Starting phenix.real_space_refine on Tue Mar 26 12:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdh_21636/03_2024/6wdh_21636_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdh_21636/03_2024/6wdh_21636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdh_21636/03_2024/6wdh_21636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdh_21636/03_2024/6wdh_21636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdh_21636/03_2024/6wdh_21636_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdh_21636/03_2024/6wdh_21636_updated.pdb" } resolution = 4.3 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= 0.115 sd= 0.882 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: 5 Type Number sf(0) Gaussians P 4800 5.49 5 S 154 5.16 5 C 75449 2.51 5 N 27949 2.21 5 O 41797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b GLU 184": "OE1" <-> "OE2" Residue "b ASP 228": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d GLU 51": "OE1" <-> "OE2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "d GLU 197": "OE1" <-> "OE2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "e ASP 9": "OD1" <-> "OD2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 55": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 70": "OE1" <-> "OE2" Residue "h PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 116": "OE1" <-> "OE2" Residue "h ASP 124": "OD1" <-> "OD2" Residue "i PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i GLU 129": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ASP 70": "OD1" <-> "OD2" 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 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 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 8": "OE1" <-> "OE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" 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 ARG 69": "NH1" <-> "NH2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ASP 55": "OD1" <-> "OD2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 95": "OD1" <-> "OD2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t GLU 52": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 87": "OE1" <-> "OE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "w ASP 11": "OD1" <-> "OD2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "x ASP 59": "OD1" <-> "OD2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "y GLU 5": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "S PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "X PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150149 Number of models: 1 Model: "" Number of chains: 59 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" 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: "h" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} 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: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} 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: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} 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: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" 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: "F" 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: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" 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: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" 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: "N" 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: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" 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: "U" 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: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" 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: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 90, 'rna2p_pyr': 49, 'rna3p_pur': 784, 'rna3p_pyr': 616} Link IDs: {'rna2p': 139, 'rna3p': 1399} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 210, 'rna2p_pyr': 92, 'rna3p_pur': 1464, 'rna3p_pyr': 1137} Link IDs: {'rna2p': 302, 'rna3p': 2600} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "7" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 60} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} 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 Time building chain proxies: 58.26, per 1000 atoms: 0.39 Number of scatterers: 150149 At special positions: 0 Unit cell: (279.93, 267.933, 243.939, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 4800 15.00 O 41797 8.00 N 27949 7.00 C 75449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.69 Conformation dependent library (CDL) restraints added in 6.9 seconds 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11074 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: 184 helices and 70 sheets defined 38.4% alpha, 16.8% beta 1360 base pairs and 2983 stacking pairs defined. Time for finding SS restraints: 76.95 Creating SS restraints... Processing helix chain 'b' and resid 9 through 15 removed outlier: 6.563A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 removed outlier: 4.073A pdb=" N ILE b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Proline residue: b 135 - end of helix No H-bonds generated for 'chain 'b' and resid 130 through 135' Processing helix chain 'b' and resid 198 through 203 removed outlier: 4.005A pdb=" N ARG b 202 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL b 203 " --> pdb=" O HIS b 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 198 through 203' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.111A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 4.823A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.580A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.519A pdb=" N GLY c 66 " --> pdb=" O LYS c 62 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 103 removed outlier: 4.857A pdb=" N PHE c 101 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 97 through 103' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.554A pdb=" N VAL d 28 " --> pdb=" O ASN d 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA d 34 " --> pdb=" O GLN d 30 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA d 36 " --> pdb=" O VAL d 32 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.810A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP d 140 " --> pdb=" O GLN d 136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA d 142 " --> pdb=" O LEU d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 3.529A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 184 removed outlier: 3.985A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP d 184 " --> pdb=" O LEU d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.695A pdb=" N GLU d 197 " --> pdb=" O VAL d 193 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 10 Processing helix chain 'e' and resid 11 through 20 removed outlier: 4.816A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 4.080A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 105 removed outlier: 4.166A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.627A pdb=" N GLY e 165 " --> pdb=" O SER e 161 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 