed outlier: 3.596A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 11 through 15 removed outlier: 4.035A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.669A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL e 122 " --> pdb=" O GLY e 103 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.637A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.644A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 44 through 47 removed outlier: 6.336A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 57, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.244A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.678A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS h 126 " --> pdb=" O VAL h 102 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.603A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.931A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.433A pdb=" N ASN k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 28 through 31 removed outlier: 4.967A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 35 through 40 removed outlier: 5.008A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.990A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL p 19 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 6 through 10 removed outlier: 7.296A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 's' and resid 29 through 33 removed outlier: 4.246A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN s 55 " --> pdb=" O ASN s 52 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'z' and resid 64 through 71 removed outlier: 3.665A pdb=" N TYR z 69 " --> pdb=" O TYR z 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG z 74 " --> pdb=" O THR z 71 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY z 15 " --> pdb=" O GLY z 100 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'z' and resid 210 through 214 removed outlier: 6.576A pdb=" N PHE z 210 " --> pdb=" O LYS z 294 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN z 290 " --> pdb=" O ILE z 214 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'z' and resid 216 through 220 removed outlier: 3.910A pdb=" N ASP z 216 " --> pdb=" O THR z 228 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 234 through 237 removed outlier: 7.225A pdb=" N GLY z 234 " --> pdb=" O ALA z 270 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'z' and resid 336 through 341 removed outlier: 3.817A pdb=" N GLY z 339 " --> pdb=" O PRO z 328 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE z 341 " --> pdb=" O TYR z 326 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR z 326 " --> pdb=" O ILE z 341 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU z 372 " --> pdb=" O VAL z 387 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL z 387 " --> pdb=" O LEU z 372 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE z 374 " --> pdb=" O ALA z 385 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA z 385 " --> pdb=" O PHE z 374 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE z 376 " --> pdb=" O VAL z 383 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG z 381 " --> pdb=" O GLU z 378 " (cutoff:3.500A) 1796 hydrogen bonds defined for protein. 5297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3535 hydrogen bonds 5670 hydrogen bond angles 0 basepair planarities 1423 basepair parallelities 2418 stacking parallelities Total time for adding SS restraints: 389.88 Time building geometry restraints manager: 67.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 61267 1.39 - 1.61: 101498 1.61 - 1.82: 2719 1.82 - 2.03: 0 2.03 - 2.24: 1 Bond restraints: 165485 Sorted by residual: bond pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " ideal model delta sigma weight residual 1.607 2.242 -0.635 1.50e-02 4.44e+03 1.79e+03 bond pdb=" O3' U w 117 " pdb=" P G w 18 " ideal model delta sigma weight residual 1.607 1.348 0.259 1.50e-02 4.44e+03 2.97e+02 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 2.81e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " 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 ... (remaining 165480 not shown) Histogram of bond angle deviations from ideal: 81.42 - 92.65: 3 92.65 - 103.89: 16705 103.89 - 115.13: 119550 115.13 - 126.36: 96442 126.36 - 137.60: 14517 Bond angle restraints: 247217 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 104.00 136.50 -32.50 1.50e+00 4.44e-01 4.69e+02 angle pdb=" N ILE z 49 " pdb=" CA ILE z 49 " pdb=" C ILE z 49 " ideal model delta sigma weight residual 110.72 98.49 12.23 1.01e+00 9.80e-01 1.47e+02 angle pdb=" O3' G A 242 " pdb=" C3' G A 242 " pdb=" C2' G A 242 " ideal model delta sigma weight residual 109.50 126.49 -16.99 1.50e+00 4.44e-01 1.28e+02 angle pdb=" C3' 6MZ A1618 " pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " ideal model delta sigma weight residual 120.20 103.53 16.67 1.50e+00 4.44e-01 1.23e+02 angle pdb=" O3' 6MZ A1618 " pdb=" P G A1619 " pdb=" O5' G A1619 " ideal model delta sigma weight residual 104.00 88.11 15.89 1.50e+00 4.44e-01 1.12e+02 ... (remaining 247212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 92313 35.79 - 71.58: 11968 71.58 - 107.37: 1436 107.37 - 143.16: 44 143.16 - 178.94: 43 Dihedral angle restraints: 105804 sinusoidal: 87803 harmonic: 18001 Sorted by residual: dihedral pdb=" C5' U w 27 " pdb=" C4' U w 27 " pdb=" C3' U w 27 " pdb=" O3' U w 27 " ideal model delta sinusoidal sigma weight residual 147.00 74.55 72.45 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' G a1305 " pdb=" C4' G a1305 " pdb=" C3' G a1305 " pdb=" O3' G a1305 " ideal model delta sinusoidal sigma weight residual 147.00 74.94 72.06 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' C a 280 " pdb=" C4' C a 280 " pdb=" C3' C a 280 " pdb=" O3' C a 280 " ideal model delta sinusoidal sigma weight residual 147.00 77.80 69.20 1 8.00e+00 1.56e-02 9.67e+01 ... (remaining 105801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 28209 0.177 - 0.354: 3172 0.354 - 0.530: 14 0.530 - 0.707: 12 0.707 - 0.884: 7 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 -1.86 -0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" C3' G A1022 " pdb=" C4' G A1022 " pdb=" O3' G A1022 " pdb=" C2' G A1022 " both_signs ideal model delta sigma weight residual False -2.74 -1.90 -0.85 2.00e-01 2.50e+01 1.79e+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 -1.96 -0.79 2.00e-01 2.50e+01 1.56e+01 ... (remaining 31411 not shown) Planarity restraints: 13505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2069 " 0.040 2.00e-02 2.50e+03 6.27e-01 8.85e+03 pdb=" C4' 7MG A2069 " 0.459 2.00e-02 2.50e+03 pdb=" O4' 7MG A2069 " 0.753 2.00e-02 2.50e+03 pdb=" C3' 7MG A2069 " -0.621 2.00e-02 2.50e+03 pdb=" O3' 7MG A2069 " -0.643 2.00e-02 2.50e+03 pdb=" C2' 7MG A2069 " -0.182 2.00e-02 2.50e+03 pdb=" O2' 7MG A2069 " 0.961 2.00e-02 2.50e+03 pdb=" C1' 7MG A2069 " 0.212 2.00e-02 2.50e+03 pdb=" N9 7MG A2069 " -0.981 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " -0.025 2.00e-02 2.50e+03 6.06e-01 8.27e+03 pdb=" C4' 2MG A2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.774 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.614 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.588 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.882 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.230 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.951 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.044 2.00e-02 2.50e+03 6.06e-01 8.26e+03 pdb=" C4' 5MC a1407 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.653 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.605 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.653 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.167 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.981 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.216 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.919 2.00e-02 2.50e+03 ... (remaining 13502 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.29: 268 2.29 - 3.00: 70541 3.00 - 3.71: 329704 3.71 - 4.43: 541765 4.43 - 5.14: 742108 Nonbonded interactions: 1684386 Sorted by model distance: nonbonded pdb=" N1 A A1021 " pdb=" O4 U A1141 " model vdw 1.575 2.496 nonbonded pdb=" OP1 G A1332 " pdb="MG MG A3068 " model vdw 1.762 2.170 nonbonded pdb=" N1 A A2013 " pdb=" O4 U A2613 " model vdw 1.771 2.496 nonbonded pdb=" O4 U a 827 " pdb=" N1 A a 872 " model vdw 1.807 2.496 nonbonded pdb=" OP2 G a 331 " pdb="MG MG a1722 " model vdw 1.818 2.170 ... (remaining 1684381 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) selection = (chain 'w' and resid 1 through 76) } 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 18.360 Check model and map are aligned: 1.660 Set scattering table: 1.110 Process input model: 699.690 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 731.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 0.635 165485 Z= 0.509 Angle : 1.142 32.501 247217 Z= 0.752 Chirality : 0.097 0.884 31414 Planarity : 0.024 0.627 13505 Dihedral : 24.215 178.944 94198 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 2.27 % Allowed : 9.79 % Favored : 87.94 % Rotamer: Outliers : 3.52 % Allowed : 7.18 % Favored : 89.30 % Cbeta Deviations : 0.05 % 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: -4.03 (0.08), residues: 6219 helix: -2.54 (0.09), residues: 1801 sheet: -2.90 (0.14), residues: 963 loop : -2.72 (0.09), residues: 3455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 212 HIS 0.009 0.001 HIS J 47 PHE 0.020 0.002 PHE u 36 TYR 0.024 0.002 TYR G 156 ARG 0.023 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 1910 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1728 time to evaluate : 6.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.7784 (mttt) cc_final: 0.7238 (mmtm) REVERT: C 34 GLU cc_start: 0.7935 (pt0) cc_final: 0.7715 (pt0) REVERT: C 67 LYS cc_start: 0.8383 (mttt) cc_final: 0.8162 (mttp) REVERT: C 78 GLU cc_start: 0.8015 (tt0) cc_final: 0.7738 (mm-30) REVERT: C 110 LYS cc_start: 0.7591 (mttt) cc_final: 0.6931 (tptp) REVERT: C 114 GLN cc_start: 0.7821 (tt0) cc_final: 0.7338 (pp30) REVERT: C 144 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 184 GLU cc_start: 0.7482 (tt0) cc_final: 0.7225 (tt0) REVERT: C 193 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: C 198 GLU cc_start: 0.8043 (mp0) cc_final: 0.7810 (mp0) REVERT: C 200 MET cc_start: 0.8388 (ptt) cc_final: 0.8060 (ptm) REVERT: C 235 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 255 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7767 (mmtt) REVERT: C 263 ASP cc_start: 0.8119 (m-30) cc_final: 0.7617 (m-30) REVERT: C 269 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7599 (mmm160) REVERT: D 46 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7519 (ttp-110) REVERT: D 81 GLU cc_start: 0.8223 (tt0) cc_final: 0.7869 (mt-10) REVERT: D 128 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7951 (mtp180) REVERT: D 157 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8243 (mmtt) REVERT: D 168 GLU cc_start: 0.7826 (tt0) cc_final: 0.7479 (tt0) REVERT: E 67 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7286 (mtp85) REVERT: E 69 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7387 (ptp-170) REVERT: E 171 ASP cc_start: 0.6765 (t70) cc_final: 0.6347 (t0) REVERT: E 189 THR cc_start: 0.7432 (m) cc_final: 0.7209 (t) REVERT: E 193 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8084 (t) REVERT: E 197 GLU cc_start: 0.7042 (tp30) cc_final: 0.6771 (mt-10) REVERT: E 198 GLU cc_start: 0.7802 (tt0) cc_final: 0.7457 (pt0) REVERT: F 10 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7114 (mm-30) REVERT: F 31 GLU cc_start: 0.7583 (tt0) cc_final: 0.7320 (tt0) REVERT: F 46 LYS cc_start: 0.7046 (mttt) cc_final: 0.6738 (mmtm) REVERT: F 62 GLN cc_start: 0.7785 (pt0) cc_final: 0.7136 (pt0) REVERT: F 71 LYS cc_start: 0.7020 (mtmt) cc_final: 0.6407 (pttm) REVERT: F 73 VAL cc_start: 0.6255 (m) cc_final: 0.5925 (p) REVERT: F 77 LYS cc_start: 0.7219 (mtmt) cc_final: 0.6854 (mmtp) REVERT: F 126 ASN cc_start: 0.7083 (m-40) cc_final: 0.6860 (m-40) REVERT: F 132 ARG cc_start: 0.6668 (mtt-85) cc_final: 0.6286 (mpp80) REVERT: F 164 GLU cc_start: 0.7836 (tt0) cc_final: 0.7629 (tt0) REVERT: G 36 LEU cc_start: 0.7350 (tp) cc_final: 0.6972 (mp) REVERT: G 129 GLU cc_start: 0.6502 (tt0) cc_final: 0.5945 (mt-10) REVERT: G 150 TYR cc_start: 0.8088 (m-80) cc_final: 0.7869 (m-80) REVERT: H 37 VAL cc_start: 0.7037 (t) cc_final: 0.6801 (p) REVERT: I 11 GLN cc_start: 0.1981 (OUTLIER) cc_final: 0.0810 (mp10) REVERT: J 17 VAL cc_start: 0.8816 (t) cc_final: 0.8525 (m) REVERT: J 53 TYR cc_start: 0.8702 (m-80) cc_final: 0.8395 (m-80) REVERT: J 85 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (mmtp) REVERT: J 91 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6971 (mm-30) REVERT: J 98 GLU cc_start: 0.7690 (mp0) cc_final: 0.7462 (mp0) REVERT: J 106 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8020 (tttt) REVERT: J 138 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: K 17 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7428 (tpp80) REVERT: K 18 ARG cc_start: 0.7849 (mmt180) cc_final: 0.7493 (mmm160) REVERT: K 37 ASP cc_start: 0.7630 (m-30) cc_final: 0.7055 (m-30) REVERT: K 66 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8530 (mtpp) REVERT: K 105 ARG cc_start: 0.7822 (mmt180) cc_final: 0.7184 (mmm-85) REVERT: K 113 MET cc_start: 0.5890 (tpp) cc_final: 0.5583 (tpp) REVERT: K 114 LYS cc_start: 0.7566 (tptt) cc_final: 0.7252 (mmtp) REVERT: K 115 ILE cc_start: 0.8172 (mt) cc_final: 0.7861 (mm) REVERT: K 121 GLU cc_start: 0.6980 (tt0) cc_final: 0.6698 (tt0) REVERT: L 60 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8320 (ptp90) REVERT: L 70 LYS cc_start: 0.8603 (tttp) cc_final: 0.8222 (ttmt) REVERT: L 78 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5995 (ttm170) REVERT: L 80 SER cc_start: 0.8476 (t) cc_final: 0.8050 (p) REVERT: L 92 LEU cc_start: 0.5901 (mt) cc_final: 0.3847 (pp) REVERT: L 94 THR cc_start: 0.7543 (p) cc_final: 0.7230 (p) REVERT: L 123 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7405 (ttp-110) REVERT: L 136 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6316 (tp30) REVERT: M 18 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6656 (mtp-110) REVERT: M 51 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7503 (mtt-85) REVERT: M 84 LYS cc_start: 0.8047 (mttt) cc_final: 0.7795 (mttp) REVERT: M 133 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7260 (tmtt) REVERT: N 35 LYS cc_start: 0.8889 (tttt) cc_final: 0.8610 (tttp) REVERT: N 54 LEU cc_start: 0.8174 (tp) cc_final: 0.7969 (tt) REVERT: N 57 THR cc_start: 0.7679 (m) cc_final: 0.7164 (p) REVERT: N 65 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7773 (mm) REVERT: N 74 GLU cc_start: 0.7474 (tt0) cc_final: 0.7236 (tp30) REVERT: N 107 ASN cc_start: 0.8500 (t0) cc_final: 0.7983 (t0) REVERT: N 116 VAL cc_start: 0.8288 (t) cc_final: 0.7674 (t) REVERT: O 13 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7670 (tpp-160) REVERT: O 94 ARG cc_start: 0.8341 (ptt90) cc_final: 0.7429 (ptt-90) REVERT: O 98 GLN cc_start: 0.8192 (tt0) cc_final: 0.7790 (tp40) REVERT: P 6 GLN cc_start: 0.7560 (tt0) cc_final: 0.7084 (tp40) REVERT: P 9 GLN cc_start: 0.8413 (tt0) cc_final: 0.7771 (tp40) REVERT: P 26 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: P 28 LYS cc_start: 0.7963 (mttt) cc_final: 0.7573 (mmmt) REVERT: P 36 LYS cc_start: 0.6809 (mmmt) cc_final: 0.6583 (mmmm) REVERT: P 45 VAL cc_start: 0.8735 (t) cc_final: 0.8407 (p) REVERT: P 70 GLU cc_start: 0.7266 (tt0) cc_final: 0.6811 (mt-10) REVERT: P 87 ARG cc_start: 0.7646 (mtp-110) cc_final: 0.7166 (mtp180) REVERT: P 88 ARG cc_start: 0.7474 (mtp180) cc_final: 0.7121 (mtp-110) REVERT: P 110 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7620 (tptm) REVERT: Q 14 LYS cc_start: 0.8702 (tttt) cc_final: 0.8256 (mtpp) REVERT: Q 15 LYS cc_start: 0.8713 (tttt) cc_final: 0.8434 (tttm) REVERT: Q 18 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8023 (mtmt) REVERT: Q 48 ASP cc_start: 0.8348 (m-30) cc_final: 0.7964 (m-30) REVERT: Q 77 LYS cc_start: 0.8114 (mttt) cc_final: 0.7768 (mtmt) REVERT: Q 80 ASN cc_start: 0.8470 (t0) cc_final: 0.8191 (t0) REVERT: Q 83 LYS cc_start: 0.8626 (ttpp) cc_final: 0.7549 (mttt) REVERT: Q 92 LYS cc_start: 0.7941 (tttp) cc_final: 0.7663 (tttm) REVERT: R 2 TYR cc_start: 0.7709 (p90) cc_final: 0.6974 (p90) REVERT: R 40 MET cc_start: 0.8458 (ttp) cc_final: 0.8155 (ttp) REVERT: R 60 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7623 (mmmm) REVERT: R 73 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7495 (tppt) REVERT: R 86 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7908 (mm-40) REVERT: S 98 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7786 (mmmt) REVERT: T 51 PHE cc_start: 0.7849 (m-80) cc_final: 0.7451 (m-80) REVERT: T 52 GLU cc_start: 0.8132 (pt0) cc_final: 0.7212 (mm-30) REVERT: U 5 ARG cc_start: 0.6662 (ptp-170) cc_final: 0.6160 (mtt90) REVERT: U 9 GLU cc_start: 0.7703 (tp30) cc_final: 0.7143 (tp30) REVERT: U 18 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7622 (ttpp) REVERT: U 25 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: U 71 ILE cc_start: 0.9117 (pt) cc_final: 0.8818 (mt) REVERT: V 76 ASP cc_start: 0.8101 (t0) cc_final: 0.7798 (t0) REVERT: W 21 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.8061 (mmt90) REVERT: W 64 LYS cc_start: 0.8228 (tptm) cc_final: 0.7415 (mmtm) REVERT: W 74 LYS cc_start: 0.7667 (mttt) cc_final: 0.7430 (mttm) REVERT: W 77 SER cc_start: 0.8487 (m) cc_final: 0.7821 (p) REVERT: X 38 TRP cc_start: 0.8241 (t-100) cc_final: 0.7997 (t-100) REVERT: X 59 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7057 (t70) REVERT: X 67 LEU cc_start: 0.8351 (mp) cc_final: 0.8107 (mm) REVERT: Y 28 LEU cc_start: 0.8254 (mt) cc_final: 0.8012 (mt) REVERT: Y 37 LEU cc_start: 0.7005 (tp) cc_final: 0.6728 (tp) REVERT: Z 20 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8196 (mmtt) REVERT: 1 31 GLU cc_start: 0.5328 (pm20) cc_final: 0.5097 (pt0) REVERT: 1 32 LYS cc_start: 0.8076 (mttt) cc_final: 0.7658 (mttt) REVERT: 1 37 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7256 (mtpt) REVERT: 1 47 ILE cc_start: 0.7711 (mm) cc_final: 0.7469 (mm) REVERT: 1 49 