3.853A pdb=" N VAL e 27 " --> pdb=" O VAL e 24 " (cutoff:3.500A) Proline residue: e 28 - end of helix Processing helix chain 'e' and resid 39 through 44 removed outlier: 5.213A pdb=" N ALA e 42 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE e 43 " --> pdb=" O GLY e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 5.247A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE e 137 " --> pdb=" O GLN e 134 " (cutoff:3.500A) Proline residue: e 138 - end of helix No H-bonds generated for 'chain 'e' and resid 133 through 138' Processing helix chain 'f' and resid 1 through 7 removed outlier: 3.776A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.745A pdb=" N THR f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.701A pdb=" N ILE f 140 " --> pdb=" O ASP f 136 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG f 152 " --> pdb=" O ARG f 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.638A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.713A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 73 removed outlier: 5.986A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA g 59 " --> pdb=" O GLU g 55 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 3.991A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 22 removed outlier: 3.779A pdb=" N ASP h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY h 21 " --> pdb=" O GLU h 17 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA h 22 " --> pdb=" O VAL h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.905A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Proline residue: h 68 - end of helix Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.741A pdb=" N PHE h 76 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 72 through 78' Processing helix chain 'h' and resid 94 through 106 removed outlier: 4.381A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS h 105 " --> pdb=" O LYS h 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 114 removed outlier: 5.785A pdb=" N ALA h 112 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 31 removed outlier: 4.836A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 49 removed outlier: 3.521A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.606A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 114 removed outlier: 4.123A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.639A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 removed outlier: 3.727A pdb=" N ASP j 71 " --> pdb=" O ASN j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.722A pdb=" N ALA j 94 " --> pdb=" O GLU j 90 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.361A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.882A 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 122 removed outlier: 4.381A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 104 through 109 removed outlier: 4.126A pdb=" N ARG k 108 " --> pdb=" O THR k 104 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER k 109 " --> pdb=" O ARG k 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 104 through 109' Processing helix chain 'k' and resid 112 through 119 removed outlier: 3.628A pdb=" N ALA k 119 " --> pdb=" O ILE k 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 74 removed outlier: 4.589A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 74' Processing helix chain 'l' and resid 93 through 99 removed outlier: 5.580A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.602A pdb=" N ILE l 135 " --> pdb=" O ALA l 131 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 84 removed outlier: 5.082A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS l 84 " --> pdb=" O ASP l 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.635A pdb=" N ALA m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.859A pdb=" N GLU m 115 " --> pdb=" O GLU m 111 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 15 through 32 removed outlier: 3.539A pdb=" N SER n 27 " --> pdb=" O ASN n 23 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 58 removed outlier: 3.802A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.406A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.794A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.001A pdb=" N VAL n 76 " --> pdb=" O ASP n 72 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY n 84 " --> pdb=" O PHE n 80 " (cutoff:3.500A) Proline residue: n 85 - end of helix Processing helix chain 'o' and resid 2 through 22 removed outlier: 5.085A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 3.789A pdb=" N ALA o 59 " --> pdb=" O GLU o 55 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.508A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS o 85 " --> pdb=" O ARG o 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY o 86 " --> pdb=" O ALA o 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.511A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 13 removed outlier: 4.315A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 103 removed outlier: 4.570A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 97 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.465A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA q 11 " --> pdb=" O VAL q 7 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 30 removed outlier: 4.062A pdb=" N SER q 28 " --> pdb=" O TYR q 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 60 removed outlier: 4.532A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 70 Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.598A pdb=" N LEU q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL q 99 " --> pdb=" O ALA q 95 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE q 100 " --> pdb=" O ASP q 96 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP q 101 " --> pdb=" O ILE q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.783A pdb=" N LEU q 108 " --> pdb=" O ALA q 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA q 114 " --> pdb=" O GLU q 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 4.050A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG s 18 " --> pdb=" O ALA s 14 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 3.831A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.795A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU s 51 " --> pdb=" O VAL s 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER s 53 " --> pdb=" O LYS s 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU s 59 " --> pdb=" O ILE s 55 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 11 removed outlier: 4.125A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.585A pdb=" N ALA t 23 " --> pdb=" O LYS t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 removed outlier: 3.503A pdb=" N ALA t 45 " --> pdb=" O ALA t 41 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA t 46 " --> pdb=" O GLU t 42 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.437A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.412A 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: 3.704A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 4.525A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.912A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL x 57 " --> pdb=" O LYS x 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 1 through 7 removed outlier: 5.088A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 4.057A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET y 30 " --> pdb=" O PHE y 26 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 63 removed outlier: 4.724A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA y 63 " --> pdb=" O GLU y 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.527A pdb=" N ALA z 49 " --> pdb=" O GLY z 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER z 51 " --> pdb=" O ILE z 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.703A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Proline residue: C 30 - end of helix No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.651A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 4.265A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.849A pdb=" N ARG D 33 " --> pdb=" O GLN D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.714A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.576A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.408A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'F' and resid 30 through 35 removed outlier: 3.868A pdb=" N LYS F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 35' Processing helix chain 'G' and resid 4 through 12 removed outlier: 4.041A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 63 Proline residue: G 47 - end of helix removed outlier: 4.110A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 4.123A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 3.710A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.721A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.783A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.568A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.713A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.533A pdb=" N ILE H 9 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 5 through 12' Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.740A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP H 35 " --> pdb=" O ASN H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.684A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.866A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.563A pdb=" N VAL H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.794A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.365A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.830A pdb=" N ARG I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG I 61 " --> pdb=" O LYS I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 4.926A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.944A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.613A pdb=" N ARG I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 164 removed outlier: 5.876A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 3.900A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 191' Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.162A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.532A pdb=" N LYS J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.355A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 147 removed outlier: 3.582A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.004A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.723A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 19 removed outlier: 3.817A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 20 through 33 removed outlier: 4.083A pdb=" N ALA K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.583A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.512A pdb=" N ALA L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.754A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.785A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.573A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 132 through 148 removed outlier: 4.163A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.805A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU M 10 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.376A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.637A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 53 Proline residue: N 50 - end of helix removed outlier: 4.239A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 46 through 53' Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.763A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 5.855A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 removed outlier: 5.367A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 4.379A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.916A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.318A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) Proline residue: P 59 - end of helix No H-bonds generated for 'chain 'P' and resid 53 through 59' Processing helix chain 'P' and resid 60 through 73 removed outlier: 3.518A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.810A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.522A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.148A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.808A pdb=" N LEU R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.845A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 61 removed outlier: 5.281A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.526A pdb=" N ASP R 81 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.778A pdb=" N LEU R 88 " --> pdb=" O CYS R 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG R 89 " --> pdb=" O TYR R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 24 removed outlier: 3.743A pdb=" N LYS S 6 " --> pdb=" O LYS S 2 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA S 24 " --> pdb=" O PHE S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.577A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU S 45 " --> pdb=" O TRP S 41 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 55 through 60 removed outlier: 4.417A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 55 through 60' Processing helix chain 'S' and resid 79 through 90 removed outlier: 4.701A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 4.658A pdb=" N SER S 31 " --> pdb=" O LEU S 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 removed outlier: 3.567A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 42 removed outlier: 4.557A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.842A pdb=" N ARG T 53 " --> pdb=" O HIS T 49 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU T 55 " --> pdb=" O SER T 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR T 68 " --> pdb=" O LYS T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 83 removed outlier: 4.023A pdb=" N LEU T 80 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.573A pdb=" N ILE U 75 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 17 removed outlier: 4.041A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 12 through 17' Processing helix chain 'W' and resid 24 through 33 removed outlier: 4.251A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 