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6581 (mmmt) REVERT: 2 25 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8443 (ttpp) REVERT: 3 50 SER cc_start: 0.8552 (t) cc_final: 0.8211 (m) REVERT: 3 63 TYR cc_start: 0.8366 (m-80) cc_final: 0.8164 (m-80) REVERT: 4 19 ARG cc_start: 0.7330 (mtt180) cc_final: 0.7092 (mtt180) REVERT: 4 30 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6751 (mp0) REVERT: 5 1 MET cc_start: 0.1757 (tpt) cc_final: 0.1454 (ptp) REVERT: 5 36 ASP cc_start: 0.0505 (OUTLIER) cc_final: -0.1002 (t0) REVERT: 5 38 MET cc_start: 0.1065 (mtm) cc_final: 0.0150 (tpp) REVERT: 6 9 TYR cc_start: 0.6526 (t80) cc_final: 0.6044 (t80) REVERT: 6 25 ARG cc_start: 0.6469 (ttp-170) cc_final: 0.5684 (ptm160) REVERT: 6 61 ASN cc_start: 0.6393 (m110) cc_final: 0.6161 (m-40) REVERT: b 135 MET cc_start: 0.7197 (ttm) cc_final: 0.6514 (tpt) REVERT: b 136 ARG cc_start: 0.6641 (mmm-85) cc_final: 0.5696 (tmm160) REVERT: b 152 ASP cc_start: 0.7440 (m-30) cc_final: 0.7165 (p0) REVERT: b 170 ILE cc_start: 0.8087 (pt) cc_final: 0.7733 (mp) REVERT: b 174 GLU cc_start: 0.7542 (tt0) cc_final: 0.7167 (tt0) REVERT: b 183 PHE cc_start: 0.6954 (p90) cc_final: 0.6751 (p90) REVERT: b 193 ASP cc_start: 0.6656 (t70) cc_final: 0.6164 (t0) REVERT: c 2 GLN cc_start: 0.8266 (pt0) cc_final: 0.7772 (pt0) REVERT: c 7 ASN cc_start: 0.7840 (t0) cc_final: 0.7502 (t0) REVERT: c 37 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7967 (mmmm) REVERT: c 39 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.6838 (mtt90) REVERT: c 48 LYS cc_start: 0.7759 (mttt) cc_final: 0.7432 (mmtm) REVERT: c 75 VAL cc_start: 0.8195 (t) cc_final: 0.7962 (m) REVERT: c 107 LYS cc_start: 0.7804 (mttt) cc_final: 0.7144 (tppt) REVERT: c 113 LYS cc_start: 0.7697 (tptt) cc_final: 0.7220 (ttmm) REVERT: c 156 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7319 (pp) REVERT: c 163 ARG cc_start: 0.6299 (mtt90) cc_final: 0.5959 (ptt-90) REVERT: c 184 ASN cc_start: 0.8787 (t0) cc_final: 0.8564 (t0) REVERT: c 185 THR cc_start: 0.8785 (m) cc_final: 0.8464 (p) REVERT: c 203 LYS cc_start: 0.7894 (mttt) cc_final: 0.7646 (mtpt) REVERT: d 64 TYR cc_start: 0.6896 (m-80) cc_final: 0.6486 (m-80) REVERT: d 72 ARG cc_start: 0.7415 (ttp80) cc_final: 0.7047 (tpt-90) REVERT: d 75 TYR cc_start: 0.7678 (t80) cc_final: 0.7445 (t80) REVERT: d 94 GLU cc_start: 0.5962 (tp30) cc_final: 0.5746 (tp30) REVERT: d 103 ARG cc_start: 0.6924 (mmt-90) cc_final: 0.6672 (mmt90) REVERT: d 112 GLU cc_start: 0.5920 (tt0) cc_final: 0.5374 (tp30) REVERT: d 123 MET cc_start: 0.6772 (ttt) cc_final: 0.6507 (ttt) REVERT: d 142 VAL cc_start: 0.7081 (p) cc_final: 0.6725 (m) REVERT: d 177 MET cc_start: 0.2839 (mmp) cc_final: 0.2364 (mtt) REVERT: e 11 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7721 (tp40) REVERT: e 60 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7765 (mm-40) REVERT: e 65 LYS cc_start: 0.7785 (mttm) cc_final: 0.7311 (mmmm) REVERT: e 129 SER cc_start: 0.8035 (p) cc_final: 0.7732 (p) REVERT: f 5 GLU cc_start: 0.7833 (tt0) cc_final: 0.7585 (tm-30) REVERT: f 39 LEU cc_start: 0.4421 (OUTLIER) cc_final: 0.3584 (mp) REVERT: f 72 ASP cc_start: 0.6931 (m-30) cc_final: 0.6679 (m-30) REVERT: g 4 ARG cc_start: 0.6127 (mmt180) cc_final: 0.5530 (mmm-85) REVERT: g 58 LEU cc_start: 0.7248 (mt) cc_final: 0.6345 (tt) REVERT: g 89 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: g 91 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7100 (ttp80) REVERT: g 117 LEU cc_start: 0.7350 (tp) cc_final: 0.7035 (tp) REVERT: g 129 ASN cc_start: 0.6890 (p0) cc_final: 0.6428 (p0) REVERT: g 136 LYS cc_start: 0.7600 (tttp) cc_final: 0.7392 (tptt) REVERT: g 137 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6526 (ttp-170) REVERT: g 143 MET cc_start: 0.6347 (mmm) cc_final: 0.5943 (mmp) REVERT: h 2 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7660 (tpp) REVERT: h 8 ASP cc_start: 0.7950 (t0) cc_final: 0.7691 (t0) REVERT: h 28 SER cc_start: 0.8539 (t) cc_final: 0.8180 (m) REVERT: h 45 ILE cc_start: 0.8463 (mt) cc_final: 0.8243 (mm) REVERT: h 59 GLU cc_start: 0.7307 (pm20) cc_final: 0.6254 (pm20) REVERT: h 72 GLU cc_start: 0.7953 (tt0) cc_final: 0.7148 (mm-30) REVERT: h 73 SER cc_start: 0.8444 (t) cc_final: 0.8036 (p) REVERT: h 112 ASP cc_start: 0.7896 (p0) cc_final: 0.7687 (p0) REVERT: h 125 ILE cc_start: 0.8320 (mt) cc_final: 0.7818 (mm) REVERT: i 34 LEU cc_start: 0.8024 (tp) cc_final: 0.7720 (tt) REVERT: i 36 GLN cc_start: 0.6096 (pt0) cc_final: 0.5339 (pm20) REVERT: i 109 GLN cc_start: 0.7809 (mt0) cc_final: 0.7378 (mp10) REVERT: j 18 ILE cc_start: 0.7105 (tt) cc_final: 0.6884 (tt) REVERT: j 88 MET cc_start: 0.6394 (mmm) cc_final: 0.5758 (tmm) REVERT: k 27 ASN cc_start: 0.8402 (m-40) cc_final: 0.8144 (m-40) REVERT: k 49 SER cc_start: 0.8492 (m) cc_final: 0.8148 (t) REVERT: k 125 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7616 (tttp) REVERT: l 8 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8002 (mtp-110) REVERT: l 9 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6831 (ptmm) REVERT: l 30 ARG cc_start: 0.6524 (ttm110) cc_final: 0.6298 (ttp-170) REVERT: l 55 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7274 (ttp80) REVERT: m 32 ILE cc_start: 0.7349 (mm) cc_final: 0.6927 (mt) REVERT: m 56 ARG cc_start: 0.7106 (mtt90) cc_final: 0.6786 (mtt90) REVERT: n 5 MET cc_start: 0.8152 (mmm) cc_final: 0.7773 (mmm) REVERT: n 17 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: n 41 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7600 (mtm-85) REVERT: n 62 ASN cc_start: 0.8390 (t0) cc_final: 0.7548 (t0) REVERT: n 89 MET cc_start: 0.7687 (ptp) cc_final: 0.7475 (mtp) REVERT: n 90 ARG cc_start: 0.7752 (ttt90) cc_final: 0.7533 (ttp80) REVERT: o 3 SER cc_start: 0.7673 (t) cc_final: 0.7044 (p) REVERT: p 50 THR cc_start: 0.7308 (m) cc_final: 0.6980 (t) REVERT: q 7 LEU cc_start: 0.7584 (mt) cc_final: 0.7362 (mp) REVERT: q 10 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7387 (ttm170) REVERT: q 18 LYS cc_start: 0.7436 (mttt) cc_final: 0.7153 (mttp) REVERT: q 71 SER cc_start: 0.7556 (m) cc_final: 0.7029 (t) REVERT: r 27 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6661 (p) REVERT: r 47 ARG cc_start: 0.6986 (mmt-90) cc_final: 0.6581 (mmt90) REVERT: s 54 ARG cc_start: 0.8060 (ptt-90) cc_final: 0.7721 (ptt90) REVERT: s 62 THR cc_start: 0.7494 (p) cc_final: 0.7144 (p) REVERT: t 12 GLN cc_start: 0.7112 (tt0) cc_final: 0.6867 (tt0) REVERT: t 15 LYS cc_start: 0.8251 (tttm) cc_final: 0.7720 (tptt) REVERT: t 20 ASN cc_start: 0.8314 (t0) cc_final: 0.8062 (m-40) REVERT: t 26 MET cc_start: 0.7100 (ttp) cc_final: 0.6787 (ttp) REVERT: t 51 ASN cc_start: 0.7489 (m-40) cc_final: 0.7055 (m110) REVERT: t 53 MET cc_start: 0.6543 (ptm) cc_final: 0.6270 (tmm) REVERT: t 68 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7624 (ttpt) REVERT: z 9 LYS cc_start: 0.4244 (mttt) cc_final: 0.3488 (mmtt) REVERT: z 24 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6246 (ttpp) REVERT: z 48 GLN cc_start: 0.4257 (OUTLIER) cc_final: 0.3919 (mp-120) REVERT: z 112 MET cc_start: 0.4860 (OUTLIER) cc_final: 0.4592 (mmp) REVERT: z 136 LYS cc_start: 0.4790 (mptp) cc_final: 0.3618 (mmtp) REVERT: z 152 GLU cc_start: 0.5632 (mt-10) cc_final: 0.5400 (mt-10) REVERT: z 196 ASP cc_start: 0.4737 (m-30) cc_final: 0.4429 (m-30) REVERT: z 237 LYS cc_start: 0.4495 (mtmt) cc_final: 0.4268 (tptp) REVERT: z 260 MET cc_start: 0.5109 (tpp) cc_final: 0.4353 (mmm) REVERT: z 282 LYS cc_start: 0.4824 (mttt) cc_final: 0.4445 (mtpt) outliers start: 182 outliers final: 28 residues processed: 1840 average time/residue: 1.4828 time to fit residues: 4530.8252 Evaluate side-chains 1288 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1224 time to evaluate : 6.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain L residue 3 LEU 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 M residue 18 ARG Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 110 LYS Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 18 LYS Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 37 LYS Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 4 residue 36 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 137 ARG Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain o residue 87 ARG Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain t residue 68 LYS Chi-restraints excluded: chain z residue 22 HIS Chi-restraints excluded: chain z residue 24 LYS Chi-restraints excluded: chain z residue 48 GLN Chi-restraints excluded: chain z residue 49 ILE Chi-restraints excluded: chain z residue 112 MET Chi-restraints excluded: chain z residue 306 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 917 optimal weight: 0.9990 chunk 823 optimal weight: 5.9990 chunk 457 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 555 optimal weight: 3.9990 chunk 440 optimal weight: 0.7980 chunk 851 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 518 optimal weight: 2.9990 chunk 634 optimal weight: 10.0000 chunk 987 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 85 ASN C 114 GLN C 133 ASN D 150 GLN D 173 GLN D 185 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN G 37 ASN G 63 GLN G 103 ASN J 128 ASN K 29 HIS L 54 GLN N 18 GLN N 62 ASN P 11 GLN P 74 GLN P 114 ASN Q 71 ASN R 6 GLN T 70 HIS V 78 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 39 GLN Y 45 GLN Z 19 HIS 2 6 GLN 5 4 ASN 6 41 HIS b 35 ASN c 138 GLN c 189 HIS d 35 GLN d 115 GLN d 135 GLN e 72 ASN e 76 ASN f 3 HIS f 68 GLN f 81 ASN g 27 ASN g 141 HIS ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 GLN l 111 GLN n 3 GLN n 60 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 77 ASN ** z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 114 GLN z 135 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 165485 Z= 0.204 Angle : 0.767 20.671 247217 Z= 0.408 Chirality : 0.040 0.457 31414 Planarity : 0.007 0.131 13505 Dihedral : 24.274 178.873 82010 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.06 % Favored : 92.17 % Rotamer: Outliers : 3.79 % Allowed : 14.15 % Favored : 82.06 % 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: -2.48 (0.10), residues: 6219 helix: -0.25 (0.11), residues: 1928 sheet: -2.17 (0.14), residues: 1117 loop : -2.37 (0.09), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 212 HIS 0.010 0.001 HIS z 118 PHE 0.027 0.002 PHE Y 26 TYR 0.015 0.002 TYR F 21 ARG 0.006 0.001 ARG K 17 *********************** 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 1535 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1339 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 SER cc_start: 0.7901 (t) cc_final: 0.7642 (p) REVERT: C 27 LYS cc_start: 0.7995 (mttt) cc_final: 0.7441 (mmtm) REVERT: C 34 GLU cc_start: 0.7957 (pt0) cc_final: 0.7703 (pt0) REVERT: C 110 LYS cc_start: 0.7654 (mttt) cc_final: 0.6971 (tptp) REVERT: C 114 GLN cc_start: 0.7635 (tt0) cc_final: 0.7267 (mm-40) REVERT: C 200 MET cc_start: 0.8390 (ptt) cc_final: 0.8030 (ptm) REVERT: C 255 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7625 (mmtt) REVERT: C 263 ASP cc_start: 0.8010 (m-30) cc_final: 0.7442 (m-30) REVERT: C 269 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7772 (mmm160) REVERT: D 20 VAL cc_start: 0.8410 (t) cc_final: 0.8185 (p) REVERT: D 128 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7961 (mtp180) REVERT: D 150 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: D 157 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (mmtt) REVERT: E 24 ASN cc_start: 0.8359 (t0) cc_final: 0.7902 (t0) REVERT: E 67 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7266 (mtp85) REVERT: E 111 GLU cc_start: 0.8094 (tp30) cc_final: 0.7782 (tp30) REVERT: E 184 ASP cc_start: 0.8418 (m-30) cc_final: 0.7298 (t0) REVERT: E 195 GLN cc_start: 0.7616 (tt0) cc_final: 0.7285 (tt0) REVERT: E 198 GLU cc_start: 0.7827 (tt0) cc_final: 0.7556 (pt0) REVERT: E 199 MET cc_start: 0.7936 (ttp) cc_final: 0.7413 (tmm) REVERT: F 18 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6532 (tt0) REVERT: F 31 GLU cc_start: 0.7347 (tt0) cc_final: 0.7091 (tt0) REVERT: F 45 ASP cc_start: 0.5556 (m-30) cc_final: 0.5235 (t0) REVERT: F 46 LYS cc_start: 0.6999 (mttt) cc_final: 0.6723 (mmtm) REVERT: G 63 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7476 (mm110) REVERT: G 129 GLU cc_start: 0.6101 (tt0) cc_final: 0.5648 (mt-10) REVERT: G 130 ILE cc_start: 0.8514 (mt) cc_final: 0.8303 (tp) REVERT: G 133 LYS cc_start: 0.7065 (mttp) cc_final: 0.6821 (mtmm) REVERT: G 150 TYR cc_start: 0.7816 (m-80) cc_final: 0.7476 (m-80) REVERT: J 57 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8231 (pp) REVERT: J 85 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7867 (mmpt) REVERT: J 91 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6886 (mt-10) REVERT: J 92 MET cc_start: 0.8120 (tpt) cc_final: 0.7856 (mmm) REVERT: J 96 ARG cc_start: 0.6615 (mmm160) cc_final: 0.6197 (ttm-80) REVERT: J 98 GLU cc_start: 0.7797 (mp0) cc_final: 0.7233 (mp0) REVERT: J 131 ASN cc_start: 0.8096 (t0) cc_final: 0.7872 (t0) REVERT: J 138 GLN cc_start: 0.8201 (pt0) cc_final: 0.7723 (pm20) REVERT: K 32 TYR cc_start: 0.9002 (m-80) cc_final: 0.8546 (m-80) REVERT: K 37 ASP cc_start: 0.7610 (m-30) cc_final: 0.6904 (m-30) REVERT: K 69 VAL cc_start: 0.8701 (t) cc_final: 0.8431 (m) REVERT: K 105 ARG cc_start: 0.7427 (mmt180) cc_final: 0.6852 (mmm-85) REVERT: K 111 LYS cc_start: 0.7365 (ptpt) cc_final: 0.7094 (ptmm) REVERT: K 113 MET cc_start: 0.5807 (tpp) cc_final: 0.5592 (tpp) REVERT: L 12 SER cc_start: 0.8607 (t) cc_final: 0.8238 (p) REVERT: L 70 LYS cc_start: 0.8636 (tttp) cc_final: 0.8313 (ttmt) REVERT: L 80 SER cc_start: 0.8450 (t) cc_final: 0.8009 (p) REVERT: L 120 VAL cc_start: 0.8218 (t) cc_final: 0.7961 (p) REVERT: L 123 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7121 (ttp-110) REVERT: M 6 ARG cc_start: 0.7056 (ptm160) cc_final: 0.6458 (ttp-110) REVERT: M 18 ARG cc_start: 0.7473 (mtp180) cc_final: 0.6754 (mtp-110) REVERT: M 50 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7866 (ttp80) REVERT: M 51 ARG cc_start: 0.7843 (mtt90) cc_final: 0.7280 (mtt-85) REVERT: M 84 LYS cc_start: 0.8106 (mttt) cc_final: 0.7890 (mttp) REVERT: M 119 LEU cc_start: 0.8140 (mt) cc_final: 0.7931 (mt) REVERT: M 133 LYS cc_start: 0.7610 (ttpp) cc_final: 0.7292 (tmtt) REVERT: N 14 SER cc_start: 0.8914 (t) cc_final: 0.8612 (m) REVERT: N 35 LYS cc_start: 0.8749 (tttt) cc_final: 0.8458 (tttp) REVERT: N 37 THR cc_start: 0.8759 (p) cc_final: 0.8469 (p) REVERT: N 74 GLU cc_start: 0.7777 (tt0) cc_final: 0.7504 (tp30) REVERT: O 98 GLN cc_start: 0.8190 (tt0) cc_final: 0.7836 (tp40) REVERT: P 6 GLN cc_start: 0.7583 (tt0) cc_final: 0.7144 (tp40) REVERT: P 9 GLN cc_start: 0.8202 (tt0) cc_final: 0.7567 (tp40) REVERT: P 26 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6973 (tp30) REVERT: P 28 LYS cc_start: 0.7974 (mttt) cc_final: 0.7564 (mmmt) REVERT: P 36 LYS cc_start: 0.6827 (mmmt) cc_final: 0.6526 (mmmm) REVERT: P 45 VAL cc_start: 0.8643 (t) cc_final: 0.8344 (p) REVERT: P 70 GLU cc_start: 0.6941 (tt0) cc_final: 0.6597 (mt-10) REVERT: P 87 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7392 (mtp180) REVERT: Q 14 LYS cc_start: 0.8308 (tttt) cc_final: 0.8018 (mtpp) REVERT: Q 15 LYS cc_start: 0.8576 (tttt) cc_final: 0.8333 (tttm) REVERT: Q 18 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7866 (mtmt) REVERT: Q 48 ASP cc_start: 0.8304 (m-30) cc_final: 0.7934 (m-30) REVERT: Q 77 LYS cc_start: 0.8279 (mttt) cc_final: 0.7906 (mtpt) REVERT: Q 94 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8509 (mt) REVERT: R 2 TYR cc_start: 0.8010 (p90) cc_final: 0.7670 (p90) REVERT: R 11 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8989 (mt0) REVERT: R 60 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7518 (mmmm) REVERT: R 70 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7462 (mm-30) REVERT: R 71 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8503 (tttp) REVERT: T 52 GLU cc_start: 0.8038 (pt0) cc_final: 0.6976 (mm-30) REVERT: U 5 ARG cc_start: 0.6538 (ptp-170) cc_final: 0.6156 (mtt180) REVERT: U 9 GLU cc_start: 0.7755 (tp30) cc_final: 0.7257 (tp30) REVERT: U 71 ILE cc_start: 0.8875 (pt) cc_final: 0.8430 (mt) REVERT: U 100 GLU cc_start: 0.7380 (mp0) cc_final: 0.7082 (mp0) REVERT: V 38 LEU cc_start: 0.7784 (tp) cc_final: 0.7579 (tp) REVERT: V 51 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: W 21 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7980 (mmt90) REVERT: W 77 SER cc_start: 0.8333 (m) cc_final: 0.7655 (p) REVERT: X 44 ARG cc_start: 0.7300 (ptt90) cc_final: 0.7092 (ptm-80) REVERT: X 55 MET cc_start: 0.8509 (mtp) cc_final: 0.7943 (mtp) REVERT: X 59 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: 0 47 TYR cc_start: 0.8150 (m-80) cc_final: 0.7588 (m-80) REVERT: 0 51 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7492 (tmm160) REVERT: 1 47 ILE cc_start: 0.8022 (mm) cc_final: 0.7807 (mm) REVERT: 1 49 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6633 (mmmt) REVERT: 2 1 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7771 (ptp) REVERT: 2 25 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8303 (ttpp) REVERT: 3 50 SER cc_start: 0.8295 (t) cc_final: 0.7610 (m) REVERT: 3 53 ASP cc_start: 0.7931 (m-30) cc_final: 0.7713 (p0) REVERT: 3 61 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8252 (pp) REVERT: 4 30 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6743 (mp0) REVERT: 5 36 ASP cc_start: -0.0516 (OUTLIER) cc_final: -0.1338 (t0) REVERT: 5 38 MET cc_start: 0.0573 (mtm) cc_final: -0.0556 (tpp) REVERT: 6 25 ARG cc_start: 0.5816 (ttp-170) cc_final: 0.4899 (ptp-170) REVERT: 6 61 ASN cc_start: 0.6201 (m110) cc_final: 0.5947 (m110) REVERT: b 18 GLN cc_start: 0.5161 (mm110) cc_final: 0.4900 (mm-40) REVERT: b 48 MET cc_start: 0.5652 (mmm) cc_final: 0.5355 (mmm) REVERT: b 50 ASN cc_start: 0.6316 (t0) cc_final: 0.5959 (m-40) REVERT: b 136 ARG cc_start: 0.6313 (mmm-85) cc_final: 0.5457 (tmm160) REVERT: b 170 ILE cc_start: 0.7801 (pt) cc_final: 0.7569 (mm) REVERT: b 183 PHE cc_start: 0.6461 (p90) cc_final: 0.6164 (p90) REVERT: c 2 GLN cc_start: 0.8615 (pt0) cc_final: 0.8392 (pt0) REVERT: c 7 ASN cc_start: 0.7378 (t0) cc_final: 0.7103 (t0) REVERT: c 17 TRP cc_start: 0.7957 (m-90) cc_final: 0.7552 (m-90) REVERT: c 37 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8018 (mmmm) REVERT: c 57 GLU cc_start: 0.7118 (mp0) cc_final: 0.6898 (mp0) REVERT: c 61 LYS cc_start: 0.5778 (tptp) cc_final: 0.5461 (mtmm) REVERT: c 84 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6842 (tm-30) REVERT: c 107 LYS cc_start: 0.7811 (mttt) cc_final: 0.7292 (tppt) REVERT: c 113 LYS cc_start: 0.7623 (tptt) cc_final: 0.7384 (tppt) REVERT: c 122 GLN cc_start: 0.7744 (mt0) cc_final: 0.7519 (mt0) REVERT: c 163 ARG cc_start: 0.5846 (mtt90) cc_final: 0.5299 (mtm110) REVERT: c 182 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8224 (t0) REVERT: c 185 THR cc_start: 0.8720 (m) cc_final: 0.8505 (p) REVERT: c 187 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7610 (mt-10) REVERT: c 203 LYS cc_start: 0.7846 (mttt) cc_final: 0.7579 (mtpt) REVERT: d 32 LYS cc_start: 0.4059 (mttt) cc_final: 0.3735 (ptmt) REVERT: d 71 PHE cc_start: 0.7963 (t80) cc_final: 0.7736 (t80) REVERT: d 72 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6866 (tpt-90) REVERT: d 94 GLU cc_start: 0.5580 (tp30) cc_final: 0.5190 (tp30) REVERT: d 103 ARG cc_start: 0.6887 (mmt-90) cc_final: 0.6392 (mmt90) REVERT: d 123 MET cc_start: 0.6521 (ttt) cc_final: 0.6318 (ttt) REVERT: e 11 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7669 (tp40) REVERT: e 44 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7411 (mmm160) REVERT: e 65 LYS cc_start: 0.7658 (mttm) cc_final: 0.7174 (mmmm) REVERT: e 85 LYS cc_start: 0.8456 (mptt) cc_final: 0.8256 (mttm) REVERT: e 115 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7294 (tm-30) REVERT: e 129 SER cc_start: 0.7988 (p) cc_final: 0.7737 (p) REVERT: f 25 TYR cc_start: 0.6785 (m-10) cc_final: 0.6570 (m-10) REVERT: g 4 ARG cc_start: 0.6384 (mmt180) cc_final: 0.5636 (mmm-85) REVERT: g 39 GLU cc_start: 0.8022 (pt0) cc_final: 0.7766 (pt0) REVERT: g 67 ASN cc_start: 0.7218 (m-40) cc_final: 0.6536 (t0) REVERT: g 77 ARG cc_start: 0.5069 (ttt-90) cc_final: 0.4193 (mtm180) REVERT: g 89 GLU cc_start: 0.7642 (mp0) cc_final: 0.7054 (tm-30) REVERT: g 91 ARG cc_start: 0.7629 (mmm160) cc_final: 0.6972 (ptt-90) REVERT: g 100 MET cc_start: 0.7635 (mtm) cc_final: 0.7322 (mpp) REVERT: g 135 LYS cc_start: 0.7767 (tppp) cc_final: 0.7516 (tppt) REVERT: g 137 ARG cc_start: 0.6753 (ttt90) cc_final: 0.6405 (ttp-170) REVERT: g 148 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8610 (mtpp) REVERT: h 28 SER cc_start: 0.8567 (t) cc_final: 0.8308 (t) REVERT: h 45 ILE cc_start: 0.8280 (mt) cc_final: 0.8039 (mm) REVERT: h 72 GLU cc_start: 0.8004 (tt0) cc_final: 0.7202 (mm-30) REVERT: h 73 SER cc_start: 0.8311 (t) cc_final: 0.8010 (p) REVERT: h 125 ILE cc_start: 0.8168 (mt) cc_final: 0.7713 (mm) REVERT: i 35 GLU cc_start: 0.7073 (pm20) cc_final: 0.6812 (pm20) REVERT: j 72 ARG cc_start: 0.7421 (mmt-90) cc_final: 0.7198 (mmt180) REVERT: j 88 MET cc_start: 0.6568 (mmm) cc_final: 0.5954 (ttp) REVERT: k 27 ASN cc_start: 0.8467 (m-40) cc_final: 0.8198 (m-40) REVERT: k 37 GLN cc_start: 0.7572 (mp10) cc_final: 0.7356 (mp10) REVERT: k 49 SER cc_start: 0.8355 (m) cc_final: 0.7937 (t) REVERT: k 107 THR cc_start: 0.6551 (m) cc_final: 0.6337 (p) REVERT: k 125 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7542 (tttp) REVERT: l 9 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6593 (ptmm) REVERT: l 26 CYS cc_start: 0.7902 (p) cc_final: 0.7534 (m) REVERT: l 55 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7735 (tmt170) REVERT: l 61 GLU cc_start: 0.8013 (tp30) cc_final: 0.7743 (mt-10) REVERT: l 76 HIS cc_start: 0.6154 (m-70) cc_final: 0.5811 (m-70) REVERT: l 87 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6718 (tptp) REVERT: l 95 HIS cc_start: 0.8343 (m170) cc_final: 0.8086 (m-70) REVERT: m 71 GLU cc_start: 0.7720 (tt0) cc_final: 0.7196 (tp30) REVERT: n 13 VAL cc_start: 0.7864 (t) cc_final: 0.7094 (m) REVERT: n 17 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7114 (m-30) REVERT: n 62 ASN cc_start: 0.8543 (t0) cc_final: 0.7766 (t0) REVERT: o 4 THR cc_start: 0.6660 (m) cc_final: 0.6312 (m) REVERT: o 47 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7306 (mmtm) REVERT: p 18 GLN cc_start: 0.7285 (mm110) cc_final: 0.6181 (tt0) REVERT: q 10 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7295 (ttm170) REVERT: q 18 LYS cc_start: 0.7541 (mttt) cc_final: 0.7258 (mttp) REVERT: q 71 SER cc_start: 0.7646 (m) cc_final: 0.7162 (t) REVERT: r 69 TYR cc_start: 0.9072 (m-80) cc_final: 0.8680 (m-80) REVERT: s 20 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6830 (mmtm) REVERT: s 36 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6383 (ptm160) REVERT: s 54 ARG cc_start: 0.8058 (ptt-90) cc_final: 0.7834 (ptt90) REVERT: t 12 GLN cc_start: 0.6860 (tt0) cc_final: 0.6579 (tt0) REVERT: t 23 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7707 (tpp-160) REVERT: t 26 MET cc_start: 0.6536 (ttp) cc_final: 0.6333 (ttp) REVERT: t 35 TYR cc_start: 0.7094 (m-80) cc_final: 0.6511 (m-10) REVERT: t 43 LYS cc_start: 0.4387 (tttt) cc_final: 0.4065 (ptmm) REVERT: t 51 ASN cc_start: 0.7552 (m-40) cc_final: 0.7216 (m110) REVERT: u 33 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7365 (mtm110) REVERT: u 34 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7516 (tpt170) REVERT: u 44 ARG cc_start: 0.7209 (mtt180) cc_final: 0.7001 (mtt180) REVERT: z 9 LYS cc_start: 0.4466 (mttt) cc_final: 0.3589 (mmtt) REVERT: z 17 ILE cc_start: 0.4979 (mt) cc_final: 0.4277 (tp) REVERT: z 48 GLN cc_start: 0.4442 (OUTLIER) cc_final: 0.4226 (mp-120) REVERT: z 75 HIS cc_start: 0.6671 (t70) cc_final: 0.6438 (t70) REVERT: z 237 LYS cc_start: 0.4465 (mtmt) cc_final: 0.4243 (tptp) REVERT: z 243 GLU cc_start: 0.6540 (tt0) cc_final: 0.6334 (tt0) REVERT: z 282 LYS cc_start: 0.4962 (mttt) cc_final: 0.4584 (mtpt) REVERT: z 284 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5892 (mp0) REVERT: z 323 PHE cc_start: 0.5294 (t80) cc_final: 0.5037 (m-80) REVERT: z 332 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5396 (t80) outliers start: 196 outliers final: 102 residues processed: 1462 average time/residue: 1.4807 time to fit residues: 3663.6920 Evaluate side-chains 1305 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1180 time to evaluate : 6.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 2 residue 25 LYS Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 41 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 11 GLN Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain o residue 87 ARG Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 22 HIS Chi-restraints excluded: chain z residue 48 GLN Chi-restraints excluded: chain z residue 89 LYS Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 306 SER Chi-restraints excluded: chain z residue 332 PHE Chi-restraints excluded: chain z residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 548 optimal weight: 7.9990 chunk 306 optimal weight: 0.0010 chunk 821 optimal weight: 9.9990 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 988 optimal weight: 10.0000 chunk 1068 optimal weight: 6.9990 chunk 880 optimal weight: 6.9990 chunk 980 optimal weight: 8.9990 chunk 337 optimal weight: 3.9990 chunk 793 optimal weight: 8.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 HIS C 199 HIS E 136 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 72 ASN G 103 ASN H 73 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 76 HIS J 131 ASN N 18 GLN P 11 GLN R 6 GLN R 66 HIS R 89 HIS S 31 GLN T 15 HIS T 70 HIS V 75 GLN V 78 GLN Y 20 ASN Y 31 GLN Z 33 HIS 0 4 GLN b 167 HIS ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 122 GLN c 138 GLN d 115 GLN e 121 ASN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 109 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 ASN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS s 56 HIS t 54 GLN t 69 ASN t 74 HIS z 13 ASN ** z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 329 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 165485 Z= 0.386 Angle : 0.838 18.261 247217 Z= 0.439 Chirality : 0.045 0.417 31414 Planarity : 0.008 0.144 13505 Dihedral : 24.308 179.306 81897 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.80 % Favored : 90.58 % Rotamer: Outliers : 5.69 % Allowed : 15.75 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 6219 helix: -0.24 (0.11), residues: 1956 sheet: -1.85 (0.14), residues: 1099 loop : -2.25 (0.10), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 22 HIS 0.039 0.002 HIS T 70 PHE 0.034 0.003 PHE j 13 TYR 0.038 0.003 TYR c 167 ARG 0.011 0.001 ARG m 2 *********************** 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 1526 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1232 time to evaluate : 6.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8096 (mttt) cc_final: 0.7462 (mmtm) REVERT: C 114 GLN cc_start: 0.7607 (tt0) cc_final: 0.7045 (mt0) REVERT: C 115 ILE cc_start: 0.8421 (mt) cc_final: 0.7954 (mm) REVERT: C 144 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7739 (mt-10) REVERT: C 152 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8341 (mm-40) REVERT: C 263 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: C 269 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7740 (mmm160) REVERT: D 7 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8033 (ttpp) REVERT: D 42 ASN cc_start: 0.6665 (m-40) cc_final: 0.6408 (t0) REVERT: D 128 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7969 (mtp180) REVERT: D 157 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8182 (mmtt) REVERT: E 16 GLU cc_start: 0.7456 (tp30) cc_final: 0.6981 (tp30) REVERT: E 67 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7221 (mtp85) REVERT: E 111 GLU cc_start: 0.8670 (tp30) cc_final: 0.7798 (tp30) REVERT: E 115 GLN cc_start: 0.7722 (mt0) cc_final: 0.7212 (mt0) REVERT: E 141 MET cc_start: 0.7472 (ttm) cc_final: 0.7121 (ttm) REVERT: E 183 PHE cc_start: 0.8764 (m-80) cc_final: 0.8541 (m-80) REVERT: E 198 GLU cc_start: 0.7893 (tt0) cc_final: 0.7403 (tm-30) REVERT: E 199 MET cc_start: 0.8045 (ttp) cc_final: 0.7670 (tmm) REVERT: F 18 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6769 (tt0) REVERT: F 46 LYS cc_start: 0.7142 (mttt) cc_final: 0.6800 (mmtm) REVERT: F 93 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7102 (tm-30) REVERT: G 133 LYS cc_start: 0.7038 (mttp) cc_final: 0.6623 (tptp) REVERT: G 150 TYR cc_start: 0.7761 (m-80) cc_final: 0.7224 (m-80) REVERT: I 124 MET cc_start: 0.1082 (mtm) cc_final: 0.0754 (ppp) REVERT: J 1 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7200 (ppp) REVERT: J 57 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8081 (pp) REVERT: J 85 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7826 (mmpt) REVERT: J 91 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6974 (mt-10) REVERT: J 138 GLN cc_start: 0.7734 (pt0) cc_final: 0.7339 (pm20) REVERT: K 37 ASP cc_start: 0.7921 (m-30) cc_final: 0.7175 (m-30) REVERT: K 56 ASP cc_start: 0.7941 (t0) cc_final: 0.7714 (t0) REVERT: K 105 ARG cc_start: 0.7328 (mmt180) cc_final: 0.6961 (mmm-85) REVERT: L 12 SER cc_start: 0.8742 (t) cc_final: 0.8380 (p) REVERT: L 70 LYS cc_start: 0.8734 (tttp) cc_final: 0.8419 (ttmt) REVERT: L 80 SER cc_start: 0.8600 (t) cc_final: 0.8131 (p) REVERT: L 123 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7097 (ttp-110) REVERT: L 126 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.7300 (mtm180) REVERT: M 6 ARG cc_start: 0.7509 (ptm160) cc_final: 0.7108 (ptm160) REVERT: M 18 ARG cc_start: 0.7615 (mtp180) cc_final: 0.6938 (mtp-110) REVERT: M 51 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7308 (mtt-85) REVERT: M 84 LYS cc_start: 0.8188 (mttt) cc_final: 0.7918 (mttp) REVERT: M 133 LYS cc_start: 0.7694 (ttpp) cc_final: 0.7276 (tmtt) REVERT: N 14 SER cc_start: 0.8903 (t) cc_final: 0.8700 (m) REVERT: N 35 LYS cc_start: 0.8781 (tttt) cc_final: 0.8444 (tttp) REVERT: N 37 THR cc_start: 0.8807 (p) cc_final: 0.8588 (p) REVERT: O 12 THR cc_start: 0.8523 (m) cc_final: 0.8110 (m) REVERT: O 98 GLN cc_start: 0.8256 (tt0) cc_final: 0.7911 (tp40) REVERT: P 6 GLN cc_start: 0.7530 (tt0) cc_final: 0.7103 (tp40) REVERT: P 9 GLN cc_start: 0.8104 (tt0) cc_final: 0.7358 (tp40) REVERT: P 26 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: P 28 LYS cc_start: 0.8032 (mttt) cc_final: 0.7637 (mmmt) REVERT: P 31 VAL cc_start: 0.8492 (p) cc_final: 0.8136 (m) REVERT: P 70 GLU cc_start: 0.7267 (tt0) cc_final: 0.6823 (mt-10) REVERT: P 114 ASN cc_start: 0.6761 (OUTLIER) cc_final: 0.5955 (t0) REVERT: Q 14 LYS cc_start: 0.8490 (tttt) cc_final: 0.8253 (mtpp) REVERT: Q 15 LYS cc_start: 0.8665 (tttt) cc_final: 0.8422 (tttm) REVERT: Q 18 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7796 (mtmt) REVERT: Q 48 ASP cc_start: 0.8400 (m-30) cc_final: 0.8083 (m-30) REVERT: Q 77 LYS cc_start: 0.8415 (mttt) cc_final: 0.7968 (mtmt) REVERT: Q 94 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8321 (mp) REVERT: Q 106 THR cc_start: 0.8218 (m) cc_final: 0.7948 (m) REVERT: R 13 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7894 (ttt-90) REVERT: R 40 MET cc_start: 0.8396 (ttp) cc_final: 0.8030 (ttp) REVERT: S 57 ASN cc_start: 0.7796 (m-40) cc_final: 0.7535 (m-40) REVERT: T 52 GLU cc_start: 0.8109 (pt0) cc_final: 0.6984 (mm-30) REVERT: U 8 ASP cc_start: 0.7672 (m-30) cc_final: 0.7454 (m-30) REVERT: U 9 GLU cc_start: 0.7749 (tp30) cc_final: 0.7263 (tp30) REVERT: U 100 GLU cc_start: 0.7014 (mp0) cc_final: 0.6667 (mp0) REVERT: V 73 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7734 (mmmt) REVERT: W 74 LYS cc_start: 0.7673 (mttp) cc_final: 0.7393 (mtmm) REVERT: X 55 MET cc_start: 0.8458 (mtp) cc_final: 0.7963 (mtt) REVERT: X 59 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: Y 26 PHE cc_start: 0.8824 (t80) cc_final: 0.8529 (t80) REVERT: 0 11 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8458 (mmtm) REVERT: 0 49 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7668 (mmm160) REVERT: 1 31 GLU cc_start: 0.5189 (pm20) cc_final: 0.4834 (tt0) REVERT: 1 49 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6664 (mmmt) REVERT: 2 1 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7993 (ptp) REVERT: 3 14 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8133 (mptt) REVERT: 3 53 ASP cc_start: 0.7893 (m-30) cc_final: 0.7669 (p0) REVERT: 4 30 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7042 (mp0) REVERT: 5 36 ASP cc_start: 0.0316 (OUTLIER) cc_final: -0.1430 (t0) REVERT: 5 38 MET cc_start: 0.0298 (mtm) cc_final: -0.0764 (tpt) REVERT: 5 40 GLU cc_start: 0.3577 (OUTLIER) cc_final: 0.2364 (pm20) REVERT: 6 35 ASP cc_start: 0.4735 (OUTLIER) cc_final: 0.4361 (m-30) REVERT: b 50 ASN cc_start: 0.5668 (t0) cc_final: 0.5353 (m-40) REVERT: b 86 CYS cc_start: 0.4599 (t) cc_final: 0.4396 (t) REVERT: b 107 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6716 (ptm-80) REVERT: b 108 GLN cc_start: 0.7586 (pt0) cc_final: 0.6975 (mm110) REVERT: b 135 MET cc_start: 0.7184 (tpt) cc_final: 0.6757 (tpp) REVERT: b 136 ARG cc_start: 0.6296 (mmm-85) cc_final: 0.5237 (tmm160) REVERT: b 183 PHE cc_start: 0.6542 (p90) cc_final: 0.5812 (p90) REVERT: b 191 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7950 (t70) REVERT: b 202 ASN cc_start: 0.7213 (p0) cc_final: 0.6816 (t0) REVERT: c 7 ASN cc_start: 0.7703 (t0) cc_final: 0.7426 (t0) REVERT: c 37 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8193 (mmmm) REVERT: c 84 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6933 (tm-30) REVERT: c 107 LYS cc_start: 0.7829 (mttt) cc_final: 0.7328 (tppt) REVERT: c 122 GLN cc_start: 0.7904 (mt0) cc_final: 0.7648 (mt0) REVERT: c 163 ARG cc_start: 0.6023 (mtt90) cc_final: 0.5328 (mtm110) REVERT: d 56 GLU cc_start: 0.7045 (tp30) cc_final: 0.6722 (tp30) REVERT: d 68 GLU cc_start: 0.6481 (tp30) cc_final: 0.6107 (tp30) REVERT: d 72 ARG cc_start: 0.7259 (ttp80) cc_final: 0.7043 (tpt-90) REVERT: d 123 MET cc_start: 0.6413 (ttt) cc_final: 0.6202 (ttt) REVERT: e 65 LYS cc_start: 0.7701 (mttm) cc_final: 0.7207 (mmmm) REVERT: e 129 SER cc_start: 0.8319 (p) cc_final: 0.7991 (p) REVERT: e 155 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7402 (ttmm) REVERT: f 5 GLU cc_start: 0.7609 (tt0) cc_final: 0.7341 (tt0) REVERT: f 8 PHE cc_start: 0.7804 (p90) cc_final: 0.7505 (p90) REVERT: f 45 ARG cc_start: 0.7117 (mtp-110) cc_final: 0.6886 (mtp-110) REVERT: g 39 GLU cc_start: 0.7929 (pt0) cc_final: 0.7095 (pt0) REVERT: g 67 ASN cc_start: 0.7159 (m-40) cc_final: 0.6469 (t0) REVERT: g 77 ARG cc_start: 0.5253 (ttt-90) cc_final: 0.3586 (mtm180) REVERT: g 91 ARG cc_start: 0.7607 (mmm160) cc_final: 0.6883 (ptt-90) REVERT: g 100 MET cc_start: 0.7486 (mtm) cc_final: 0.7251 (mpp) REVERT: h 28 SER cc_start: 0.8665 (t) cc_final: 0.8449 (t) REVERT: h 42 GLU cc_start: 0.7532 (tp30) cc_final: 0.7127 (mm-30) REVERT: h 45 ILE cc_start: 0.8338 (mt) cc_final: 0.8028 (mm) REVERT: h 73 SER cc_start: 0.8315 (t) cc_final: 0.7905 (p) REVERT: i 30 ASN cc_start: 0.6922 (m-40) cc_final: 0.6537 (t0) REVERT: k 84 MET cc_start: 0.7862 (mmt) cc_final: 0.7363 (mmm) REVERT: k 100 ASN cc_start: 0.6222 (m-40) cc_final: 0.5731 (m110) REVERT: k 125 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7435 (tttp) REVERT: l 9 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6847 (ptmm) REVERT: l 23 LEU cc_start: 0.7169 (mt) cc_final: 0.6643 (mt) REVERT: l 26 CYS cc_start: 0.8009 (p) cc_final: 0.7805 (m) REVERT: m 22 TYR cc_start: 0.8534 (t80) cc_final: 0.8262 (t80) REVERT: m 71 GLU cc_start: 0.7733 (tt0) cc_final: 0.7380 (tp30) REVERT: n 17 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: n 47 LYS cc_start: 0.7298 (mttt) cc_final: 0.7093 (tptt) REVERT: n 62 ASN cc_start: 0.8619 (t0) cc_final: 0.8065 (t0) REVERT: o 4 THR cc_start: 0.6781 (m) cc_final: 0.6551 (m) REVERT: o 57 ARG cc_start: 0.7509 (ttp80) cc_final: 0.6855 (ttp-110) REVERT: p 39 PHE cc_start: 0.7753 (t80) cc_final: 0.7269 (t80) REVERT: q 5 ARG cc_start: 0.7551 (mtt-85) cc_final: 0.7329 (mtt-85) REVERT: q 10 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7398 (ttm110) REVERT: q 18 LYS cc_start: 0.7258 (mttt) cc_final: 0.7052 (mttp) REVERT: q 71 SER cc_start: 0.7923 (m) cc_final: 0.7271 (t) REVERT: s 20 LYS cc_start: 0.7470 (ttpt) cc_final: 0.7048 (mmtm) REVERT: s 36 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6736 (ptm160) REVERT: t 12 GLN cc_start: 0.7123 (tt0) cc_final: 0.6845 (tt0) REVERT: t 15 LYS cc_start: 0.8163 (tttt) cc_final: 0.7506 (tptt) REVERT: t 23 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7798 (tpp-160) REVERT: t 35 TYR cc_start: 0.6866 (m-80) cc_final: 0.6434 (m-10) REVERT: t 43 LYS cc_start: 0.5028 (tttt) cc_final: 0.4556 (ptmm) REVERT: u 33 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7368 (mtm180) REVERT: u 44 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7188 (mtt180) REVERT: z 54 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6072 (pt0) REVERT: z 75 HIS cc_start: 0.6703 (t70) cc_final: 0.6253 (t-90) REVERT: z 89 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5965 (mtmt) REVERT: z 165 ASP cc_start: 0.5460 (t0) cc_final: 0.5064 (p0) REVERT: z 249 GLU cc_start: 0.4101 (tp30) cc_final: 0.3554 (mp0) REVERT: z 252 LYS cc_start: 0.6570 (mmmt) cc_final: 0.6333 (mtmm) REVERT: z 279 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.4723 (ttp80) REVERT: z 282 LYS cc_start: 0.4503 (mttt) cc_final: 0.4170 (mtpt) REVERT: z 284 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6442 (pm20) REVERT: z 323 PHE cc_start: 0.5093 (t80) cc_final: 0.4820 (m-80) outliers start: 294 outliers final: 185 residues processed: 1423 average time/residue: 1.4418 time to fit residues: 3494.5697 Evaluate side-chains 1361 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1152 time to evaluate : 6.