4.175A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 removed outlier: 3.598A pdb=" N ARG W 52 " --> pdb=" O ALA W 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.688A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.571A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 7 through 41 removed outlier: 3.624A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS Y 15 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 64 Proline residue: Y 55 - end of helix removed outlier: 3.525A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA Y 62 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.194A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.359A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 32 removed outlier: 5.173A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix removed outlier: 3.993A pdb=" N ARG Z 44 " --> pdb=" O PRO Z 40 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 16 removed outlier: 4.217A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU a 13 " --> pdb=" O ARG a 9 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 35 removed outlier: 3.810A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.790A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.827A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY b 126 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN b 116 " --> pdb=" O GLY b 126 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY b 118 " --> pdb=" O THR b 128 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 137 through 141 removed outlier: 3.839A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL b 183 " --> pdb=" O VAL b 171 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU b 173 " --> pdb=" O ARG b 181 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG b 181 " --> pdb=" O LEU b 173 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU b 175 " --> pdb=" O GLU b 179 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.238A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 11 through 15 removed outlier: 3.884A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL c 109 " --> pdb=" O VAL c 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL c 172 " --> pdb=" O VAL c 109 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 32 through 35 removed outlier: 3.626A pdb=" N ARG c 33 " --> pdb=" O THR c 51 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 179 through 182 Processing sheet with id= 8, first strand: chain 'c' and resid 23 through 28 removed outlier: 3.695A pdb=" N VAL c 189 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE c 27 " --> pdb=" O LEU c 187 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 46 through 51 removed outlier: 5.681A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.815A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'd' and resid 1 through 5 removed outlier: 6.151A pdb=" N MET d 1 " --> pdb=" O THR d 13 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR d 13 " --> pdb=" O MET d 1 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU d 3 " --> pdb=" O ALA d 11 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA d 11 " --> pdb=" O LEU d 3 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU d 5 " --> pdb=" O GLN d 9 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.577A pdb=" N VAL d 186 " --> pdb=" O ARG d 117 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE d 119 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL d 187 " --> pdb=" O LEU d 147 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.969A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR e 154 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN e 36 " --> pdb=" O ASP e 152 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU e 151 " --> pdb=" O VAL e 131 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET e 129 " --> pdb=" O ILE e 153 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 15, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 16, first strand: chain 'f' and resid 81 through 88 removed outlier: 5.744A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 18, first strand: chain 'g' and resid 16 through 20 removed outlier: 6.196A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'g' and resid 76 through 81 removed outlier: 6.143A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU g 114 " --> pdb=" O GLN g 133 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'h' and resid 23 through 28 removed outlier: 4.658A pdb=" N LEU h 23 " --> pdb=" O GLU h 87 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA h 25 " --> pdb=" O SER h 85 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'i' and resid 6 through 12 removed outlier: 4.852A pdb=" N ALA i 6 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL i 60 " --> pdb=" O ALA i 6 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE i 58 " --> pdb=" O VAL i 8 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL i 12 " --> pdb=" O ILE i 54 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE i 54 " --> pdb=" O VAL i 12 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS i 71 " --> pdb=" O PRO i 55 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'i' and resid 98 through 101 removed outlier: 3.698A pdb=" N VAL i 138 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE i 100 " --> pdb=" O VAL i 138 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'j' and resid 52 through 57 removed outlier: 3.573A pdb=" N LEU j 57 " --> pdb=" O VAL j 18 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'j' and resid 74 through 78 removed outlier: 7.535A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'k' and resid 17 through 21 removed outlier: 6.655A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY k 81 " --> pdb=" O LYS k 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS k 66 " --> pdb=" O GLY k 81 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'k' and resid 39 through 42 removed outlier: 3.732A pdb=" N LEU k 58 " --> pdb=" O ILE k 41 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'm' and resid 62 through 65 removed outlier: 3.504A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS m 100 " --> pdb=" O ALA m 35 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'm' and resid 30 through 35 removed outlier: 7.940A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'n' and resid 95 through 99 Processing sheet with id= 30, first strand: chain 'o' and resid 34 through 41 removed outlier: 4.106A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR o 31 " --> pdb=" O HIS o 34 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU o 26 " --> pdb=" O SER o 91 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'p' and resid 37 through 43 removed outlier: 6.275A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'p' and resid 48 through 52 removed outlier: 3.736A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'r' and resid 18 through 22 removed outlier: 4.503A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN r 91 " --> pdb=" O ARG r 68 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG r 68 " --> pdb=" O GLN r 91 