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 57 LEU 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 J residue 124 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 49 LYS Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 40 GLU Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain 6 residue 41 HIS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 80 LYS Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ARG Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 22 HIS Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain z residue 62 ILE Chi-restraints excluded: chain z residue 89 LYS Chi-restraints excluded: chain z residue 93 THR Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 216 ASP Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 263 LYS Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 977 optimal weight: 3.9990 chunk 743 optimal weight: 30.0000 chunk 513 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 471 optimal weight: 3.9990 chunk 664 optimal weight: 30.0000 chunk 992 optimal weight: 10.0000 chunk 1050 optimal weight: 7.9990 chunk 518 optimal weight: 7.9990 chunk 940 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN E 163 ASN E 195 GLN G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN O 104 GLN T 70 HIS Y 20 ASN 0 4 GLN ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 HIS ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN i 4 GLN ** i 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 109 GLN j 35 GLN k 27 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN t 19 HIS ** z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 114 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 165485 Z= 0.408 Angle : 0.824 17.557 247217 Z= 0.431 Chirality : 0.045 0.409 31414 Planarity : 0.008 0.141 13505 Dihedral : 24.256 179.691 81885 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.22 % Favored : 91.17 % Rotamer: Outliers : 6.00 % Allowed : 18.50 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.10), residues: 6219 helix: -0.28 (0.11), residues: 1963 sheet: -1.68 (0.14), residues: 1088 loop : -2.17 (0.10), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP z 184 HIS 0.016 0.002 HIS 6 41 PHE 0.024 0.003 PHE E 183 TYR 0.020 0.002 TYR d 134 ARG 0.010 0.001 ARG E 61 *********************** 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 1500 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1190 time to evaluate : 6.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8123 (mttt) cc_final: 0.7517 (mmtm) REVERT: C 78 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: C 110 LYS cc_start: 0.7390 (mttm) cc_final: 0.6986 (mmtm) REVERT: C 114 GLN cc_start: 0.7595 (tt0) cc_final: 0.7089 (mt0) REVERT: C 115 ILE cc_start: 0.8420 (mt) cc_final: 0.7942 (mm) REVERT: C 119 VAL cc_start: 0.7864 (t) cc_final: 0.7526 (p) REVERT: C 144 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 152 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8367 (mm-40) REVERT: C 166 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.7176 (mtp85) REVERT: C 263 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: C 266 ILE cc_start: 0.8840 (mt) cc_final: 0.8524 (mp) REVERT: C 269 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7734 (mmm160) REVERT: D 7 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8039 (ttpp) REVERT: D 128 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8009 (mtp180) REVERT: D 157 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8129 (mmtt) REVERT: E 67 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7274 (mtp85) REVERT: E 74 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8458 (mttt) REVERT: E 115 GLN cc_start: 0.7815 (mt0) cc_final: 0.7600 (mt0) REVERT: E 141 MET cc_start: 0.7499 (ttm) cc_final: 0.7198 (ttm) REVERT: E 144 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: E 198 GLU cc_start: 0.7928 (tt0) cc_final: 0.7413 (tm-30) REVERT: E 199 MET cc_start: 0.8118 (ttp) cc_final: 0.7834 (tmm) REVERT: F 18 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6849 (tt0) REVERT: F 46 LYS cc_start: 0.7140 (mttt) cc_final: 0.6835 (mmtm) REVERT: G 105 SER cc_start: 0.8502 (t) cc_final: 0.8255 (m) REVERT: G 129 GLU cc_start: 0.6381 (mm-30) cc_final: 0.6119 (mp0) REVERT: H 27 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6399 (ptt-90) REVERT: J 1 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6786 (ppp) REVERT: J 85 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7899 (mmpt) REVERT: J 91 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7023 (mt-10) REVERT: J 96 ARG cc_start: 0.6779 (ttt-90) cc_final: 0.6234 (tpp80) REVERT: J 138 GLN cc_start: 0.7827 (pt0) cc_final: 0.7267 (pm20) REVERT: K 7 MET cc_start: 0.7810 (tpp) cc_final: 0.7598 (tpp) REVERT: K 18 ARG cc_start: 0.8293 (mmm160) cc_final: 0.8020 (mmm160) REVERT: K 37 ASP cc_start: 0.7908 (m-30) cc_final: 0.7153 (m-30) REVERT: K 45 GLU cc_start: 0.8645 (tt0) cc_final: 0.8180 (pt0) REVERT: K 105 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7074 (mmm-85) REVERT: L 12 SER cc_start: 0.8748 (t) cc_final: 0.8460 (p) REVERT: L 70 LYS cc_start: 0.8527 (tttp) cc_final: 0.8102 (ttmt) REVERT: L 80 SER cc_start: 0.8547 (t) cc_final: 0.8196 (p) REVERT: L 123 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7067 (ttp-110) REVERT: L 126 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7026 (mtp85) REVERT: M 6 ARG cc_start: 0.7665 (ptm160) cc_final: 0.7106 (ptm160) REVERT: M 18 ARG cc_start: 0.7587 (mtp180) cc_final: 0.6865 (mtp-110) REVERT: M 51 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7281 (mtt-85) REVERT: M 84 LYS cc_start: 0.8171 (mttt) cc_final: 0.7949 (mttp) REVERT: N 14 SER cc_start: 0.8851 (t) cc_final: 0.8648 (m) REVERT: N 35 LYS cc_start: 0.8817 (tttt) cc_final: 0.8523 (tttp) REVERT: N 37 THR cc_start: 0.8777 (p) cc_final: 0.8573 (p) REVERT: N 65 LEU cc_start: 0.8313 (mp) cc_final: 0.7986 (mm) REVERT: N 103 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8189 (ttm170) REVERT: O 12 THR cc_start: 0.8450 (m) cc_final: 0.8086 (m) REVERT: O 98 GLN cc_start: 0.8286 (tt0) cc_final: 0.7964 (tp40) REVERT: P 6 GLN cc_start: 0.7504 (tt0) cc_final: 0.7132 (tp40) REVERT: P 26 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7018 (tp30) REVERT: P 28 LYS cc_start: 0.8036 (mttt) cc_final: 0.7707 (mmmt) REVERT: P 31 VAL cc_start: 0.8528 (p) cc_final: 0.8168 (m) REVERT: P 70 GLU cc_start: 0.7229 (tt0) cc_final: 0.6804 (mt-10) REVERT: P 114 ASN cc_start: 0.6644 (OUTLIER) cc_final: 0.6033 (t0) REVERT: Q 14 LYS cc_start: 0.8447 (tttt) cc_final: 0.8238 (mtpp) REVERT: Q 15 LYS cc_start: 0.8685 (tttt) cc_final: 0.8449 (tttm) REVERT: Q 18 LYS cc_start: 0.8327 (ttpp) cc_final: 0.7806 (mtmt) REVERT: Q 48 ASP cc_start: 0.8403 (m-30) cc_final: 0.8048 (m-30) REVERT: Q 77 LYS cc_start: 0.8429 (mttt) cc_final: 0.7994 (mtmt) REVERT: Q 94 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8283 (mp) REVERT: R 40 MET cc_start: 0.8130 (ttp) cc_final: 0.7882 (ttp) REVERT: R 60 LYS cc_start: 0.8148 (mmtp) cc_final: 0.7781 (mmmm) REVERT: R 66 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7750 (t-90) REVERT: R 73 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8075 (ttmt) REVERT: T 52 GLU cc_start: 0.8149 (pt0) cc_final: 0.6983 (mm-30) REVERT: U 8 ASP cc_start: 0.7791 (m-30) cc_final: 0.7558 (m-30) REVERT: U 9 GLU cc_start: 0.7832 (tp30) cc_final: 0.7456 (tp30) REVERT: U 59 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: U 100 GLU cc_start: 0.7159 (mp0) cc_final: 0.6826 (mp0) REVERT: V 71 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7858 (mmtm) REVERT: W 74 LYS cc_start: 0.7689 (mttp) cc_final: 0.7325 (mtmt) REVERT: X 55 MET cc_start: 0.8407 (mtp) cc_final: 0.7882 (mtt) REVERT: X 59 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: 0 4 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8927 (tp40) REVERT: 1 31 GLU cc_start: 0.5085 (pm20) cc_final: 0.4877 (tt0) REVERT: 3 53 ASP cc_start: 0.7907 (m-30) cc_final: 0.7631 (p0) REVERT: 4 30 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6886 (mp0) REVERT: 5 36 ASP cc_start: -0.0121 (OUTLIER) cc_final: -0.1386 (t0) REVERT: 5 38 MET cc_start: 0.0405 (OUTLIER) cc_final: -0.0615 (tpt) REVERT: b 50 ASN cc_start: 0.5668 (t0) cc_final: 0.5333 (m-40) REVERT: b 108 GLN cc_start: 0.7569 (pt0) cc_final: 0.7136 (mm110) REVERT: b 136 ARG cc_start: 0.6228 (mmm-85) cc_final: 0.5198 (tmm160) REVERT: b 183 PHE cc_start: 0.6687 (p90) cc_final: 0.5790 (p90) REVERT: b 191 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7889 (t70) REVERT: b 202 ASN cc_start: 0.7239 (p0) cc_final: 0.6825 (t0) REVERT: c 7 ASN cc_start: 0.7636 (t0) cc_final: 0.7375 (t0) REVERT: c 37 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8166 (mmmm) REVERT: c 84 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6829 (tm-30) REVERT: c 107 LYS cc_start: 0.7875 (mttt) cc_final: 0.7460 (tppt) REVERT: c 122 GLN cc_start: 0.7956 (mt0) cc_final: 0.7676 (mt0) REVERT: c 133 MET cc_start: 0.6223 (ptp) cc_final: 0.5730 (ptm) REVERT: c 163 ARG cc_start: 0.5763 (mtt90) cc_final: 0.5173 (mtm110) REVERT: c 187 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7556 (mt-10) REVERT: d 49 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6906 (t70) REVERT: d 56 GLU cc_start: 0.6942 (tp30) cc_final: 0.6580 (tp30) REVERT: d 72 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7080 (tpt-90) REVERT: d 87 GLU cc_start: 0.6644 (pp20) cc_final: 0.6413 (mt-10) REVERT: d 123 MET cc_start: 0.6609 (ttt) cc_final: 0.6391 (ttt) REVERT: d 190 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6580 (pp) REVERT: e 65 LYS cc_start: 0.7643 (mttm) cc_final: 0.7332 (mtpp) REVERT: e 129 SER cc_start: 0.8353 (p) cc_final: 0.8040 (p) REVERT: f 38 ARG cc_start: 0.7400 (ttm170) cc_final: 0.7100 (ttm110) REVERT: g 39 GLU cc_start: 0.7982 (pt0) cc_final: 0.7145 (pt0) REVERT: g 67 ASN cc_start: 0.6926 (m-40) cc_final: 0.6407 (t0) REVERT: g 77 ARG cc_start: 0.5183 (ttt-90) cc_final: 0.3311 (mmm160) REVERT: g 91 ARG cc_start: 0.7626 (mmm160) cc_final: 0.6856 (mtm-85) REVERT: g 128 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7516 (mp0) REVERT: h 45 ILE cc_start: 0.8231 (mt) cc_final: 0.7962 (mm) REVERT: h 73 SER cc_start: 0.8334 (t) cc_final: 0.8003 (p) REVERT: h 103 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8096 (m) REVERT: i 30 ASN cc_start: 0.6681 (m-40) cc_final: 0.6296 (t0) REVERT: k 84 MET cc_start: 0.8104 (mmt) cc_final: 0.7343 (mmm) REVERT: k 125 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7392 (tttp) REVERT: l 42 LYS cc_start: 0.6971 (mttt) cc_final: 0.6736 (mtmt) REVERT: l 61 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7858 (mt-10) REVERT: m 22 TYR cc_start: 0.8537 (t80) cc_final: 0.8308 (t80) REVERT: m 71 GLU cc_start: 0.7819 (tt0) cc_final: 0.7489 (tp30) REVERT: m 113 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7119 (mtpp) REVERT: n 11 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7881 (ttpt) REVERT: n 17 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: n 62 ASN cc_start: 0.8622 (t0) cc_final: 0.8047 (t0) REVERT: n 66 GLN cc_start: 0.7823 (mt0) cc_final: 0.7504 (mt0) REVERT: o 57 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7038 (ttp-110) REVERT: p 34 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: p 39 PHE cc_start: 0.7739 (t80) cc_final: 0.7439 (t80) REVERT: q 10 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7389 (ttm110) REVERT: q 18 LYS cc_start: 0.7291 (mttt) cc_final: 0.7004 (mttp) REVERT: q 71 SER cc_start: 0.7941 (m) cc_final: 0.7204 (t) REVERT: r 19 GLU cc_start: 0.7363 (tt0) cc_final: 0.7091 (mp0) REVERT: r 69 TYR cc_start: 0.9146 (m-80) cc_final: 0.8785 (m-80) REVERT: s 20 LYS cc_start: 0.7393 (ttpt) cc_final: 0.6968 (mmtm) REVERT: s 36 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6792 (ptm160) REVERT: t 20 ASN cc_start: 0.8513 (m-40) cc_final: 0.8273 (m110) REVERT: t 23 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7698 (tpp-160) REVERT: t 26 MET cc_start: 0.7099 (ttp) cc_final: 0.6759 (ttp) REVERT: t 43 LYS cc_start: 0.4890 (tttt) cc_final: 0.4662 (ptmm) REVERT: u 33 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7569 (mtm180) REVERT: u 45 LYS cc_start: 0.7357 (ttpp) cc_final: 0.7007 (mtmm) REVERT: u 55 HIS cc_start: 0.5806 (m-70) cc_final: 0.5544 (m170) REVERT: z 54 GLU cc_start: 0.6437 (mt-10) cc_final: 0.6109 (pt0) REVERT: z 75 HIS cc_start: 0.6663 (t70) cc_final: 0.6264 (t-90) REVERT: z 89 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5719 (tppt) REVERT: z 165 ASP cc_start: 0.5339 (t0) cc_final: 0.4886 (p0) REVERT: z 181 ASP cc_start: 0.4192 (m-30) cc_final: 0.3806 (t0) REVERT: z 232 GLU cc_start: 0.6481 (tt0) cc_final: 0.5564 (mm-30) REVERT: z 249 GLU cc_start: 0.4262 (tp30) cc_final: 0.3405 (mp0) REVERT: z 252 LYS cc_start: 0.6303 (mmmt) cc_final: 0.6057 (mmtm) REVERT: z 279 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.4467 (ttp80) REVERT: z 282 LYS cc_start: 0.5254 (mttt) cc_final: 0.4824 (mtpt) REVERT: z 284 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6619 (pm20) REVERT: z 298 ILE cc_start: 0.6618 (tt) cc_final: 0.6333 (tp) outliers start: 310 outliers final: 216 residues processed: 1382 average time/residue: 1.4339 time to fit residues: 3398.7047 Evaluate side-chains 1379 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1133 time to evaluate : 6.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 38 MET Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 178 GLU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 34 GLN Chi-restraints excluded: chain o residue 38 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 22 HIS Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 37 LYS Chi-restraints excluded: chain z residue 62 ILE Chi-restraints excluded: chain z residue 89 LYS Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 263 LYS Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 875 optimal weight: 3.9990 chunk 596 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 782 optimal weight: 8.9990 chunk 433 optimal weight: 5.9990 chunk 896 optimal weight: 8.9990 chunk 726 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 536 optimal weight: 1.9990 chunk 943 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 GLN E 163 ASN E 165 HIS E 195 GLN G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN T 91 GLN W 8 ASN Y 20 ASN Y 31 GLN 0 4 GLN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 ASN d 151 GLN e 121 ASN f 46 GLN g 67 ASN g 85 GLN g 121 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN i 109 GLN j 35 GLN j 56 HIS k 27 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 HIS ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 63 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN t 19 HIS t 47 GLN ** z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 165485 Z= 0.302 Angle : 0.747 17.238 247217 Z= 0.398 Chirality : 0.040 0.412 31414 Planarity : 0.007 0.136 13505 Dihedral : 24.166 179.769 81873 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.51 % Favored : 90.93 % Rotamer: Outliers : 5.83 % Allowed : 19.80 % Favored : 74.38 % 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: -1.99 (0.10), residues: 6219 helix: -0.08 (0.12), residues: 1969 sheet: -1.55 (0.15), residues: 1078 loop : -2.07 (0.10), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 212 HIS 0.027 0.002 HIS t 19 PHE 0.022 0.002 PHE E 183 TYR 0.021 0.002 TYR d 75 ARG 0.007 0.001 ARG C 79 *********************** 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 1449 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1148 time to evaluate : 6.