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA r 65 " --> pdb=" O THR r 29 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR r 29 " --> pdb=" O ALA r 65 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 71 through 78 removed outlier: 3.719A pdb=" N HIS r 89 " --> pdb=" O VAL r 72 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 's' and resid 2 through 8 removed outlier: 4.717A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY s 79 " --> pdb=" O THR s 100 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE s 75 " --> pdb=" O THR s 104 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 't' and resid 12 through 15 removed outlier: 5.536A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'u' and resid 8 through 13 removed outlier: 4.797A pdb=" N ASP u 8 " --> pdb=" O VAL u 24 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS u 20 " --> pdb=" O VAL u 12 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'u' and resid 81 through 86 removed outlier: 4.826A pdb=" N ARG u 81 " --> pdb=" O LYS u 96 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'v' and resid 2 through 5 Processing sheet with id= 40, first strand: chain 'v' and resid 37 through 41 removed outlier: 4.480A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE v 29 " --> pdb=" O ILE v 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'w' and resid 62 through 67 Processing sheet with id= 42, first strand: chain 'x' and resid 11 through 16 removed outlier: 4.516A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'x' and resid 33 through 40 removed outlier: 3.510A pdb=" N VAL x 46 " --> pdb=" O PHE x 37 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'z' and resid 4 through 9 removed outlier: 4.007A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU z 57 " --> pdb=" O LYS z 5 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR z 7 " --> pdb=" O LYS z 55 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS z 55 " --> pdb=" O THR z 7 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 27 through 30 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'C' and resid 7 through 12 removed outlier: 5.176A pdb=" N HIS C 18 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 33 through 38 removed outlier: 6.256A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 50 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 37 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 14 through 19 removed outlier: 3.757A pdb=" N ILE F 26 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG F 19 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'G' and resid 14 through 17 removed outlier: 5.305A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.682A pdb=" N ILE G 163 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'H' and resid 18 through 21 removed outlier: 5.811A pdb=" N ASN H 18 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG H 58 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE H 67 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.617A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'I' and resid 140 through 143 removed outlier: 6.737A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP I 173 " --> pdb=" O GLU I 178 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'J' and resid 11 through 15 removed outlier: 4.061A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'J' and resid 93 through 97 Processing sheet with id= 56, first strand: chain 'J' and resid 31 through 35 removed outlier: 4.416A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'K' and resid 39 through 42 removed outlier: 3.663A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 59, first strand: chain 'M' and resid 22 through 28 removed outlier: 6.685A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'M' and resid 122 through 125 removed outlier: 6.736A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE M 100 " --> pdb=" O VAL M 128 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS M 126 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.709A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'O' and resid 44 through 50 removed outlier: 3.691A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE O 67 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'P' and resid 29 through 34 removed outlier: 3.566A pdb=" N ILE P 30 " --> pdb=" O HIS P 23 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 35 through 40 removed outlier: 4.863A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.729A pdb=" N VAL U 19 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 6 through 10 removed outlier: 3.612A pdb=" N GLY V 9 " --> pdb=" O VAL V 58 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'V' and resid 18 through 27 removed outlier: 4.633A pdb=" N LYS V 18 " --> pdb=" O ASP V 47 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP V 47 " --> pdb=" O LYS V 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE V 24 " --> pdb=" O THR V 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR V 41 " --> pdb=" O ILE V 24 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'X' and resid 29 through 33 removed outlier: 4.039A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 59 through 65 removed outlier: 6.389A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 169 through 176 removed outlier: 5.624A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) 1559 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3328 hydrogen bonds 5550 hydrogen bond angles 0 basepair planarities 1360 basepair parallelities 2983 stacking parallelities Total time for adding SS restraints: 305.52 Time building geometry restraints manager: 67.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 31423 1.34 - 1.46: 66109 1.46 - 1.58: 55729 1.58 - 1.71: 9600 1.71 - 1.83: 278 Bond restraints: 163139 Sorted by residual: bond pdb=" CN FME 5 101 " pdb=" O1 FME 5 101 " ideal model delta sigma weight residual 1.221 1.296 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CA PRO i 73 " pdb=" C PRO i 73 " ideal model delta sigma weight residual 1.514 1.533 -0.018 5.50e-03 3.31e+04 1.11e+01 bond pdb=" N GLY C 3 " pdb=" CA GLY C 3 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.50e+00 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.17e+00 bond pdb=" CA PRO i 21 " pdb=" C PRO i 21 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.04e+00 ... (remaining 163134 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.05: 27417 106.05 - 113.03: 91842 113.03 - 120.01: 61703 120.01 - 127.00: 50932 127.00 - 133.98: 12188 Bond angle restraints: 244082 Sorted by residual: angle pdb=" N GLY r 50 " pdb=" CA GLY r 50 " pdb=" C GLY r 50 " ideal model delta sigma weight residual 114.16 102.40 11.76 1.21e+00 6.83e-01 9.44e+01 angle pdb=" N ARG G 20 " pdb=" CA ARG G 20 " pdb=" C ARG G 20 " ideal model delta sigma weight residual 113.50 102.67 10.83 1.23e+00 6.61e-01 7.75e+01 angle pdb=" N ARG J 92 " pdb=" CA ARG J 92 " pdb=" C ARG J 92 " ideal model delta sigma weight residual 113.50 102.79 10.71 1.23e+00 6.61e-01 7.57e+01 angle pdb=" N ILE g 72 " pdb=" CA ILE g 72 " pdb=" C ILE g 72 " ideal model delta sigma weight residual 111.58 102.75 8.83 1.06e+00 8.90e-01 6.94e+01 angle pdb=" N LEU h 117 " pdb=" CA LEU h 117 " pdb=" C LEU h 117 " ideal model delta sigma weight residual 109.06 123.12 -14.06 1.70e+00 3.46e-01 6.84e+01 ... (remaining 244077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 93788 35.99 - 71.98: 9603 71.98 - 107.97: 1181 107.97 - 143.96: 10 143.96 - 179.95: 17 Dihedral angle restraints: 104599 sinusoidal: 87439 harmonic: 17160 Sorted by residual: dihedral pdb=" O4' C 2 12 " pdb=" C1' C 2 12 " pdb=" N1 C 2 12 " pdb=" C2 C 2 12 " ideal model delta sinusoidal sigma weight residual 200.00 26.55 173.45 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 5 55 " pdb=" C1' U 5 55 " pdb=" N1 U 5 55 " pdb=" C2 U 5 55 " ideal model delta sinusoidal sigma weight residual 200.00 43.67 156.33 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U 12552 " pdb=" C1' U 12552 " pdb=" N1 U 12552 " pdb=" C2 U 12552 " ideal model delta sinusoidal sigma weight residual 200.00 45.62 154.38 1 1.50e+01 4.44e-03 8.11e+01 ... (remaining 104596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 17855 0.078 - 0.156: 12019 0.156 - 0.234: 1162 0.234 - 0.311: 164 0.311 - 0.389: 20 Chirality restraints: 31220 Sorted by residual: chirality pdb=" C3' A 31201 " pdb=" C4' A 31201 " pdb=" O3' A 31201 " pdb=" C2' A 31201 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA PRO b 217 " pdb=" N PRO b 217 " pdb=" C PRO b 217 " pdb=" CB PRO b 217 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU h 117 " pdb=" N LEU h 117 " pdb=" C LEU h 117 " pdb=" CB LEU h 117 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 31217 not shown) Planarity restraints: 13080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12629 " 0.077 2.00e-02 2.50e+03 4.26e-02 4.08e+01 pdb=" N1 U 12629 " -0.002 2.00e-02 2.50e+03 pdb=" C2 U 12629 " -0.015 2.00e-02 2.50e+03 pdb=" O2 U 12629 " -0.028 2.00e-02 2.50e+03 pdb=" N3 U 12629 " -0.016 2.00e-02 2.50e+03 pdb=" C4 U 12629 " -0.015 2.00e-02 2.50e+03 pdb=" O4 U 12629 " 0.077 2.00e-02 2.50e+03 pdb=" C5 U 12629 " -0.041 2.00e-02 2.50e+03 pdb=" C6 U 12629 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11647 " 0.073 2.00e-02 2.50e+03 4.19e-02 3.94e+01 pdb=" N1 U 11647 " -0.001 2.00e-02 2.50e+03 pdb=" C2 U 11647 " -0.015 2.00e-02 2.50e+03 pdb=" O2 U 11647 " -0.026 2.00e-02 2.50e+03 pdb=" N3 U 11647 " -0.018 2.00e-02 2.50e+03 pdb=" C4 U 11647 " -0.019 2.00e-02 2.50e+03 pdb=" O4 U 11647 " 0.078 2.00e-02 2.50e+03 pdb=" C5 U 11647 " -0.041 2.00e-02 2.50e+03 pdb=" C6 U 11647 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 810 " 0.077 2.00e-02 2.50e+03 4.11e-02 3.79e+01 pdb=" N1 U 1 810 " -0.006 2.00e-02 2.50e+03 pdb=" C2 U 1 810 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U 1 810 " -0.027 2.00e-02 2.50e+03 pdb=" N3 U 1 810 " -0.014 2.00e-02 2.50e+03 pdb=" C4 U 1 810 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U 1 810 " 0.071 2.00e-02 2.50e+03 pdb=" C5 U 1 810 " -0.038 2.00e-02 2.50e+03 pdb=" C6 U 1 810 " -0.038 2.00e-02 2.50e+03 ... (remaining 13077 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 20487 2.76 - 3.30: 132866 3.30 - 3.83: 292297 3.83 - 4.37: 372371 4.37 - 4.90: 502190 Nonbonded interactions: 1320211 Sorted by model distance: nonbonded pdb=" O LYS T 64 " pdb=" OD1 ASP T 67 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR c 129 " pdb=" O HIS c 140 " model vdw 2.229 2.440 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.253 2.440 nonbonded pdb=" O2' U 11130 " pdb=" OP1 G 11131 " model vdw 2.301 2.440 nonbonded pdb=" O2' C 12326 " pdb=" OP1 A 12327 " model vdw 2.309 2.440 ... (remaining 1320206 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 '5' and resid 1 through 76) selection = chain '6' } 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=0.52 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 11.010 Check model and map are aligned: 1.610 Set scattering table: 1.040 Process input model: 611.190 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 633.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.006 0.075 163139 Z= 0.345 Angle : 0.997 14.057 244082 Z= 0.656 Chirality : 0.083 0.389 31220 Planarity : 0.007 0.079 13080 Dihedral : 21.927 179.951 93525 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 2.15 % Allowed : 12.52 % Favored : 85.34 % Rotamer: Outliers : 1.02 % Allowed : 7.60 % Favored : 91.38 % 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: -4.94 (0.08), residues: 5919 helix: -3.67 (0.08), residues: 1666 sheet: -2.94 (0.15), residues: 916 loop : -3.25 (0.09), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.006 TRP c 80 HIS 0.002 0.000 HIS G 169 PHE 0.034 0.005 PHE d 85 TYR 0.047 0.007 TYR N 5 ARG 0.007 0.001 ARG L 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2157 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 2107 time to evaluate : 6.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 145 MET cc_start: 0.6674 (mmm) cc_final: 0.5979 (ptt) REVERT: b 163 ILE cc_start: 0.7405 (mt) cc_final: 0.6999 (mt) REVERT: b 250 GLN cc_start: 0.7976 (tp40) cc_final: 0.7342 (tm-30) REVERT: c 46 ARG cc_start: 0.7435 (ptm160) cc_final: 0.7074 (ptm-80) REVERT: c 51 THR cc_start: 0.6561 (t) cc_final: 0.5805 (m) REVERT: d 1 MET cc_start: 0.8354 (tpt) cc_final: 0.7519 (mmm) REVERT: d 109 LEU cc_start: 0.9321 (mm) cc_final: 0.9042 (tt) REVERT: d 123 LYS cc_start: 0.8257 (tptt) cc_final: 0.7987 (tppt) REVERT: d 124 PHE cc_start: 0.4190 (t80) cc_final: 0.2727 (t80) REVERT: d 183 PHE cc_start: 0.7673 (m-80) cc_final: 0.7191 (m-80) REVERT: d 184 ASP cc_start: 0.6435 (m-30) cc_final: 0.6092 (m-30) REVERT: e 3 LEU cc_start: 0.7611 (mm) cc_final: 0.7363 (mt) REVERT: e 82 TYR cc_start: 0.7994 (t80) cc_final: 0.7569 (t80) REVERT: e 87 LYS cc_start: 0.5730 (ttpt) cc_final: 0.5016 (tttt) REVERT: e 135 ILE cc_start: 0.9053 (pt) cc_final: 0.8806 (mp) REVERT: e 136 ILE cc_start: 0.6932 (pt) cc_final: 0.6296 (pt) REVERT: e 139 GLU cc_start: 0.8271 (mp0) cc_final: 0.7446 (mt-10) REVERT: e 174 PHE cc_start: 0.8316 (m-80) cc_final: 0.7836 (m-10) REVERT: f 50 THR cc_start: 0.7174 (p) cc_final: 0.6580 (p) REVERT: f 73 SER cc_start: 0.8301 (t) cc_final: 0.7747 (p) REVERT: g 5 LEU cc_start: 0.7764 (mp) cc_final: 0.7158 (tp) REVERT: g 147 VAL cc_start: 0.8060 (t) cc_final: 0.7783 (m) REVERT: h 1 MET cc_start: 0.1536 (ptm) cc_final: 0.1195 (ppp) REVERT: h 52 MET cc_start: -0.0133 (mtm) cc_final: -0.1874 (tmm) REVERT: h 86 MET cc_start: -0.1095 (tpt) cc_final: -0.2321 (mmt) REVERT: j 16 TYR cc_start: 0.6862 (m-10) cc_final: 0.6167 (m-80) REVERT: j 17 VAL cc_start: 0.6107 (t) cc_final: 0.5771 (p) REVERT: j 88 THR cc_start: 0.4685 (p) cc_final: 0.4310 (m) REVERT: j 103 ILE cc_start: 0.7425 (mt) cc_final: 0.6943 (mt) REVERT: k 7 MET cc_start: 0.6813 (mmm) cc_final: 0.6216 (tpp) REVERT: k 8 LEU cc_start: 0.7583 (mt) cc_final: 0.6755 (mt) REVERT: l 56 PRO cc_start: 0.7921 (Cg_exo) cc_final: 0.7662 (Cg_endo) REVERT: l 73 ILE cc_start: 0.6665 (pt) cc_final: 0.6429 (pt) REVERT: m 12 MET cc_start: 0.7317 (ppp) cc_final: 0.6886 (ptp) REVERT: m 106 ASP cc_start: 0.7641 (t70) cc_final: 0.7229 (t0) REVERT: n 29 VAL cc_start: 0.7096 (t) cc_final: 0.6815 (t) REVERT: n 116 