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8117 (mttt) cc_final: 0.7527 (mmtm) REVERT: C 78 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: C 110 LYS cc_start: 0.7384 (mttm) cc_final: 0.6999 (mmtm) REVERT: C 114 GLN cc_start: 0.7564 (tt0) cc_final: 0.7157 (mt0) REVERT: C 115 ILE cc_start: 0.8501 (mt) cc_final: 0.8036 (mm) REVERT: C 119 VAL cc_start: 0.7822 (t) cc_final: 0.7497 (p) REVERT: C 144 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 152 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8418 (mm-40) REVERT: C 166 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.7322 (mtp85) REVERT: C 263 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: C 269 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7707 (mmm160) REVERT: D 7 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8037 (ttpp) REVERT: D 128 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7966 (mtp180) REVERT: D 157 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8161 (mmtt) REVERT: E 67 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7259 (mtp85) REVERT: E 74 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8304 (mtpt) REVERT: E 144 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: E 183 PHE cc_start: 0.8734 (m-80) cc_final: 0.8479 (m-80) REVERT: E 198 GLU cc_start: 0.7958 (tt0) cc_final: 0.7422 (tm-30) REVERT: E 199 MET cc_start: 0.8200 (ttp) cc_final: 0.7975 (tmm) REVERT: F 39 VAL cc_start: 0.5644 (OUTLIER) cc_final: 0.5236 (t) REVERT: G 105 SER cc_start: 0.8449 (t) cc_final: 0.8169 (m) REVERT: H 27 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6531 (ptt-90) REVERT: J 1 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6796 (ppp) REVERT: J 85 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7863 (mmpt) REVERT: J 91 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6997 (mt-10) REVERT: J 96 ARG cc_start: 0.6824 (ttt-90) cc_final: 0.6285 (tpp80) REVERT: J 138 GLN cc_start: 0.7678 (pt0) cc_final: 0.7151 (pm20) REVERT: K 37 ASP cc_start: 0.7735 (m-30) cc_final: 0.6900 (m-30) REVERT: K 45 GLU cc_start: 0.8617 (tt0) cc_final: 0.8125 (pt0) REVERT: K 53 LYS cc_start: 0.7823 (pttp) cc_final: 0.6832 (mmtp) REVERT: K 105 ARG cc_start: 0.7526 (mmt180) cc_final: 0.6655 (mtp85) REVERT: L 12 SER cc_start: 0.8708 (t) cc_final: 0.8479 (p) REVERT: L 41 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.7622 (mpt180) REVERT: L 70 LYS cc_start: 0.8528 (tttp) cc_final: 0.8124 (ttmt) REVERT: L 80 SER cc_start: 0.8441 (t) cc_final: 0.8121 (p) REVERT: L 123 ARG cc_start: 0.7617 (mtt180) cc_final: 0.6931 (ttp-110) REVERT: L 126 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7334 (mtm180) REVERT: M 6 ARG cc_start: 0.7572 (ptm160) cc_final: 0.7089 (ptm160) REVERT: M 18 ARG cc_start: 0.7528 (mtp180) cc_final: 0.6820 (mtp-110) REVERT: M 51 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7265 (mtt-85) REVERT: M 84 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7955 (mttp) REVERT: N 37 THR cc_start: 0.8783 (p) cc_final: 0.8574 (p) REVERT: N 65 LEU cc_start: 0.8324 (mp) cc_final: 0.7994 (mm) REVERT: O 12 THR cc_start: 0.8429 (m) cc_final: 0.8061 (m) REVERT: O 98 GLN cc_start: 0.8225 (tt0) cc_final: 0.7936 (tp40) REVERT: P 6 GLN cc_start: 0.7470 (tt0) cc_final: 0.7081 (tp40) REVERT: P 26 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6973 (tp30) REVERT: P 28 LYS cc_start: 0.7975 (mttt) cc_final: 0.7700 (mmmt) REVERT: P 70 GLU cc_start: 0.7197 (tt0) cc_final: 0.6783 (mt-10) REVERT: Q 14 LYS cc_start: 0.8402 (tttt) cc_final: 0.8163 (mtpp) REVERT: Q 15 LYS cc_start: 0.8626 (tttt) cc_final: 0.8310 (tttm) REVERT: Q 18 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7826 (mtmt) REVERT: Q 48 ASP cc_start: 0.8339 (m-30) cc_final: 0.7976 (m-30) REVERT: Q 77 LYS cc_start: 0.8375 (mttt) cc_final: 0.7910 (mtmt) REVERT: Q 94 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8260 (mp) REVERT: R 40 MET cc_start: 0.8083 (ttp) cc_final: 0.7841 (ttp) REVERT: R 60 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7636 (mmmm) REVERT: R 66 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7737 (t-90) REVERT: S 57 ASN cc_start: 0.7900 (m-40) cc_final: 0.7661 (m-40) REVERT: S 83 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7941 (mmtp) REVERT: T 52 GLU cc_start: 0.8158 (pt0) cc_final: 0.7117 (mm-30) REVERT: T 91 GLN cc_start: 0.5600 (OUTLIER) cc_final: 0.5106 (tt0) REVERT: U 5 ARG cc_start: 0.6617 (ptp-170) cc_final: 0.5762 (mtt180) REVERT: U 9 GLU cc_start: 0.7804 (tp30) cc_final: 0.7442 (tp30) REVERT: U 100 GLU cc_start: 0.7101 (mp0) cc_final: 0.6747 (mp0) REVERT: V 71 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7834 (mmtm) REVERT: W 7 ARG cc_start: 0.7663 (tpt170) cc_final: 0.6809 (mtt-85) REVERT: X 55 MET cc_start: 0.8412 (mtp) cc_final: 0.8049 (mtt) REVERT: X 71 ARG cc_start: 0.7328 (mtm110) cc_final: 0.7029 (mtm110) REVERT: Z 5 LYS cc_start: 0.7098 (mmtm) cc_final: 0.6897 (mmtp) REVERT: 0 39 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8264 (tpt170) REVERT: 3 50 SER cc_start: 0.8195 (t) cc_final: 0.7678 (m) REVERT: 3 53 ASP cc_start: 0.7889 (m-30) cc_final: 0.7651 (p0) REVERT: 4 30 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6883 (mp0) REVERT: 5 36 ASP cc_start: 0.0201 (OUTLIER) cc_final: -0.1130 (t70) REVERT: 5 38 MET cc_start: 0.0094 (OUTLIER) cc_final: -0.0879 (tpt) REVERT: 6 35 ASP cc_start: 0.4915 (OUTLIER) cc_final: 0.4685 (m-30) REVERT: b 8 MET cc_start: 0.5396 (tmm) cc_final: 0.5119 (tmm) REVERT: b 29 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: b 48 MET cc_start: 0.5518 (mmm) cc_final: 0.5216 (mmm) REVERT: b 50 ASN cc_start: 0.5540 (t0) cc_final: 0.5184 (m-40) REVERT: b 108 GLN cc_start: 0.7498 (pt0) cc_final: 0.7155 (mm-40) REVERT: b 136 ARG cc_start: 0.6331 (mmm-85) cc_final: 0.5282 (tmm160) REVERT: b 156 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6825 (tp) REVERT: b 183 PHE cc_start: 0.6690 (p90) cc_final: 0.5786 (p90) REVERT: b 191 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7746 (t70) REVERT: b 202 ASN cc_start: 0.7319 (p0) cc_final: 0.6908 (t0) REVERT: c 7 ASN cc_start: 0.7594 (t0) cc_final: 0.7300 (t0) REVERT: c 37 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8157 (mmmm) REVERT: c 84 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6806 (tm-30) REVERT: c 107 LYS cc_start: 0.7846 (mttt) cc_final: 0.7383 (tppt) REVERT: c 122 GLN cc_start: 0.7960 (mt0) cc_final: 0.7652 (mt0) REVERT: c 163 ARG cc_start: 0.6095 (mtt90) cc_final: 0.5384 (mtm110) REVERT: c 187 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7484 (mt-10) REVERT: d 56 GLU cc_start: 0.6774 (tp30) cc_final: 0.6479 (tp30) REVERT: d 87 GLU cc_start: 0.6666 (pp20) cc_final: 0.6418 (mt-10) REVERT: d 123 MET cc_start: 0.6716 (ttt) cc_final: 0.6359 (ttt) REVERT: d 153 ARG cc_start: 0.4195 (OUTLIER) cc_final: 0.3844 (ptm160) REVERT: e 65 LYS cc_start: 0.7689 (mttm) cc_final: 0.7297 (mtpp) REVERT: e 129 SER cc_start: 0.8347 (p) cc_final: 0.8054 (p) REVERT: g 39 GLU cc_start: 0.7979 (pt0) cc_final: 0.7165 (pt0) REVERT: g 67 ASN cc_start: 0.6936 (m110) cc_final: 0.6410 (t0) REVERT: g 77 ARG cc_start: 0.5215 (ttt-90) cc_final: 0.3335 (mmm160) REVERT: g 91 ARG cc_start: 0.7568 (mmm160) cc_final: 0.6813 (mtm-85) REVERT: g 100 MET cc_start: 0.7774 (mpp) cc_final: 0.7390 (mpp) REVERT: g 128 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7533 (mp0) REVERT: h 45 ILE cc_start: 0.8301 (mt) cc_final: 0.8037 (mm) REVERT: h 73 SER cc_start: 0.8304 (t) cc_final: 0.8006 (p) REVERT: i 45 MET cc_start: 0.5987 (ptt) cc_final: 0.5591 (ptp) REVERT: j 7 ARG cc_start: 0.6117 (mtm-85) cc_final: 0.5905 (mtm-85) REVERT: j 45 ARG cc_start: 0.6969 (ttt-90) cc_final: 0.6387 (tpt-90) REVERT: k 84 MET cc_start: 0.8065 (mmt) cc_final: 0.7373 (mmm) REVERT: k 125 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7418 (tttm) REVERT: l 72 ASN cc_start: 0.6821 (OUTLIER) cc_final: 0.5835 (p0) REVERT: m 22 TYR cc_start: 0.8484 (t80) cc_final: 0.8262 (t80) REVERT: m 71 GLU cc_start: 0.7801 (tt0) cc_final: 0.7486 (tp30) REVERT: n 11 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7917 (ttpt) REVERT: n 62 ASN cc_start: 0.8587 (t0) cc_final: 0.8030 (t0) REVERT: n 76 LYS cc_start: 0.8275 (tptt) cc_final: 0.7687 (tppt) REVERT: o 57 ARG cc_start: 0.7499 (ttp80) cc_final: 0.6869 (ttp-110) REVERT: p 34 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6769 (pp20) REVERT: p 63 GLN cc_start: 0.7103 (mm110) cc_final: 0.6449 (mm-40) REVERT: q 10 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7399 (ttm110) REVERT: q 18 LYS cc_start: 0.7414 (mttt) cc_final: 0.7179 (mttp) REVERT: q 71 SER cc_start: 0.7958 (m) cc_final: 0.7129 (t) REVERT: r 19 GLU cc_start: 0.7335 (tt0) cc_final: 0.7040 (mp0) REVERT: r 69 TYR cc_start: 0.9126 (m-80) cc_final: 0.8785 (m-80) REVERT: s 20 LYS cc_start: 0.7226 (ttpt) cc_final: 0.6826 (mmtm) REVERT: s 36 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7085 (ptm160) REVERT: t 20 ASN cc_start: 0.8484 (m-40) cc_final: 0.8183 (m110) REVERT: t 23 ARG cc_start: 0.8011 (tpp-160) cc_final: 0.7684 (tpp-160) REVERT: t 26 MET cc_start: 0.7088 (ttp) cc_final: 0.6764 (ttp) REVERT: u 33 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7572 (mtm180) REVERT: u 55 HIS cc_start: 0.5849 (m-70) cc_final: 0.5560 (m170) REVERT: z 17 ILE cc_start: 0.5371 (mt) cc_final: 0.4930 (tp) REVERT: z 54 GLU cc_start: 0.6364 (mt-10) cc_final: 0.6141 (pt0) REVERT: z 91 MET cc_start: 0.5412 (tmm) cc_final: 0.5184 (tmm) REVERT: z 165 ASP cc_start: 0.5420 (t0) cc_final: 0.4933 (p0) REVERT: z 181 ASP cc_start: 0.4080 (m-30) cc_final: 0.3739 (t0) REVERT: z 184 TRP cc_start: 0.4383 (m100) cc_final: 0.4083 (m100) REVERT: z 232 GLU cc_start: 0.6347 (tt0) cc_final: 0.5504 (mm-30) REVERT: z 249 GLU cc_start: 0.4164 (tp30) cc_final: 0.3595 (mm-30) REVERT: z 252 LYS cc_start: 0.6482 (mmmt) cc_final: 0.6197 (mmtm) REVERT: z 279 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.4450 (ttp80) REVERT: z 282 LYS cc_start: 0.4773 (mttt) cc_final: 0.4410 (mtpt) REVERT: z 284 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6620 (pm20) REVERT: z 298 ILE cc_start: 0.6766 (tt) cc_final: 0.6448 (tp) REVERT: z 327 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5703 (mtm110) outliers start: 301 outliers final: 210 residues processed: 1336 average time/residue: 1.4057 time to fit residues: 3205.0375 Evaluate side-chains 1367 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1127 time to evaluate : 5.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 39 ARG Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 38 MET Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 105 ILE 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 f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 85 GLN Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 34 GLN Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 130 ILE Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 302 THR Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 353 optimal weight: 2.9990 chunk 946 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 616 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 1051 optimal weight: 4.9990 chunk 873 optimal weight: 9.9990 chunk 486 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 2.9990 chunk 552 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS E 41 GLN E 163 ASN E 195 GLN G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS J 131 ASN U 73 ASN Y 20 ASN 0 5 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN k 27 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 HIS o 34 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN t 19 HIS t 74 HIS ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 165485 Z= 0.176 Angle : 0.665 16.921 247217 Z= 0.362 Chirality : 0.035 0.471 31414 Planarity : 0.007 0.127 13505 Dihedral : 24.021 179.720 81867 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.29 % Favored : 92.18 % Rotamer: Outliers : 4.86 % Allowed : 21.27 % Favored : 73.87 % 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: -1.63 (0.10), residues: 6219 helix: 0.31 (0.12), residues: 1988 sheet: -1.38 (0.15), residues: 1093 loop : -1.92 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 212 HIS 0.013 0.001 HIS e 120 PHE 0.026 0.002 PHE d 71 TYR 0.019 0.001 TYR d 75 ARG 0.008 0.000 ARG o 88 *********************** 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 1417 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1166 time to evaluate : 6.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8097 (mttt) cc_final: 0.7509 (mmtm) REVERT: C 78 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: C 110 LYS cc_start: 0.7483 (mttm) cc_final: 0.7064 (mmtm) REVERT: C 114 GLN cc_start: 0.7694 (tt0) cc_final: 0.7214 (mm-40) REVERT: C 115 ILE cc_start: 0.8476 (mt) cc_final: 0.8098 (mm) REVERT: C 119 VAL cc_start: 0.7739 (t) cc_final: 0.7451 (p) REVERT: C 144 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7823 (mt-10) REVERT: C 166 ARG cc_start: 0.7687 (mtp-110) cc_final: 0.7320 (mtp85) REVERT: C 266 ILE cc_start: 0.8796 (mt) cc_final: 0.8469 (mp) REVERT: C 269 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7669 (mmm160) REVERT: D 7 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8030 (ttpp) REVERT: D 55 LYS cc_start: 0.6640 (tttp) cc_final: 0.6379 (ttpt) REVERT: D 128 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7751 (mtp180) REVERT: D 157 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (mmtt) REVERT: E 24 ASN cc_start: 0.8451 (t0) cc_final: 0.7980 (t0) REVERT: E 67 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7273 (mtp85) REVERT: E 69 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6618 (ptp-170) REVERT: E 74 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8257 (mtpt) REVERT: E 111 GLU cc_start: 0.8409 (tp30) cc_final: 0.7576 (tp30) REVERT: E 141 MET cc_start: 0.7290 (ttm) cc_final: 0.7055 (ttm) REVERT: E 144 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6577 (pm20) REVERT: E 199 MET cc_start: 0.8223 (ttp) cc_final: 0.7887 (tmm) REVERT: F 39 VAL cc_start: 0.5803 (OUTLIER) cc_final: 0.5383 (t) REVERT: F 73 VAL cc_start: 0.6763 (OUTLIER) cc_final: 0.6519 (p) REVERT: G 105 SER cc_start: 0.8430 (t) cc_final: 0.8166 (m) REVERT: I 124 MET cc_start: 0.0396 (mtt) cc_final: -0.0040 (ppp) REVERT: J 1 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7166 (ppp) REVERT: J 57 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8138 (pp) REVERT: J 85 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7762 (mmpt) REVERT: J 91 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6963 (mt-10) REVERT: J 92 MET cc_start: 0.8086 (tpt) cc_final: 0.7844 (mmm) REVERT: J 96 ARG cc_start: 0.6881 (ttt-90) cc_final: 0.6286 (tpp80) REVERT: J 138 GLN cc_start: 0.7794 (pt0) cc_final: 0.7264 (pm20) REVERT: K 37 ASP cc_start: 0.7633 (m-30) cc_final: 0.6808 (m-30) REVERT: K 53 LYS cc_start: 0.7677 (pttp) cc_final: 0.6665 (mmtp) REVERT: K 105 ARG cc_start: 0.7643 (mmt180) cc_final: 0.6737 (mtp85) REVERT: L 70 LYS cc_start: 0.8498 (tttp) cc_final: 0.8277 (ttmt) REVERT: L 80 SER cc_start: 0.8372 (t) cc_final: 0.8067 (p) REVERT: L 123 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7142 (ptp-110) REVERT: L 126 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7387 (mtm180) REVERT: M 18 ARG cc_start: 0.7376 (mtp180) cc_final: 0.6800 (mtp-110) REVERT: M 51 ARG cc_start: 0.7726 (mtt90) cc_final: 0.7233 (mtt-85) REVERT: N 37 THR cc_start: 0.8740 (p) cc_final: 0.8539 (p) REVERT: N 57 THR cc_start: 0.7717 (m) cc_final: 0.7373 (p) REVERT: N 65 LEU cc_start: 0.8276 (mp) cc_final: 0.7928 (mm) REVERT: O 12 THR cc_start: 0.8439 (m) cc_final: 0.8078 (m) REVERT: O 98 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7763 (tp40) REVERT: P 6 GLN cc_start: 0.7487 (tt0) cc_final: 0.7099 (tp40) REVERT: P 26 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6907 (tp30) REVERT: P 28 LYS cc_start: 0.7996 (mttt) cc_final: 0.7616 (mmmt) REVERT: Q 14 LYS cc_start: 0.8356 (tttt) cc_final: 0.8148 (mtpp) REVERT: Q 15 LYS cc_start: 0.8582 (tttt) cc_final: 0.8306 (tttm) REVERT: Q 18 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7833 (mtmt) REVERT: Q 48 ASP cc_start: 0.8276 (m-30) cc_final: 0.7927 (m-30) REVERT: Q 77 LYS cc_start: 0.8384 (mttt) cc_final: 0.7887 (mtpt) REVERT: Q 94 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8254 (mp) REVERT: Q 110 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7369 (mt-10) REVERT: R 40 MET cc_start: 0.8053 (ttp) cc_final: 0.7838 (ttp) REVERT: R 60 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7889 (mmtp) REVERT: R 66 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.7821 (t-90) REVERT: S 25 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7899 (ttm170) REVERT: S 57 ASN cc_start: 0.7876 (m-40) cc_final: 0.7584 (m-40) REVERT: S 83 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7994 (mmtp) REVERT: T 49 LYS cc_start: 0.7602 (mptt) cc_final: 0.7208 (ttmt) REVERT: T 52 GLU cc_start: 0.8163 (pt0) cc_final: 0.7134 (mm-30) REVERT: U 5 ARG cc_start: 0.6630 (ptp-170) cc_final: 0.5824 (mtt180) REVERT: U 9 GLU cc_start: 0.7779 (tp30) cc_final: 0.7453 (tp30) REVERT: U 100 GLU cc_start: 0.7110 (mp0) cc_final: 0.6756 (mp0) REVERT: V 71 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7834 (mmtm) REVERT: V 75 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7817 (tp40) REVERT: W 7 ARG cc_start: 0.7599 (tpt170) cc_final: 0.6842 (mtt-85) REVERT: W 8 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7948 (p0) REVERT: W 21 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.7897 (mmt90) REVERT: W 62 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7259 (mmmt) REVERT: W 64 LYS cc_start: 0.8272 (tppt) cc_final: 0.7556 (ttpp) REVERT: Z 5 LYS cc_start: 0.6976 (mmtm) cc_final: 0.6775 (mmtp) REVERT: 0 49 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7243 (mmm160) REVERT: 0 54 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8376 (mt) REVERT: 3 50 SER cc_start: 0.8226 (t) cc_final: 0.7712 (m) REVERT: 4 30 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6631 (mp0) REVERT: 5 36 ASP cc_start: 0.0154 (OUTLIER) cc_final: -0.1144 (t70) REVERT: 5 38 MET cc_start: 0.0221 (OUTLIER) cc_final: -0.0684 (tpt) REVERT: b 29 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6619 (m-80) REVERT: b 48 MET cc_start: 0.5537 (mmm) cc_final: 0.5336 (mmm) REVERT: b 50 ASN cc_start: 0.5627 (t0) cc_final: 0.5308 (m-40) REVERT: b 108 GLN cc_start: 0.7498 (pt0) cc_final: 0.7089 (mm-40) REVERT: b 136 ARG cc_start: 0.6282 (mmm-85) cc_final: 0.5224 (tmm160) REVERT: b 202 ASN cc_start: 0.7134 (p0) cc_final: 0.6641 (t0) REVERT: c 7 ASN cc_start: 0.7574 (t0) cc_final: 0.7218 (t0) REVERT: c 37 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8075 (mmmm) REVERT: c 107 LYS cc_start: 0.7779 (mttt) cc_final: 0.7315 (tppt) REVERT: c 120 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8254 (p) REVERT: c 122 GLN cc_start: 0.7933 (mt0) cc_final: 0.7646 (mt0) REVERT: c 163 ARG cc_start: 0.6192 (mtt90) cc_final: 0.5465 (mtm110) REVERT: c 187 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7636 (mt-10) REVERT: d 123 MET cc_start: 0.6730 (ttt) cc_final: 0.6345 (ttt) REVERT: d 153 ARG cc_start: 0.4215 (OUTLIER) cc_final: 0.3974 (ptm160) REVERT: e 65 LYS cc_start: 0.7626 (mttm) cc_final: 0.7264 (mtpp) REVERT: e 75 LEU cc_start: 0.5567 (pt) cc_final: 0.5255 (pp) REVERT: e 129 SER cc_start: 0.8225 (p) cc_final: 0.7964 (p) REVERT: f 98 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6989 (tm-30) REVERT: g 39 GLU cc_start: 0.7951 (pt0) cc_final: 0.7134 (pt0) REVERT: g 67 ASN cc_start: 0.6968 (m110) cc_final: 0.6311 (t0) REVERT: g 77 ARG cc_start: 