VAL cc_start: 0.8209 (m) cc_final: 0.6902 (m) REVERT: o 92 PHE cc_start: 0.8430 (t80) cc_final: 0.7696 (t80) REVERT: p 37 LYS cc_start: 0.7854 (ttmm) cc_final: 0.7206 (mttt) REVERT: q 18 LYS cc_start: 0.8258 (tptt) cc_final: 0.7803 (ttmt) REVERT: q 61 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7235 (tp) REVERT: q 111 LYS cc_start: 0.9311 (tptm) cc_final: 0.9021 (ptpp) REVERT: r 5 PHE cc_start: 0.7001 (p90) cc_final: 0.6308 (p90) REVERT: r 18 GLN cc_start: 0.7155 (tt0) cc_final: 0.6811 (tp-100) REVERT: r 89 HIS cc_start: 0.7345 (t-90) cc_final: 0.6987 (t-90) REVERT: s 52 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.5268 (pt0) REVERT: t 61 LEU cc_start: 0.4763 (pt) cc_final: 0.4476 (pt) REVERT: t 70 HIS cc_start: 0.5850 (t70) cc_final: 0.4264 (m-70) REVERT: u 21 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8049 (mtt90) REVERT: u 24 VAL cc_start: 0.7097 (t) cc_final: 0.5643 (t) REVERT: v 53 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8355 (mmtm) REVERT: v 76 ASP cc_start: 0.8420 (t0) cc_final: 0.8202 (t0) REVERT: w 15 LYS cc_start: 0.7222 (mmtm) cc_final: 0.6896 (mptt) REVERT: w 39 THR cc_start: 0.5003 (m) cc_final: 0.3978 (m) REVERT: w 42 HIS cc_start: 0.3766 (OUTLIER) cc_final: 0.3503 (m-70) REVERT: x 5 GLN cc_start: 0.7434 (mm110) cc_final: 0.7019 (tp40) REVERT: x 37 PHE cc_start: 0.7709 (m-10) cc_final: 0.7343 (m-80) REVERT: x 55 MET cc_start: 0.6967 (mtt) cc_final: 0.6661 (ppp) REVERT: x 66 VAL cc_start: 0.6743 (t) cc_final: 0.6442 (t) REVERT: y 31 GLN cc_start: 0.8847 (tt0) cc_final: 0.8564 (tp-100) REVERT: B 6 LYS cc_start: 0.7264 (ttmt) cc_final: 0.6960 (tttt) REVERT: B 19 ASP cc_start: 0.7652 (m-30) cc_final: 0.7325 (p0) REVERT: B 52 LYS cc_start: 0.8647 (tppp) cc_final: 0.8377 (tppp) REVERT: C 21 THR cc_start: 0.4967 (OUTLIER) cc_final: 0.4607 (p) REVERT: D 22 MET cc_start: 0.8986 (mmm) cc_final: 0.8725 (mmm) REVERT: G 5 MET cc_start: 0.7900 (ptt) cc_final: 0.6212 (tpp) REVERT: G 8 MET cc_start: 0.8584 (mtp) cc_final: 0.7949 (ptp) REVERT: G 27 LYS cc_start: 0.8984 (tttp) cc_final: 0.8713 (ttmt) REVERT: G 41 ASN cc_start: 0.7566 (t0) cc_final: 0.5960 (t0) REVERT: G 59 ILE cc_start: 0.9383 (mp) cc_final: 0.8827 (mp) REVERT: G 68 PHE cc_start: 0.8426 (m-80) cc_final: 0.8148 (m-80) REVERT: G 88 GLN cc_start: 0.5761 (mm-40) cc_final: 0.5368 (mm-40) REVERT: G 135 MET cc_start: 0.4985 (ptp) cc_final: 0.4695 (ptt) REVERT: G 199 ILE cc_start: 0.6226 (mt) cc_final: 0.5639 (mt) REVERT: H 11 LEU cc_start: 0.5836 (mt) cc_final: 0.5472 (tt) REVERT: H 68 HIS cc_start: 0.8089 (m90) cc_final: 0.7538 (m90) REVERT: H 87 ARG cc_start: 0.6812 (tmm-80) cc_final: 0.6558 (ttm110) REVERT: H 105 VAL cc_start: 0.5707 (p) cc_final: 0.5351 (p) REVERT: H 138 GLN cc_start: 0.8078 (mt0) cc_final: 0.7758 (mt0) REVERT: H 156 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6387 (pt) REVERT: H 165 GLU cc_start: 0.6352 (mp0) cc_final: 0.6031 (mp0) REVERT: H 167 TYR cc_start: 0.5517 (t80) cc_final: 0.5081 (t80) REVERT: H 171 ARG cc_start: 0.5925 (mpt-90) cc_final: 0.5592 (ttm-80) REVERT: H 187 GLU cc_start: 0.8257 (pm20) cc_final: 0.7163 (tp30) REVERT: I 89 LEU cc_start: 0.8348 (mt) cc_final: 0.8070 (mt) REVERT: I 94 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7767 (mm-30) REVERT: I 123 MET cc_start: 0.6185 (ttp) cc_final: 0.5718 (ttm) REVERT: I 167 PRO cc_start: 0.5448 (Cg_exo) cc_final: 0.3713 (Cg_endo) REVERT: I 177 MET cc_start: 0.2560 (mpp) cc_final: 0.2024 (mtp) REVERT: I 190 LEU cc_start: 0.8647 (mp) cc_final: 0.8309 (mp) REVERT: J 30 PHE cc_start: 0.7359 (m-80) cc_final: 0.6879 (m-10) REVERT: J 36 THR cc_start: 0.7752 (p) cc_final: 0.7340 (p) REVERT: J 40 ASP cc_start: 0.6766 (p0) cc_final: 0.6260 (p0) REVERT: J 51 LYS cc_start: 0.6424 (ptmm) cc_final: 0.5246 (ttpt) REVERT: J 95 MET cc_start: 0.6357 (ptp) cc_final: 0.6015 (mtm) REVERT: J 163 ILE cc_start: 0.8057 (mp) cc_final: 0.7664 (mm) REVERT: K 1 MET cc_start: 0.6651 (mtt) cc_final: 0.6191 (mmp) REVERT: K 8 PHE cc_start: 0.7085 (p90) cc_final: 0.6801 (p90) REVERT: K 67 PRO cc_start: 0.8389 (Cg_endo) cc_final: 0.6832 (Cg_exo) REVERT: L 31 VAL cc_start: 0.7239 (p) cc_final: 0.7011 (m) REVERT: L 32 ASP cc_start: 0.7197 (m-30) cc_final: 0.6864 (t70) REVERT: L 95 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7496 (ttm110) REVERT: L 122 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7442 (tp30) REVERT: L 134 VAL cc_start: 0.8184 (m) cc_final: 0.7357 (m) REVERT: L 150 PHE cc_start: 0.4511 (m-80) cc_final: 0.4011 (t80) REVERT: M 17 GLN cc_start: 0.7811 (mt0) cc_final: 0.6858 (tt0) REVERT: M 35 ILE cc_start: 0.7672 (mt) cc_final: 0.7469 (mt) REVERT: M 64 TYR cc_start: 0.3916 (m-80) cc_final: 0.3711 (m-80) REVERT: M 125 ILE cc_start: 0.7558 (mp) cc_final: 0.7123 (mp) REVERT: N 4 GLN cc_start: 0.4244 (tt0) cc_final: 0.3701 (tp-100) REVERT: N 51 LEU cc_start: 0.7282 (mt) cc_final: 0.7078 (mm) REVERT: P 41 LEU cc_start: 0.7787 (pt) cc_final: 0.7554 (pp) REVERT: P 106 ILE cc_start: 0.6808 (mm) cc_final: 0.6168 (mm) REVERT: Q 34 THR cc_start: 0.7459 (p) cc_final: 0.6965 (t) REVERT: Q 95 HIS cc_start: 0.7330 (m90) cc_final: 0.7087 (m-70) REVERT: R 81 ASP cc_start: 0.7135 (m-30) cc_final: 0.6174 (m-30) REVERT: R 84 CYS cc_start: 0.3022 (p) cc_final: 0.1023 (p) REVERT: S 40 ARG cc_start: 0.5722 (mtp180) cc_final: 0.4690 (tmt170) REVERT: T 17 ASP cc_start: 0.8473 (p0) cc_final: 0.7962 (p0) REVERT: T 47 LYS cc_start: 0.6750 (mttt) cc_final: 0.6222 (tppt) REVERT: T 60 SER cc_start: 0.6132 (t) cc_final: 0.5925 (p) REVERT: U 33 ILE cc_start: 0.7461 (mm) cc_final: 0.6941 (mm) REVERT: V 19 SER cc_start: 0.4231 (p) cc_final: 0.3890 (m) REVERT: V 39 ARG cc_start: 0.6766 (mmt90) cc_final: 0.6491 (mmt90) REVERT: X 46 LEU cc_start: 0.8143 (mt) cc_final: 0.7909 (mp) REVERT: X 61 VAL cc_start: 0.7478 (t) cc_final: 0.6472 (m) REVERT: Y 30 PHE cc_start: 0.6203 (m-80) cc_final: 0.5902 (m-80) REVERT: Y 35 TYR cc_start: 0.7591 (m-10) cc_final: 0.7255 (m-80) REVERT: Z 38 GLU cc_start: 0.8380 (tp30) cc_final: 0.7492 (tp30) REVERT: a 30 LEU cc_start: 0.3798 (pp) cc_final: 0.3442 (mm) outliers start: 50 outliers final: 10 residues processed: 2131 average time/residue: 1.4857 time to fit residues: 5199.0695 Evaluate side-chains 1401 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1386 time to evaluate : 6.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 10.0000 chunk 801 optimal weight: 9.9990 chunk 444 optimal weight: 6.9990 chunk 273 optimal weight: 0.2980 chunk 540 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 828 optimal weight: 9.9990 chunk 320 optimal weight: 6.9990 chunk 503 optimal weight: 20.0000 chunk 616 optimal weight: 10.0000 chunk 959 optimal weight: 9.