0.5150 (ttt-90) cc_final: 0.3362 (mmm160) REVERT: g 85 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6626 (mm110) REVERT: g 91 ARG cc_start: 0.7585 (mmm160) cc_final: 0.6828 (mtm-85) REVERT: g 128 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7609 (mp0) REVERT: g 148 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8336 (mtpp) REVERT: h 45 ILE cc_start: 0.8375 (mt) cc_final: 0.8153 (mm) REVERT: h 73 SER cc_start: 0.8267 (t) cc_final: 0.8012 (p) REVERT: h 103 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7883 (m) REVERT: i 45 MET cc_start: 0.6090 (ptt) cc_final: 0.5624 (ptp) REVERT: j 45 ARG cc_start: 0.6853 (ttt-90) cc_final: 0.6616 (tpt-90) REVERT: k 84 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: k 125 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7405 (tttm) REVERT: l 72 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.5780 (p0) REVERT: m 22 TYR cc_start: 0.8368 (t80) cc_final: 0.8145 (t80) REVERT: m 71 GLU cc_start: 0.7817 (tt0) cc_final: 0.7508 (tp30) REVERT: m 113 LYS cc_start: 0.7520 (mtmm) cc_final: 0.7106 (mtpp) REVERT: n 11 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7872 (ttpp) REVERT: n 17 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: n 62 ASN cc_start: 0.8397 (t0) cc_final: 0.7860 (t0) REVERT: n 76 LYS cc_start: 0.8295 (tptt) cc_final: 0.7701 (tppt) REVERT: o 57 ARG cc_start: 0.7493 (ttp80) cc_final: 0.6924 (ttp-110) REVERT: p 34 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6853 (pp20) REVERT: p 63 GLN cc_start: 0.7072 (mm110) cc_final: 0.6484 (mm-40) REVERT: q 10 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7355 (ttm170) REVERT: q 18 LYS cc_start: 0.7381 (mttt) cc_final: 0.7175 (mttp) REVERT: q 37 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7906 (pt) REVERT: q 71 SER cc_start: 0.7841 (m) cc_final: 0.7013 (t) REVERT: r 19 GLU cc_start: 0.7325 (tt0) cc_final: 0.7013 (mp0) REVERT: r 69 TYR cc_start: 0.9113 (m-80) cc_final: 0.8782 (m-80) REVERT: s 20 LYS cc_start: 0.7385 (ttpt) cc_final: 0.6965 (mmtm) REVERT: s 36 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7429 (ptm160) REVERT: t 20 ASN cc_start: 0.8521 (m-40) cc_final: 0.8250 (m110) REVERT: t 23 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7676 (tpp-160) REVERT: t 26 MET cc_start: 0.6776 (ttp) cc_final: 0.6534 (ttp) REVERT: t 51 ASN cc_start: 0.7497 (m-40) cc_final: 0.7117 (m110) REVERT: u 33 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7499 (mtm180) REVERT: u 55 HIS cc_start: 0.5863 (m-70) cc_final: 0.5561 (m170) REVERT: z 17 ILE cc_start: 0.5192 (OUTLIER) cc_final: 0.4850 (tp) REVERT: z 184 TRP cc_start: 0.4336 (m100) cc_final: 0.3998 (m100) REVERT: z 232 GLU cc_start: 0.6228 (tt0) cc_final: 0.5427 (mm-30) REVERT: z 249 GLU cc_start: 0.4136 (tp30) cc_final: 0.3580 (mm-30) REVERT: z 252 LYS cc_start: 0.6381 (mmmt) cc_final: 0.6124 (mmtm) REVERT: z 282 LYS cc_start: 0.4792 (mttt) cc_final: 0.4408 (mtpt) REVERT: z 284 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6670 (pm20) REVERT: z 298 ILE cc_start: 0.6681 (tt) cc_final: 0.6393 (tp) REVERT: z 327 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5800 (mtm110) outliers start: 251 outliers final: 156 residues processed: 1317 average time/residue: 1.4232 time to fit residues: 3203.8451 Evaluate side-chains 1319 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1130 time to evaluate : 6.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 38 MET Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 85 GLN Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 34 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 195 LEU Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 338 THR 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: 8.9990 chunk 599 optimal weight: 10.0000 chunk 768 optimal weight: 10.0000 chunk 595 optimal weight: 7.9990 chunk 885 optimal weight: 3.9990 chunk 587 optimal weight: 5.9990 chunk 1047 optimal weight: 30.0000 chunk 655 optimal weight: 10.0000 chunk 638 optimal weight: 4.9990 chunk 483 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 195 GLN F 62 GLN G 103 ASN J 58 ASN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN R 6 GLN U 98 ASN W 8 ASN X 35 HIS Y 31 GLN 5 4 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 18 GLN e 76 ASN g 51 GLN g 85 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 HIS l 95 HIS m 51 GLN o 34 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN t 74 HIS ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 165485 Z= 0.451 Angle : 0.854 17.320 247217 Z= 0.443 Chirality : 0.045 0.407 31414 Planarity : 0.008 0.145 13505 Dihedral : 24.200 179.394 81857 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.09 % Favored : 90.37 % Rotamer: Outliers : 6.19 % Allowed : 20.92 % Favored : 72.89 % 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: -1.98 (0.10), residues: 6219 helix: -0.16 (0.11), residues: 1976 sheet: -1.43 (0.15), residues: 1085 loop : -2.06 (0.10), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP z 184 HIS 0.011 0.002 HIS t 19 PHE 0.030 0.003 PHE E 183 TYR 0.022 0.002 TYR d 134 ARG 0.012 0.001 ARG C 79 *********************** 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 1462 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1142 time to evaluate : 6.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8088 (mttt) cc_final: 0.7491 (mmtm) REVERT: C 78 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: C 114 GLN cc_start: 0.7647 (tt0) cc_final: 0.7179 (mt0) REVERT: C 115 ILE cc_start: 0.8492 (mt) cc_final: 0.7978 (mm) REVERT: C 132 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7490 (ttm-80) REVERT: C 144 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 166 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7485 (mtp85) REVERT: C 263 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: C 269 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7723 (mmm160) REVERT: D 7 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8040 (ttpp) REVERT: D 128 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7975 (mtp180) REVERT: D 157 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8153 (mmtt) REVERT: D 176 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: E 67 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7245 (mtp85) REVERT: E 69 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7007 (ptp-170) REVERT: E 111 GLU cc_start: 0.8377 (tp30) cc_final: 0.8005 (tp30) REVERT: E 141 MET cc_start: 0.7377 (ttm) cc_final: 0.7103 (ttm) REVERT: E 144 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: E 195 GLN cc_start: 0.7345 (tt0) cc_final: 0.7111 (tt0) REVERT: E 199 MET cc_start: 0.8163 (ttp) cc_final: 0.7759 (tmm) REVERT: F 18 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6791 (tt0) REVERT: F 39 VAL cc_start: 0.5617 (OUTLIER) cc_final: 0.5088 (t) REVERT: F 73 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6594 (p) REVERT: G 105 SER cc_start: 0.8404 (t) cc_final: 0.8174 (m) REVERT: H 27 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6628 (ptt-90) REVERT: J 1 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6856 (ppp) REVERT: J 57 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8219 (pp) REVERT: J 85 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7852 (mmpt) REVERT: J 91 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7009 (mt-10) REVERT: J 96 ARG cc_start: 0.6846 (ttt-90) cc_final: 0.6237 (tpp80) REVERT: J 138 GLN cc_start: 0.7765 (pt0) cc_final: 0.7217 (pm20) REVERT: K 8 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8519 (mt) REVERT: K 37 ASP cc_start: 0.7801 (m-30) cc_final: 0.6975 (m-30) REVERT: K 53 LYS cc_start: 0.7860 (pttp) cc_final: 0.6837 (mmtm) REVERT: K 105 ARG cc_start: 0.7584 (mmt180) cc_final: 0.6787 (mtp85) REVERT: L 41 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8113 (mpt180) REVERT: L 70 LYS cc_start: 0.8638 (tttp) cc_final: 0.8218 (ttmt) REVERT: L 80 SER cc_start: 0.8402 (t) cc_final: 0.8076 (p) REVERT: L 123 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7040 (ttp-110) REVERT: L 126 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7377 (mtm180) REVERT: M 6 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7141 (ptm160) REVERT: M 18 ARG cc_start: 0.7600 (mtp180) cc_final: 0.6891 (mtp-110) REVERT: M 51 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7292 (mtt-85) REVERT: N 65 LEU cc_start: 0.8284 (mp) cc_final: 0.7951 (mm) REVERT: N 100 CYS cc_start: 0.8338 (p) cc_final: 0.7981 (p) REVERT: O 12 THR cc_start: 0.8488 (m) cc_final: 0.8115 (m) REVERT: O 98 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7975 (tp40) REVERT: O 104 GLN cc_start: 0.6790 (tt0) cc_final: 0.6568 (tt0) REVERT: P 6 GLN cc_start: 0.7453 (tt0) cc_final: 0.7092 (tp40) REVERT: P 26 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: P 28 LYS cc_start: 0.8065 (mttt) cc_final: 0.7774 (mmmt) REVERT: P 70 GLU cc_start: 0.7322 (tt0) cc_final: 0.6947 (mt-10) REVERT: Q 15 LYS cc_start: 0.8619 (tttt) cc_final: 0.8297 (tttm) REVERT: Q 18 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8045 (mtpp) REVERT: Q 48 ASP cc_start: 0.8406 (m-30) cc_final: 0.8088 (m-30) REVERT: Q 77 LYS cc_start: 0.8396 (mttt) cc_final: 0.7920 (mtmt) REVERT: Q 89 ILE cc_start: 0.8404 (mt) cc_final: 0.8194 (mt) REVERT: Q 94 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8258 (mp) REVERT: R 40 MET cc_start: 0.8232 (ttp) cc_final: 0.7977 (ttp) REVERT: R 60 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7695 (mmmm) REVERT: R 66 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.7545 (t-90) REVERT: S 83 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7893 (mmtp) REVERT: T 49 LYS cc_start: 0.7574 (mptt) cc_final: 0.7241 (ttmt) REVERT: T 52 GLU cc_start: 0.8200 (pt0) cc_final: 0.7224 (mm-30) REVERT: U 5 ARG cc_start: 0.6712 (ptp-170) cc_final: 0.5990 (mtt180) REVERT: U 9 GLU cc_start: 0.7806 (tp30) cc_final: 0.7487 (tp30) REVERT: U 45 GLN cc_start: 0.7837 (tp40) cc_final: 0.7498 (tp-100) REVERT: U 100 GLU cc_start: 0.6982 (mp0) cc_final: 0.6651 (mp0) REVERT: V 34 LYS cc_start: 0.7951 (pttp) cc_final: 0.7722 (pttp) REVERT: V 53 LYS cc_start: 0.6102 (mmtp) cc_final: 0.5854 (mmtt) REVERT: W 7 ARG cc_start: 0.7549 (tpt170) cc_final: 0.6831 (mtt-85) REVERT: W 64 LYS cc_start: 0.8431 (tppt) cc_final: 0.7945 (ttmt) REVERT: X 71 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6987 (mtm110) REVERT: 0 49 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7201 (mtm180) REVERT: 2 41 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7882 (mtm-85) REVERT: 3 50 SER cc_start: 0.8069 (t) cc_final: 0.7802 (m) REVERT: 4 30 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6974 (mp0) REVERT: 5 36 ASP cc_start: 0.0346 (OUTLIER) cc_final: -0.1111 (t70) REVERT: 5 38 MET cc_start: 0.0006 (OUTLIER) cc_final: -0.0933 (tpt) REVERT: b 8 MET cc_start: 0.5458 (tmm) cc_final: 0.5134 (tmm) REVERT: b 29 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: b 50 ASN cc_start: 0.5681 (t0) cc_final: 0.5340 (m-40) REVERT: b 86 CYS cc_start: 0.4560 (t) cc_final: 0.4337 (t) REVERT: b 108 GLN cc_start: 0.7613 (pt0) cc_final: 0.7242 (mm-40) REVERT: b 116 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.5165 (tt) REVERT: b 136 ARG cc_start: 0.6284 (mmm-85) cc_final: 0.5275 (ttp-170) REVERT: b 191 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7848 (t70) REVERT: b 202 ASN cc_start: 0.7337 (p0) cc_final: 0.7004 (t0) REVERT: c 7 ASN cc_start: 0.7710 (t0) cc_final: 0.7457 (t0) REVERT: c 37 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8165 (mmmm) REVERT: c 107 LYS cc_start: 0.7767 (mttt) cc_final: 0.7281 (tppt) REVERT: c 122 GLN cc_start: 0.7970 (mt0) cc_final: 0.7649 (mt0) REVERT: c 163 ARG cc_start: 0.6292 (mtt90) cc_final: 0.5592 (mtm110) REVERT: c 187 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7466 (mm-30) REVERT: d 56 GLU cc_start: 0.6898 (tp30) cc_final: 0.6521 (tp30) REVERT: d 153 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.4015 (ptm160) REVERT: d 190 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6567 (pp) REVERT: e 53 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7700 (tpp80) REVERT: e 65 LYS cc_start: 0.7628 (mttm) cc_final: 0.7280 (mtpp) REVERT: e 129 SER cc_start: 0.8417 (p) cc_final: 0.8141 (p) REVERT: g 39 GLU cc_start: 0.8039 (pt0) cc_final: 0.7179 (pt0) REVERT: g 67 ASN cc_start: 0.6859 (m110) cc_final: 0.6164 (t0) REVERT: g 77 ARG cc_start: 0.5380 (ttt-90) cc_final: 0.3401 (mtp180) REVERT: g 91 ARG cc_start: 0.7499 (mmm160) cc_final: 0.6775 (mtm-85) REVERT: g 128 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7475 (mp0) REVERT: h 9 MET cc_start: 0.7916 (ttt) cc_final: 0.7628 (ttt) REVERT: h 45 ILE cc_start: 0.8282 (mt) cc_final: 0.8007 (mm) REVERT: h 73 SER cc_start: 0.8347 (t) cc_final: 0.8000 (p) REVERT: j 45 ARG cc_start: 0.6962 (ttt-90) cc_final: 0.6609 (tpt-90) REVERT: k 84 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7407 (mmm) REVERT: l 72 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.5743 (p0) REVERT: m 71 GLU cc_start: 0.7939 (tt0) cc_final: 0.7605 (tp30) REVERT: n 11 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: n 17 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: n 62 ASN cc_start: 0.8693 (t0) cc_final: 0.8150 (t0) REVERT: o 57 ARG cc_start: 0.7555 (ttp80) cc_final: 0.6992 (ttp-110) REVERT: p 63 GLN cc_start: 0.7086 (mm110) cc_final: 0.6481 (mm-40) REVERT: q 10 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7264 (ttm110) REVERT: q 18 LYS cc_start: 0.7396 (mttt) cc_final: 0.7162 (mttp) REVERT: q 71 SER cc_start: 0.8028 (m) cc_final: 0.7180 (t) REVERT: r 19 GLU cc_start: 0.7310 (tt0) cc_final: 0.7009 (mp0) REVERT: r 29 LYS cc_start: 0.8096 (ttpp) cc_final: 0.7556 (pttm) REVERT: s 20 LYS cc_start: 0.7338 (ttpt) cc_final: 0.6951 (mmtm) REVERT: s 36 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6828 (ptm160) REVERT: t 20 ASN cc_start: 0.8377 (m-40) cc_final: 0.8097 (m110) REVERT: t 23 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.7762 (tpp-160) REVERT: u 33 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7583 (mtm180) REVERT: u 45 LYS cc_start: 0.7330 (ttpp) cc_final: 0.6978 (mtmm) REVERT: u 55 HIS cc_start: 0.6034 (m-70) cc_final: 0.5724 (m170) REVERT: z 17 ILE cc_start: 0.5344 (OUTLIER) cc_final: 0.4947 (tp) REVERT: z 232 GLU cc_start: 0.6285 (tt0) cc_final: 0.5428 (mm-30) REVERT: z 249 GLU cc_start: 0.4111 (tp30) cc_final: 0.3460 (mp0) REVERT: z 252 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6096 (mmtm) REVERT: z 262 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.5897 (mtp85) REVERT: z 279 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.4412 (ttp80) REVERT: z 282 LYS cc_start: 0.5031 (mttt) cc_final: 0.4682 (mtpt) REVERT: z 284 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6444 (pm20) REVERT: z 298 ILE cc_start: 0.6945 (tt) cc_final: 0.6648 (tp) REVERT: z 327 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5824 (mtm110) outliers start: 320 outliers final: 238 residues processed: 1330 average time/residue: 1.4427 time to fit residues: 3292.5650 Evaluate side-chains 1405 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1129 time to evaluate : 6.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 38 MET Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 53 ARG Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 51 GLN Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 85 GLN Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 49 GLN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 34 GLN Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 67 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 47 ASN Chi-restraints excluded: chain z residue 130 ILE Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 284 GLU Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 648 optimal weight: 10.0000 chunk 418 optimal weight: 30.0000 chunk 625 optimal weight: 20.0000 chunk 315 optimal weight: 0.2980 chunk 205 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 666 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 517 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 823 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 128 ASN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN 0 5 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 119 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN i 31 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 HIS m 51 GLN o 34 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN t 19 HIS t 74 HIS ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 165485 Z= 0.225 Angle : 0.693 17.095 247217 Z= 0.374 Chirality : 0.037 0.445 31414 Planarity : 0.007 0.129 13505 Dihedral : 24.047 179.228 81857 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.61 % Favored : 91.88 % Rotamer: Outliers : 5.05 % Allowed : 22.51 % Favored : 72.44 % 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: -1.69 (0.10), residues: 6219 helix: 0.21 (0.12), residues: 1972 sheet: -1.32 (0.15), residues: 1073 loop : -1.94 (0.10), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP z 184 HIS 0.014 0.001 HIS l 76 PHE 0.022 0.002 PHE V 26 TYR 0.018 0.002 TYR 5 51 ARG 0.007 0.000 ARG E 162 *********************** 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 1396 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1135 time to evaluate : 6.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8063 (mttt) cc_final: 0.7474 (mmtm) REVERT: C 78 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: C 110 LYS cc_start: 0.7479 (mttm) cc_final: 0.7046 (mmtm) REVERT: C 114 GLN cc_start: 0.7648 (tt0) cc_final: 0.7258 (mt0) REVERT: C 115 ILE cc_start: 0.8516 (mt) cc_final: 0.8057 (mm) REVERT: C 119 VAL cc_start: 0.7913 (t) cc_final: 0.7561 (p) REVERT: C 132 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7460 (ttm-80) REVERT: C 144 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 166 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7477 (mtp85) REVERT: C 263 ASP cc_start: 0.7883 (m-30) cc_final: 0.7206 (m-30) REVERT: C 266 ILE cc_start: 0.8809 (mt) cc_final: 0.8461 (mp) REVERT: C 269 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7623 (mmm160) REVERT: D 7 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7969 (ttpp) REVERT: D 128 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7931 (mtp180) REVERT: D 157 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8160 (mmtt) REVERT: E 67 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7267 (mtp85) REVERT: E 69 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6726 (ptp-170) REVERT: E 74 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8301 (mtpt) REVERT: E 111 GLU cc_start: 0.8330 (tp30) cc_final: 0.7719 (tp30) REVERT: E 141 MET cc_start: 0.7215 (ttm) cc_final: 0.6958 (ttm) REVERT: E 144 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: E 195 GLN cc_start: 0.7387 (tt0) cc_final: 0.7145 (tt0) REVERT: E 199 MET cc_start: 0.8210 (ttp) cc_final: 0.7880 (tmm) REVERT: F 39 VAL cc_start: 0.5510 (OUTLIER) cc_final: 0.5074 (t) REVERT: F 46 LYS cc_start: 0.7097 (mttt) cc_final: 0.6637 (mmtm) REVERT: F 73 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6489 (p) REVERT: G 105 SER cc_start: 0.8414 (t) cc_final: 0.8158 (m) REVERT: H 27 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6716 (ptt-90) REVERT: J 1 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7156 (ppp) REVERT: J 57 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8232 (pp) REVERT: J 85 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7793 (mmpt) REVERT: J 91 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6968 (mt-10) REVERT: J 92 MET cc_start: 0.8084 (tpt) cc_final: 0.7828 (mmm) REVERT: J 96 ARG cc_start: 0.6878 (ttt-90) cc_final: 0.6305 (tpp80) REVERT: J 138 GLN cc_start: 0.7768 (pt0) cc_final: 0.7228 (pm20) REVERT: K 8 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8503 (mt) REVERT: K 37 ASP cc_start: 0.7661 (m-30) cc_final: 0.6817 (m-30) REVERT: K 45 GLU cc_start: 0.8541 (tt0) cc_final: 0.8246 (pt0) REVERT: K 53 LYS cc_start: 0.7784 (pttp) cc_final: 0.6805 (mmtp) REVERT: K 105 ARG cc_start: 0.7571 (mmt180) cc_final: 0.6779 (mtp85) REVERT: L 70 LYS cc_start: 0.8497 (tttp) cc_final: 0.8265 (ttmt) REVERT: L 80 SER cc_start: 0.8308 (t) cc_final: 0.8027 (p) REVERT: L 123 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7017 (ttp-110) REVERT: L 126 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7391 (mtm180) REVERT: M 6 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7156 (ptm160) REVERT: M 18 ARG cc_start: 0.7496 (mtp180) cc_final: 0.6772 (mtp-110) REVERT: M 51 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7240 (mtt-85) REVERT: M 129 THR cc_start: 0.8148 (p) cc_final: 0.7444 (t) REVERT: N 57 THR cc_start: 0.7763 (m) cc_final: 0.7409 (p) REVERT: N 65 LEU cc_start: 0.8322 (mp) cc_final: 0.7986 (mm) REVERT: O 12 THR cc_start: 0.8465 (m) cc_final: 0.8094 (m) REVERT: O 31 THR cc_start: 0.7142 (m) cc_final: 0.6607 (p) REVERT: O 98 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7783 (tp40) REVERT: P 6 GLN cc_start: 0.7479 (tt0) cc_final: 0.7098 (tp40) REVERT: P 26 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6911 (tp30) REVERT: P 28 LYS cc_start: 0.8034 (mttt) cc_final: 0.7578 (mmmt) REVERT: Q 15 LYS cc_start: 0.8652 (tttt) cc_final: 0.8378 (tttm) REVERT: Q 18 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7827 (mtmt) REVERT: Q 48 ASP cc_start: 0.8312 (m-30) cc_final: 0.7971 (m-30) REVERT: Q 77 LYS cc_start: 0.8424 (mttt) cc_final: 0.7930 (mtpt) REVERT: Q 94 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8241 (mp) REVERT: Q 110 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7377 (mt-10) REVERT: R 40 MET cc_start: 0.8112 (ttp) cc_final: 0.7888 (ttp) REVERT: R 66 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.7417 (t-90) REVERT: S 57 ASN cc_start: 0.7917 (m-40) cc_final: 0.7707 (m-40) REVERT: S 83 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7951 (mmtp) REVERT: T 49 LYS cc_start: 0.7554 (mptt) cc_final: 0.7166 (ttmt) REVERT: T 52 GLU cc_start: 0.8241 (pt0) cc_final: 0.7239 (mm-30) REVERT: U 5 ARG cc_start: 0.6597 (ptp-170) cc_final: 0.5824 (mtt180) REVERT: U 9 GLU cc_start: 0.7792 (tp30) cc_final: 0.7460 (tp30) REVERT: U 45 GLN cc_start: 0.7736 (tp40) cc_final: 0.7450 (tp-100) REVERT: U 59 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: U 100 GLU cc_start: 0.7146 (mp0) cc_final: 0.6799 (mp0) REVERT: V 34 LYS cc_start: 0.7906 (pttp) cc_final: 0.7687 (pttp) REVERT: V 48 MET cc_start: 0.7662 (tpp) cc_final: 0.7438 (tpt) REVERT: W 64 LYS cc_start: 0.8301 (tppt) cc_final: 0.7889 (ttmt) REVERT: X 71 ARG cc_start: 0.7234 (mtm110) cc_final: 0.6975 (mtm110) REVERT: 0 49 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7193 (mmm160) REVERT: 2 41 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7668 (mtm180) REVERT: 3 50 SER cc_start: 0.7992 (t) cc_final: 0.7609 (m) REVERT: 4 30 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6677 (mp0) REVERT: 5 36 ASP cc_start: 0.0196 (OUTLIER) cc_final: -0.1166 (t70) REVERT: 5 38 MET cc_start: -0.0224 (OUTLIER) cc_final: -0.1085 (tpt) REVERT: 6 25 ARG cc_start: 0.6660 (ptm160) cc_final: 0.6368 (mtp-110) REVERT: b 8 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4740 (tmm) REVERT: b 29 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: b 48 MET cc_start: 0.5486 (mmm) cc_final: 0.5226 (mmm) REVERT: b 50 ASN cc_start: 0.5655 (t0) cc_final: 0.5296 (m-40) REVERT: b 108 GLN cc_start: 0.7537 (pt0) cc_final: 0.7239 (mm110) REVERT: b 116 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5209 (tt) REVERT: b 136 ARG cc_start: 0.6329 (mmm-85) cc_final: 0.5295 (ttp-170) REVERT: b 139 GLU cc_start: 0.8357 (tt0) cc_final: 0.8080 (tt0) REVERT: b 183 PHE cc_start: 0.6528 (p90) cc_final: 0.5668 (p90) REVERT: b 191 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7695 (t70) REVERT: b 202 ASN cc_start: 0.7330 (p0) cc_final: 0.6774 (t0) REVERT: c 7 ASN cc_start: 0.7566 (t0) cc_final: 0.7237 (t0) REVERT: c 37 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8139 (mmmm) REVERT: c 107 LYS cc_start: 0.7683 (mttt) cc_final: 0.7203 (tppt) REVERT: c 120 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8237 (p) REVERT: c 122 GLN cc_start: 0.7855 (mt0) cc_final: 0.7572 (mt0) REVERT: c 163 ARG cc_start: 0.6157 (mtt90) cc_final: 0.5440 (mtm110) REVERT: c 187 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7642 (mt-10) REVERT: d 56 GLU cc_start: 0.6708 (tp30) cc_final: 0.6415 (tp30) REVERT: d 106 PHE cc_start: 0.6191 (m-80) cc_final: 0.5808 (m-80) REVERT: d 153 ARG cc_start: 0.4257 (OUTLIER) cc_final: 0.3830 (ptm160) REVERT: d 159 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5761 (mm-30) REVERT: d 190 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6553 (pp) REVERT: e 65 LYS cc_start: 0.7643 (mttm) cc_final: 0.7285 (mtpp) REVERT: e 129 SER cc_start: 0.8291 (p) cc_final: 0.8025 (p) REVERT: g 39 GLU cc_start: 0.7946 (pt0) cc_final: 0.7132 (pt0) REVERT: g 67 ASN cc_start: 0.6837 (m110) cc_final: 0.6191 (t0) REVERT: g 77 ARG cc_start: 0.5274 (ttt-90) cc_final: 0.3463 (mmm160) REVERT: g 91 ARG cc_start: 0.7400 (mmm160) cc_final: 0.6770 (mtm-85) REVERT: g 100 MET cc_start: 0.7856 (mpp) cc_final: 0.7540 (mpp) REVERT: g 128 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7588 (mp0) REVERT: h 45 ILE cc_start: 0.8403 (mt) cc_final: 0.8195 (mm) REVERT: h 73 SER cc_start: 0.8255 (t) cc_final: 0.7979 (p) REVERT: h 103 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7952 (m) REVERT: i 45 MET cc_start: 0.5712 (ptt) cc_final: 0.5268 (ptp) REVERT: i 94 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5573 (ptp-110) REVERT: k 84 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7490 (mmm) REVERT: l 72 ASN cc_start: 0.6582 (OUTLIER) cc_final: 0.5577 (p0) REVERT: m 22 TYR cc_start: 0.8471 (t80) cc_final: 0.8228 (t80) REVERT: m 71 GLU cc_start: 0.7890 (tt0) cc_final: 0.7590 (tp30) REVERT: n 11 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7648 (ttpt) REVERT: n 17 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: n 62 ASN cc_start: 0.8551 (t0) cc_final: 0.7987 (t0) REVERT: n 76 LYS cc_start: 0.8356 (tptt) cc_final: 0.7731 (tppt) REVERT: o 57 ARG cc_start: 0.7545 (ttp80) cc_final: 0.6986 (ttp-110) REVERT: p 51 ARG cc_start: 0.5545 (ttm-80) cc_final: 0.5022 (ptp-170) REVERT: p 63 GLN cc_start: 0.7059 (mm110) cc_final: 0.6496 (mm-40) REVERT: q 10 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7279 (ttm170) REVERT: q 18 LYS cc_start: 0.7360 (mttt) cc_final: 0.7159 (mttp) REVERT: q 37 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7917 (pt) REVERT: q 71 SER cc_start: 0.7919 (m) cc_final: 0.7067 (t) REVERT: r 19 GLU cc_start: 0.7258 (tt0) cc_final: 0.6983 (mp0) REVERT: s 20 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6902 (mmtm) REVERT: s 36 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7448 (ptm160) REVERT: t 20 ASN cc_start: 0.8499 (m-40) cc_final: 0.8233 (m110) REVERT: t 23 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7788 (tpp-160) REVERT: t 26 MET cc_start: 0.6902 (ttp) cc_final: 0.6609 (ttp) REVERT: u 33 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7576 (mtm180) REVERT: u 55 HIS cc_start: 0.6038 (m-70) cc_final: 0.5727 (m170) REVERT: z 17 ILE cc_start: 0.5278 (OUTLIER) cc_final: 0.4888 (tp) REVERT: z 232 GLU cc_start: 0.6223 (tt0) cc_final: 0.5400 (mm-30) REVERT: z 249 GLU cc_start: 0.4042 (tp30) cc_final: 0.3383 (mp0) REVERT: z 252 LYS cc_start: 0.6435 (mmmt) cc_final: 0.6166 (mmtm) REVERT: z 262 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.5902 (mmm-85) REVERT: z 279 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.4426 (ttp80) REVERT: z 282 LYS cc_start: 0.5060 (mttt) cc_final: 0.4680 (mtpt) REVERT: z 284 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6496 (pm20) REVERT: z 298 ILE cc_start: 0.6890 (tt) cc_final: 0.6601 (tp) REVERT: z 327 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5883 (mtm110) outliers start: 261 outliers final: 192 residues processed: 1290 average time/residue: 1.4298 time to fit residues: 3167.6082 Evaluate side-chains 1347 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1116 time to evaluate : 6.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 38 MET Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 34 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 34 GLU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 63 LYS Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 237 LYS Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 ILE Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 953 optimal weight: 10.0000 chunk 1003 optimal weight: 10.0000 chunk 915 optimal weight: 0.5980 chunk 976 optimal weight: 10.0000 chunk 587 optimal weight: 6.9990 chunk 425 optimal weight: 20.0000 chunk 766 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 882 optimal weight: 2.9990 chunk 923 optimal weight: 9.9990 chunk 972 optimal weight: 6.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 128 ASN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN i 31 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 HIS o 34 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 74 HIS ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 165485 Z= 0.399 Angle : 0.806 17.308 247217 Z= 0.422 Chirality : 0.043 0.375 31414 Planarity : 0.008 0.142 13505 Dihedral : 24.133 179.739 81857 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.22 % Favored : 90.25 % Rotamer: Outliers : 5.67 % Allowed : 22.16 % Favored : 72.17 % 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: -1.90 (0.10), residues: 6219 helix: -0.07 (0.11), residues: 1990 sheet: -1.37 (0.15), residues: 1116 loop : -2.03 (0.10), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP z 184 HIS 0.010 0.002 HIS l 76 PHE 0.027 0.002 PHE E 183 TYR 0.020 0.002 TYR d 134 ARG 0.008 0.001 ARG o 88 *********************** 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 1420 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1127 time to evaluate : 6.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8078 (mttt) cc_final: 0.7486 (mmtm) REVERT: C 78 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: C 114 GLN cc_start: 0.7647 (tt0) cc_final: 0.7168 (mt0) REVERT: C 115 ILE cc_start: 0.8504 (mt) cc_final: 0.8006 (mm) REVERT: C 132 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7528 (ttm-80) REVERT: C 144 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7827 (mt-10) REVERT: C 166 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7500 (mtp85) REVERT: C 263 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: C 269 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7703 (mmm160) REVERT: D 7 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8022 (ttpp) REVERT: D 128 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7988 (mtp180) REVERT: D 157 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8153 (mmtt) REVERT: D 176 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: E 67 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7289 (mtp85) REVERT: E 69 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6882 (ptp-170) REVERT: E 74 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8326 (mtpt) REVERT: E 111 GLU cc_start: 0.8421 (tp30) cc_final: 0.8026 (tp30) REVERT: E 141 MET cc_start: 0.7323 (ttm) cc_final: 0.7052 (ttm) REVERT: E 144 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6735 (pm20) REVERT: E 195 GLN cc_start: 0.7227 (tt0) cc_final: 0.6973 (tt0) REVERT: E 199 MET cc_start: 0.8208 (ttp) cc_final: 0.7805 (tmm) REVERT: F 18 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6800 (tt0) REVERT: F 46 LYS cc_start: 0.7069 (mttt) cc_final: 0.6602 (mmtm) REVERT: G 105 SER cc_start: 0.8388 (t) cc_final: 0.8165 (m) REVERT: H 27 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6613 (ptt-90) REVERT: J 1 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6835 (ppp) REVERT: J 57 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8199 (pp) REVERT: J 85 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7811 (mmpt) REVERT: J 91 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7017 (mt-10) REVERT: J 96 ARG cc_start: 0.6828 (ttt-90) cc_final: 0.6188 (tpp80) REVERT: K 8 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8520 (mt) REVERT: K 37 ASP cc_start: 0.7774 (m-30) cc_final: 0.6946 (m-30) REVERT: K 53 LYS cc_start: 0.7839 (pttp) cc_final: 0.6873 (mmtm) REVERT: K 105 ARG cc_start: 0.7513 (mmt180) cc_final: 0.6761 (mtp85) REVERT: L 41 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8071 (mpt180) REVERT: L 70 LYS cc_start: 0.8581 (tttp) cc_final: 0.8321 (ttmt) REVERT: L 80 SER cc_start: 0.8347 (t) cc_final: 0.8042 (p) REVERT: L 123 ARG cc_start: 0.7714 (mtt180) cc_final: 0.6985 (ttp-110) REVERT: L 126 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7394 (mtm180) REVERT: M 6 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7168 (ptm160) REVERT: M 18 ARG cc_start: 0.7535 (mtp180) cc_final: 0.6858 (mtp-110) REVERT: M 51 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7255 (mtt-85) REVERT: N 65 LEU cc_start: 0.8282 (mp) cc_final: 0.7941 (mm) REVERT: O 12 THR cc_start: 0.8476 (m) cc_final: 0.8112 (m) REVERT: O 31 THR cc_start: 0.7182 (m) cc_final: 0.6698 (p) REVERT: O 98 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7975 (tp40) REVERT: P 6 GLN cc_start: 0.7348 (tt0) cc_final: 0.7008 (tp40) REVERT: P 26 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7042 (tp30) REVERT: P 28 LYS cc_start: 0.8018 (mttt) cc_final: 0.7664 (mmmt) REVERT: P 70 GLU cc_start: 0.7411 (tt0) cc_final: 0.7027 (mt-10) REVERT: Q 15 LYS cc_start: 0.8673 (tttt) cc_final: 0.8383 (tttm) REVERT: Q 18 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7822 (mtmt) REVERT: Q 48 ASP cc_start: 0.8404 (m-30) cc_final: 0.8097 (m-30) REVERT: Q 77 LYS cc_start: 0.8425 (mttt) cc_final: 0.7959 (mtmt) REVERT: Q 94 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8296 (mp) REVERT: Q 110 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7377 (mt-10) REVERT: R 40 MET cc_start: 0.8216 (ttp) cc_final: 0.7964 (ttp) REVERT: R 60 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7661 (mmtm) REVERT: S 83 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7919 (mmtp) REVERT: T 49 LYS cc_start: 0.7617 (mptt) cc_final: 0.7339 (ttmt) REVERT: T 52 GLU cc_start: 0.8246 (pt0) cc_final: 0.7276 (mm-30) REVERT: U 5 ARG cc_start: 0.6698 (ptp-170) cc_final: 0.5952 (mtt180) REVERT: U 9 GLU cc_start: 0.7739 (tp30) cc_final: 0.7409 (tp30) REVERT: U 45 GLN cc_start: 0.7841 (tp40) cc_final: 0.7483 (tp-100) REVERT: U 59 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: U 100 GLU cc_start: 0.6930 (mp0) cc_final: 0.6599 (mp0) REVERT: W 7 ARG cc_start: 0.7509 (tpt170) cc_final: 0.6747 (mtp85) REVERT: W 64 LYS cc_start: 0.8428 (tppt) cc_final: 0.7954 (ttmt) REVERT: X 71 ARG cc_start: 0.7326 (mtm110) cc_final: 0.7067 (mtm110) REVERT: Y 4 LYS cc_start: 0.8336 (mttt) cc_final: 0.7786 (pttp) REVERT: 2 41 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7726 (mtm180) REVERT: 3 50 SER cc_start: 0.8067 (t) cc_final: 0.7689 (m) REVERT: 4 30 GLU cc_start: 0.7643 (mt-10) cc_final: 0.6926 (mp0) REVERT: 5 36 ASP cc_start: 0.0307 (OUTLIER) cc_final: -0.1063 (t70) REVERT: 6 25 ARG cc_start: 0.6629 (ptm160) cc_final: 0.6389 (mtp-110) REVERT: b 8 MET cc_start: 0.5003 (tmm) cc_final: 0.4701 (tmm) REVERT: b 29 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: b 50 ASN cc_start: 0.5859 (t0) cc_final: 0.5647 (m-40) REVERT: b 108 GLN cc_start: 0.7587 (pt0) cc_final: 0.7290 (mm110) REVERT: b 116 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5166 (tt) REVERT: b 136 ARG cc_start: 0.6290 (mmm-85) cc_final: 0.5266 (ttp-170) REVERT: b 191 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7854 (t70) REVERT: c 7 ASN cc_start: 0.7676 (t0) cc_final: 0.7364 (t0) REVERT: c 37 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8048 (mmmm) REVERT: c 107 LYS cc_start: 0.7653 (mttt) cc_final: 0.7169 (tppt) REVERT: c 122 GLN cc_start: 0.7974 (mt0) cc_final: 0.7650 (mt0) REVERT: c 163 ARG cc_start: 0.6248 (mtt90) cc_final: 0.5397 (mtm-85) REVERT: c 187 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7446 (mm-30) REVERT: d 56 GLU cc_start: 0.6857 (tp30) cc_final: 0.6530 (tp30) REVERT: d 106 PHE cc_start: 0.6237 (m-80) cc_final: 0.5907 (m-80) REVERT: d 153 ARG cc_start: 0.4236 (OUTLIER) cc_final: 0.3876 (ptm160) REVERT: d 188 SER cc_start: 0.6791 (p) cc_final: 0.6303 (t) REVERT: d 190 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6592 (pp) REVERT: e 65 LYS cc_start: 0.7646 (mttm) cc_final: 0.7305 (mtpp) REVERT: e 129 SER cc_start: 0.8388 (p) cc_final: 0.8108 (p) REVERT: g 39 GLU cc_start: 0.8053 (pt0) cc_final: 0.7292 (pt0) REVERT: g 67 ASN cc_start: 0.6896 (m110) cc_final: 0.6178 (t0) REVERT: g 77 ARG cc_start: 0.5161 (ttt-90) cc_final: 0.3304 (mtp180) REVERT: g 91 ARG cc_start: 0.7382 (mmm160) cc_final: 0.6743 (mtm-85) REVERT: g 100 MET cc_start: 0.7791 (mpp) cc_final: 0.7449 (mpp) REVERT: g 128 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7471 (mp0) REVERT: h 9 MET cc_start: 0.7907 (ttt) cc_final: 0.7599 (ttt) REVERT: h 45 ILE cc_start: 0.8276 (mt) cc_final: 0.8017 (mm) REVERT: h 73 SER cc_start: 0.8308 (t) cc_final: 0.7939 (p) REVERT: i 45 MET cc_start: 0.5887 (ptt) cc_final: 0.5425 (ptp) REVERT: j 99 GLN cc_start: 0.7256 (mt0) cc_final: 0.7017 (tt0) REVERT: k 84 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7372 (mmm) REVERT: l 72 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.5614 (p0) REVERT: m 71 GLU cc_start: 0.7974 (tt0) cc_final: 0.7629 (tp30) REVERT: n 11 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7672 (ttpt) REVERT: n 17 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: n 62 ASN cc_start: 0.8678 (t0) cc_final: 0.8114 (t0) REVERT: o 57 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7019 (ttp-110) REVERT: p 63 GLN cc_start: 0.7050 (mm110) cc_final: 0.6486 (mm-40) REVERT: q 10 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7276 (ttm170) REVERT: q 18 LYS cc_start: 0.7363 (mttt) cc_final: 0.7150 (mttp) REVERT: q 37 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7929 (pt) REVERT: q 71 SER cc_start: 0.8061 (m) cc_final: 0.7171 (t) REVERT: r 19 GLU cc_start: 0.7348 (tt0) cc_final: 0.7020 (mp0) REVERT: r 29 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7663 (pttm) REVERT: s 20 LYS cc_start: 0.7317 (ttpt) cc_final: 0.6949 (mmtm) REVERT: s 36 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7123 (ptm160) REVERT: t 20 ASN cc_start: 0.8477 (m-40) cc_final: 0.8192 (m110) REVERT: t 23 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7759 (tpp-160) REVERT: t 26 MET cc_start: 0.7111 (ttp) cc_final: 0.6805 (ttp) REVERT: u 33 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7613 (mtm180) REVERT: u 44 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7356 (mmt180) REVERT: u 45 LYS cc_start: 0.7187 (ttpp) cc_final: 0.6908 (mtmm) REVERT: u 46 ARG cc_start: 0.6807 (mtt180) cc_final: 0.6335 (mtt180) REVERT: u 55 HIS cc_start: 0.6054 (m-70) cc_final: 0.5704 (m170) REVERT: z 17 ILE cc_start: 0.5324 (OUTLIER) cc_final: 0.4936 (tp) REVERT: z 208 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5537 (ptpp) REVERT: z 249 GLU cc_start: 0.4119 (tp30) cc_final: 0.3443 (mp0) REVERT: z 252 LYS cc_start: 0.6358 (mmmt) cc_final: 0.6105 (mmtm) REVERT: z 262 ARG cc_start: 0.6928 (mtm-85) cc_final: 0.5688 (mmm-85) REVERT: z 279 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.4419 (ttp80) REVERT: z 282 LYS cc_start: 0.5535 (mttt) cc_final: 0.5112 (mtpt) REVERT: z 284 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6587 (pm20) REVERT: z 298 ILE cc_start: 0.6912 (tt) cc_final: 0.6620 (tp) REVERT: z 327 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5916 (mtm110) outliers start: 293 outliers final: 224 residues processed: 1308 average time/residue: 1.4362 time to fit residues: 3210.8189 Evaluate side-chains 1372 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1114 time to evaluate : 6.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 34 GLN Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 196 ASP Chi-restraints excluded: chain z residue 208 LYS Chi-restraints excluded: chain z residue 237 LYS Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 ILE Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 641 optimal weight: 3.9990 chunk 1032 optimal weight: 10.0000 chunk 630 optimal weight: 50.0000 chunk 489 optimal weight: 0.7980 chunk 717 optimal weight: 10.0000 chunk 1082 optimal weight: 2.9990 chunk 996 optimal weight: 6.9990 chunk 862 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 528 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN i 31 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 HIS n 66 GLN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 165485 Z= 0.333 Angle : 0.812 59.083 247217 Z= 0.430 Chirality : 0.041 0.371 31414 Planarity : 0.008 0.141 13505 Dihedral : 24.134 179.620 81857 Min Nonbonded Distance : 1.014 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.17 % Favored : 90.30 % Rotamer: Outliers : 5.42 % Allowed : 22.47 % Favored : 72.11 % Cbeta Deviations : 0.02 % 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: -1.90 (0.10), residues: 6219 helix: -0.07 (0.11), residues: 1990 sheet: -1.36 (0.15), residues: 1103 loop : -2.03 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP z 184 HIS 0.012 0.001 HIS l 76 PHE 0.036 0.002 PHE b 49 TYR 0.019 0.002 TYR d 134 ARG 0.013 0.001 ARG K 18 ********************** 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 1392 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1112 time to evaluate : 6.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8077 (mttt) cc_final: 0.7485 (mmtm) REVERT: C 78 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: C 114 GLN cc_start: 0.7644 (tt0) cc_final: 0.7170 (mt0) REVERT: C 115 ILE cc_start: 0.8501 (mt) cc_final: 0.8002 (mm) REVERT: C 132 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: C 144 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7817 (mt-10) REVERT: C 166 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7497 (mtp85) REVERT: C 263 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: C 269 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7699 (mmm160) REVERT: D 7 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8017 (ttpp) REVERT: D 128 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7982 (mtp180) REVERT: D 157 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8150 (mmtt) REVERT: D 176 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: E 67 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7284 (mtp85) REVERT: E 69 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6878 (ptp-170) REVERT: E 74 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8324 (mtpt) REVERT: E 111 GLU cc_start: 0.8413 (tp30) cc_final: 0.8014 (tp30) REVERT: E 141 MET cc_start: 0.7320 (ttm) cc_final: 0.7044 (ttm) REVERT: E 144 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: E 195 GLN cc_start: 0.7278 (tt0) cc_final: 0.7034 (tt0) REVERT: E 199 MET cc_start: 0.8212 (ttp) cc_final: 0.7806 (tmm) REVERT: F 18 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6776 (tt0) REVERT: F 46 LYS cc_start: 0.7067 (mttt) cc_final: 0.6590 (mmtm) REVERT: G 105 SER cc_start: 0.8387 (t) cc_final: 0.8163 (m) REVERT: H 27 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6604 (ptt-90) REVERT: J 1 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6831 (ppp) REVERT: J 57 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8205 (pp) REVERT: J 85 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7808 (mmpt) REVERT: J 91 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7012 (mt-10) REVERT: J 96 ARG cc_start: 0.6823 (ttt-90) cc_final: 0.6268 (ttm-80) REVERT: K 8 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (mt) REVERT: K 37 ASP cc_start: 0.7775 (m-30) cc_final: 0.6944 (m-30) REVERT: K 53 LYS cc_start: 0.7837 (pttp) cc_final: 0.6872 (mmtm) REVERT: K 105 ARG cc_start: 0.7510 (mmt180) cc_final: 0.6760 (mtp85) REVERT: L 41 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7853 (mpt180) REVERT: L 70 LYS cc_start: 0.8578 (tttp) cc_final: 0.8316 (ttmt) REVERT: L 80 SER cc_start: 0.8348 (t) cc_final: 0.8043 (p) REVERT: L 123 ARG cc_start: 0.7710 (mtt180) cc_final: 0.6979 (ttp-110) REVERT: L 126 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7400 (mtm180) REVERT: M 6 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7166 (ptm160) REVERT: M 18 ARG cc_start: 0.7530 (mtp180) cc_final: 0.6854 (mtp-110) REVERT: M 51 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7251 (mtt-85) REVERT: N 65 LEU cc_start: 0.8304 (mp) cc_final: 0.7961 (mm) REVERT: O 12 THR cc_start: 0.8470 (m) cc_final: 0.8109 (m) REVERT: O 31 THR cc_start: 0.7174 (m) cc_final: 0.6695 (p) REVERT: O 98 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7972 (tp40) REVERT: P 6 GLN cc_start: 0.7347 (tt0) cc_final: 0.7008 (tp40) REVERT: P 26 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7047 (tp30) REVERT: P 28 LYS cc_start: 0.8012 (mttt) cc_final: 0.7659 (mmmt) REVERT: P 70 GLU cc_start: 0.7401 (tt0) cc_final: 0.7019 (mt-10) REVERT: Q 15 LYS cc_start: 0.8672 (tttt) cc_final: 0.8382 (tttm) REVERT: Q 18 LYS cc_start: 0.8288 (ttpp) cc_final: 0.7832 (mtmt) REVERT: Q 48 ASP cc_start: 0.8396 (m-30) cc_final: 0.8092 (m-30) REVERT: Q 77 LYS cc_start: 0.8421 (mttt) cc_final: 0.7954 (mtmt) REVERT: Q 110 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7376 (mt-10) REVERT: R 40 MET cc_start: 0.8196 (ttp) cc_final: 0.7961 (ttp) REVERT: R 60 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7654 (mmtm) REVERT: S 83 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7918 (mmtp) REVERT: T 49 LYS cc_start: 0.7614 (mptt) cc_final: 0.7336 (ttmt) REVERT: T 52 GLU cc_start: 0.8245 (pt0) cc_final: 0.7275 (mm-30) REVERT: U 5 ARG cc_start: 0.6687 (ptp-170) cc_final: 0.5936 (mtt180) REVERT: U 9 GLU cc_start: 0.7735 (tp30) cc_final: 0.7405 (tp30) REVERT: U 45 GLN cc_start: 0.7839 (tp40) cc_final: 0.7482 (tp-100) REVERT: U 53 GLN cc_start: 0.5582 (OUTLIER) cc_final: 0.4612 (pp30) REVERT: U 59 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: U 100 GLU cc_start: 0.6927 (mp0) cc_final: 0.6596 (mp0) REVERT: W 7 ARG cc_start: 0.7505 (tpt170) cc_final: 0.6744 (mtp85) REVERT: W 64 LYS cc_start: 0.8425 (tppt) cc_final: 0.7951 (ttmt) REVERT: X 71 ARG cc_start: 0.7323 (mtm110) cc_final: 0.7063 (mtm110) REVERT: Y 4 LYS cc_start: 0.8087 (mttt) cc_final: 0.7789 (pttp) REVERT: 2 41 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7725 (mtm180) REVERT: 3 50 SER cc_start: 0.8065 (t) cc_final: 0.7685 (m) REVERT: 4 30 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6922 (mp0) REVERT: 5 36 ASP cc_start: 0.0275 (OUTLIER) cc_final: -0.1066 (t70) REVERT: 6 25 ARG cc_start: 0.6628 (ptm160) cc_final: 0.6391 (mtp-110) REVERT: b 8 MET cc_start: 0.4995 (tmm) cc_final: 0.4707 (tmm) REVERT: b 29 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6384 (m-80) REVERT: b 50 ASN cc_start: 0.5887 (t0) cc_final: 0.5554 (m-40) REVERT: b 108 GLN cc_start: 0.7585 (pt0) cc_final: 0.7289 (mm110) REVERT: b 116 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5164 (tt) REVERT: b 136 ARG cc_start: 0.6272 (mmm-85) cc_final: 0.5275 (ttp-170) REVERT: b 191 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7854 (t70) REVERT: c 7 ASN cc_start: 0.7671 (t0) cc_final: 0.7360 (t0) REVERT: c 37 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8040 (mmmm) REVERT: c 107 LYS cc_start: 0.7650 (mttt) cc_final: 0.7165 (tppt) REVERT: c 122 GLN cc_start: 0.7971 (mt0) cc_final: 0.7649 (mt0) REVERT: c 163 ARG cc_start: 0.6240 (mtt90) cc_final: 0.5392 (mtm-85) REVERT: c 187 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7443 (mm-30) REVERT: d 56 GLU cc_start: 0.6855 (tp30) cc_final: 0.6528 (tp30) REVERT: d 106 PHE cc_start: 0.6203 (m-80) cc_final: 0.5867 (m-80) REVERT: d 153 ARG cc_start: 0.4230 (OUTLIER) cc_final: 0.3906 (ptm160) REVERT: d 188 SER cc_start: 0.6794 (p) cc_final: 0.6303 (t) REVERT: d 190 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6590 (pp) REVERT: e 65 LYS cc_start: 0.7639 (mttm) cc_final: 0.7303 (mtpp) REVERT: e 129 SER cc_start: 0.8384 (p) cc_final: 0.8102 (p) REVERT: g 39 GLU cc_start: 0.8051 (pt0) cc_final: 0.7287 (pt0) REVERT: g 67 ASN cc_start: 0.6893 (m110) cc_final: 0.6173 (t0) REVERT: g 77 ARG cc_start: 0.5160 (ttt-90) cc_final: 0.3305 (mtp180) REVERT: g 89 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: g 91 ARG cc_start: 0.7381 (mmm160) cc_final: 0.6776 (mtm-85) REVERT: g 100 MET cc_start: 0.7788 (mpp) cc_final: 0.7432 (mpp) REVERT: g 128 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7471 (mp0) REVERT: h 9 MET cc_start: 0.7904 (ttt) cc_final: 0.7596 (ttt) REVERT: h 45 ILE cc_start: 0.8272 (mt) cc_final: 0.8013 (mm) REVERT: h 73 SER cc_start: 0.8306 (t) cc_final: 0.7936 (p) REVERT: i 45 MET cc_start: 0.5883 (ptt) cc_final: 0.5459 (ptp) REVERT: j 99 GLN cc_start: 0.7255 (mt0) cc_final: 0.7002 (tt0) REVERT: k 84 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7368 (mmm) REVERT: l 72 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.5617 (p0) REVERT: m 71 GLU cc_start: 0.7971 (tt0) cc_final: 0.7625 (tp30) REVERT: n 11 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7670 (ttpt) REVERT: n 17 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: n 62 ASN cc_start: 0.8674 (t0) cc_final: 0.8111 (t0) REVERT: o 57 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7015 (ttp-110) REVERT: p 63 GLN cc_start: 0.7045 (mm110) cc_final: 0.6483 (mm-40) REVERT: q 10 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7277 (ttm170) REVERT: q 18 LYS cc_start: 0.7361 (mttt) cc_final: 0.7147 (mttp) REVERT: q 37 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7927 (pt) REVERT: q 71 SER cc_start: 0.8061 (m) cc_final: 0.7171 (t) REVERT: r 19 GLU cc_start: 0.7347 (tt0) cc_final: 0.7022 (mp0) REVERT: r 29 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7662 (pttm) REVERT: s 20 LYS cc_start: 0.7350 (ttpt) cc_final: 0.6957 (mmtm) REVERT: s 36 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7189 (ptm160) REVERT: t 20 ASN cc_start: 0.8472 (m-40) cc_final: 0.8193 (m110) REVERT: t 23 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7771 (tpp-160) REVERT: t 26 MET cc_start: 0.7105 (ttp) cc_final: 0.6802 (ttp) REVERT: u 32 ARG cc_start: 0.7997 (tpt90) cc_final: 0.7452 (tpt170) REVERT: u 33 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7535 (mtm180) REVERT: u 44 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7354 (mmt180) REVERT: u 45 LYS cc_start: 0.7184 (ttpp) cc_final: 0.6904 (mtmm) REVERT: u 46 ARG cc_start: 0.6808 (mtt180) cc_final: 0.6341 (mtt180) REVERT: u 55 HIS cc_start: 0.6053 (m-70) cc_final: 0.5704 (m170) REVERT: z 17 ILE cc_start: 0.5319 (OUTLIER) cc_final: 0.4936 (tp) REVERT: z 208 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5536 (ptpp) REVERT: z 249 GLU cc_start: 0.4116 (tp30) cc_final: 0.3439 (mp0) REVERT: z 252 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6104 (mmtm) REVERT: z 262 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.5687 (mmm-85) REVERT: z 279 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.4420 (ttp80) REVERT: z 282 LYS cc_start: 0.5534 (mttt) cc_final: 0.5103 (mtpt) REVERT: z 284 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6616 (pm20) REVERT: z 298 ILE cc_start: 0.6909 (tt) cc_final: 0.6619 (tp) REVERT: z 327 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.5913 (mtm110) outliers start: 280 outliers final: 238 residues processed: 1283 average time/residue: 1.4391 time to fit residues: 3159.5638 Evaluate side-chains 1382 residues out of total 5165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1109 time to evaluate : 6.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 37 CYS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 81 ASP Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 113 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 137 THR Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain b residue 225 SER Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 153 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 178 GLU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 94 ARG Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain n residue 10 VAL Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 49 GLN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 38 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 20 VAL Chi-restraints excluded: chain z residue 26 THR Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 130 ILE Chi-restraints excluded: chain z residue 138 ASP Chi-restraints excluded: chain z residue 139 MET Chi-restraints excluded: chain z residue 149 VAL Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 175 LEU Chi-restraints excluded: chain z residue 208 LYS Chi-restraints excluded: chain z residue 237 LYS Chi-restraints excluded: chain z residue 247 ILE Chi-restraints excluded: chain z residue 279 ARG Chi-restraints excluded: chain z residue 286 ILE Chi-restraints excluded: chain z residue 320 THR Chi-restraints excluded: chain z residue 327 ARG Chi-restraints excluded: chain z residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1087 random chunks: chunk 684 optimal weight: 20.0000 chunk 918 optimal weight: 0.3980 chunk 264 optimal weight: 10.0000 chunk 795 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 863 optimal weight: 9.9990 chunk 361 optimal weight: 4.9990 chunk 886 optimal weight: 0.5980 chunk 109 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN G 103 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN i 31 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 95 HIS ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 74 HIS ** z 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124364 restraints weight = 220997.605| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 0.53 r_work: 0.3214 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 165485 Z= 0.325 Angle : 0.752 17.203 247217 Z= 0.399 Chirality : 0.040 0.404 31414 Planarity : 0.007 0.137 13505 Dihedral : 24.100 178.662 81857 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.28 % Favored : 91.20 % Rotamer: Outliers : 5.52 % Allowed : 22.35 % Favored : 72.13 % 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: -1.85 (0.10), residues: 6219 helix: -0.01 (0.11), residues: 1992 sheet: -1.38 (0.15), residues: 1094 loop : -2.00 (0.10), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP z 184 HIS 0.008 0.001 HIS z 22 PHE 0.027 0.002 PHE E 183 TYR 0.021 0.002 TYR s 79 ARG 0.012 0.001 ARG E 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47438.13 seconds wall clock time: 825 minutes 23.85 seconds (49523.85 seconds total)