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 HIS b 89 ASN b 116 GLN b 127 ASN b 196 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 ASN c 150 GLN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN d 115 GLN e 4 HIS ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN g 145 ASN i 29 GLN i 33 ASN i 42 ASN ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 ASN k 13 ASN m 3 GLN m 22 GLN n 62 ASN o 104 GLN q 19 GLN q 55 GLN q 71 ASN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 40 ASN u 73 ASN w 42 HIS w 53 HIS y 20 ASN B 3 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS E 23 HIS G 50 ASN G 119 GLN G 121 GLN H 5 HIS H 31 ASN H 139 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 35 GLN I 39 GLN I 88 ASN I 115 GLN I 119 HIS ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN N 74 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 GLN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS T 27 GLN T 50 HIS ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN Y 47 GLN ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN Y 69 ASN a 24 ASN a 160 GLN a 172 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.234 163139 Z= 0.408 Angle : 0.880 15.788 244082 Z= 0.448 Chirality : 0.047 0.352 31220 Planarity : 0.007 0.209 13080 Dihedral : 22.814 176.990 81722 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 0.47 % Allowed : 7.42 % Favored : 92.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.75 (0.09), residues: 5919 helix: -2.10 (0.10), residues: 1820 sheet: -2.18 (0.16), residues: 949 loop : -2.87 (0.10), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP b 212 HIS 0.030 0.003 HIS P 23 PHE 0.051 0.004 PHE q 56 TYR 0.032 0.003 TYR K 25 ARG 0.040 0.001 ARG o 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1871 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1848 time to evaluate : 5.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 29 PHE cc_start: 0.7158 (t80) cc_final: 0.6916 (t80) REVERT: b 63 ILE cc_start: 0.8424 (mt) cc_final: 0.8066 (mt) REVERT: b 146 LYS cc_start: 0.6978 (mttm) cc_final: 0.6408 (mttp) REVERT: b 163 ILE cc_start: 0.8499 (mt) cc_final: 0.8166 (mt) REVERT: b 187 CYS cc_start: 0.8028 (m) cc_final: 0.7711 (m) REVERT: c 11 MET cc_start: 0.7056 (ttm) cc_final: 0.6238 (ttm) REVERT: c 14 ILE cc_start: 0.8066 (tp) cc_final: 0.7615 (mp) REVERT: c 80 TRP cc_start: 0.7033 (m-90) cc_final: 0.6750 (m-90) REVERT: c 96 ILE cc_start: 0.8500 (tp) cc_final: 0.8177 (mt) REVERT: c 125 TRP cc_start: 0.8086 (m100) cc_final: 0.7841 (m100) REVERT: d 1 MET cc_start: 0.8769 (tpt) cc_final: 0.7885 (mmm) REVERT: d 30 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8120 (tm-30) REVERT: d 43 THR cc_start: 0.7132 (p) cc_final: 0.6822 (p) REVERT: d 145 ASP cc_start: 0.7255 (t0) cc_final: 0.6689 (t0) REVERT: d 175 ILE cc_start: 0.6353 (mm) cc_final: 0.6072 (mm) REVERT: d 183 PHE cc_start: 0.7949 (m-80) cc_final: 0.7606 (m-80) REVERT: d 184 ASP cc_start: 0.7232 (m-30) cc_final: 0.6528 (m-30) REVERT: e 62 GLN cc_start: 0.6592 (pt0) cc_final: 0.6333 (pt0) REVERT: e 65 LEU cc_start: 0.9004 (tt) cc_final: 0.8800 (tt) REVERT: e 86 CYS cc_start: 0.5499 (m) cc_final: 0.5121 (m) REVERT: e 99 PHE cc_start: 0.8334 (t80) cc_final: 0.7957 (t80) REVERT: e 113 PHE cc_start: 0.4875 (t80) cc_final: 0.4367 (t80) REVERT: e 119 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8202 (pttm) REVERT: e 129 MET cc_start: 0.7066 (tmm) cc_final: 0.6575 (tmm) REVERT: e 174 PHE cc_start: 0.8130 (m-80) cc_final: 0.7753 (m-10) REVERT: f 43 LYS cc_start: 0.8448 (pttm) cc_final: 0.8207 (ptpp) REVERT: f 73 SER cc_start: 0.8520 (t) cc_final: 0.7850 (p) REVERT: f 80 GLU cc_start: 0.8772 (tp30) cc_final: 0.8109 (tm-30) REVERT: f 137 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6022 (tptp) REVERT: f 148 ARG cc_start: 0.8027 (ttt-90) cc_final: 0.7675 (ttt180) REVERT: g 46 PHE cc_start: 0.8999 (m-80) cc_final: 0.8629 (m-80) REVERT: g 55 GLU cc_start: 0.7314 (mp0) cc_final: 0.6607 (tp30) REVERT: g 147 VAL cc_start: 0.8428 (t) cc_final: 0.8194 (p) REVERT: h 38 MET cc_start: -0.1969 (tpp) cc_final: -0.2178 (tpp) REVERT: h 52 MET cc_start: -0.0609 (mtp) cc_final: -0.2202 (tmm) REVERT: j 7 LYS cc_start: 0.6835 (mttt) cc_final: 0.6106 (tttp) REVERT: j 32 LEU cc_start: 0.8198 (tt) cc_final: 0.7927 (tt) REVERT: j 58 ASN cc_start: 0.7962 (m-40) cc_final: 0.7542 (t0) REVERT: j 64 VAL cc_start: 0.6588 (m) cc_final: 0.6358 (m) REVERT: j 139 VAL cc_start: 0.7119 (t) cc_final: 0.6226 (t) REVERT: k 71 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8327 (mmm160) REVERT: k 88 ASN cc_start: 0.8711 (t0) cc_final: 0.8500 (t0) REVERT: k 113 MET cc_start: 0.8516 (ttt) cc_final: 0.8278 (ttp) REVERT: l 95 LEU cc_start: 0.7032 (mt) cc_final: 0.6756 (mt) REVERT: l 101 ILE cc_start: 0.8741 (pt) cc_final: 0.8316 (tt) REVERT: l 125 LEU cc_start: 0.8017 (mp) cc_final: 0.7662 (mt) REVERT: l 127 VAL cc_start: 0.8442 (t) cc_final: 0.8237 (p) REVERT: m 2 LEU cc_start: 0.6675 (mm) cc_final: 0.6259 (mt) REVERT: m 18 ARG cc_start: 0.8340 (mtm110) cc_final: 0.7808 (mtp85) REVERT: m 84 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8207 (mtmt) REVERT: m 104 GLU cc_start: 0.7619 (tt0) cc_final: 0.6609 (tt0) REVERT: m 105 MET cc_start: 0.7495 (mtm) cc_final: 0.7098 (mpp) REVERT: m 106 ASP cc_start: 0.7753 (t70) cc_final: 0.7366 (t0) REVERT: m 110 GLU cc_start: 0.6418 (tm-30) cc_final: 0.6076 (tm-30) REVERT: n 35 LYS cc_start: 0.6759 (tttp) cc_final: 0.6364 (tttp) REVERT: n 53 THR cc_start: 0.8711 (m) cc_final: 0.8490 (p) REVERT: o 31 THR cc_start: 0.8220 (m) cc_final: 0.7929 (p) REVERT: o 63 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8373 (tmtt) REVERT: o 92 PHE cc_start: 0.8632 (t80) cc_final: 0.7877 (t80) REVERT: p 37 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7355 (mttt) REVERT: q 18 LYS cc_start: 0.8464 (tptt) cc_final: 0.8186 (ttpt) REVERT: q 97 ILE cc_start: 0.8627 (pt) cc_final: 0.8301 (pt) REVERT: q 111 LYS cc_start: 0.9503 (tptm) cc_final: 0.9119 (ptpp) REVERT: r 5 PHE cc_start: 0.7148 (p90) cc_final: 0.6836 (p90) REVERT: r 13 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7622 (ptm160) REVERT: r 48 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7497 (ptpp) REVERT: r 73 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7403 (tptt) REVERT: r 92 TRP cc_start: 0.7522 (m100) cc_final: 0.6733 (m100) REVERT: s 3 THR cc_start: 0.7533 (m) cc_final: 0.6806 (p) REVERT: s 6 LYS cc_start: 0.8682 (tttm) cc_final: 0.8325 (tttm) REVERT: s 40 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.6781 (p0) REVERT: s 86 MET cc_start: 0.8022 (tpt) cc_final: 0.7755 (tpt) REVERT: s 92 ARG cc_start: 0.6339 (mpp80) cc_final: 0.6106 (mtt180) REVERT: s 105 VAL cc_start: 0.8878 (t) cc_final: 0.8353 (m) REVERT: v 1 MET cc_start: 0.8640 (pmm) cc_final: 0.7032 (ppp) REVERT: v 59 GLU cc_start: 0.6712 (pt0) cc_final: 0.6467 (pt0) REVERT: v 71 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8727 (ptpp) REVERT: v 87 GLN cc_start: 0.8076 (mt0) cc_final: 0.7649 (mt0) REVERT: w 36 GLN cc_start: 0.8072 (pp30) cc_final: 0.7318 (pp30) REVERT: x 5 GLN cc_start: 0.8192 (mm110) cc_final: 0.7699 (tp40) REVERT: x 11 PRO cc_start: 0.8875 (Cg_exo) cc_final: 0.8580 (Cg_endo) REVERT: x 37 PHE cc_start: 0.7936 (m-10) cc_final: 0.7612 (m-80) REVERT: x 53 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8590 (mtpt) REVERT: y 1 MET cc_start: 0.7215 (ptm) cc_final: 0.6968 (ptm) REVERT: y 12 GLU cc_start: 0.8720 (tp30) cc_final: 0.8510 (mm-30) REVERT: y 31 GLN cc_start: 0.9123 (tt0) cc_final: 0.8733 (tp-100) REVERT: y 41 HIS cc_start: 0.7658 (p-80) cc_final: 0.7437 (p-80) REVERT: z 2 LYS cc_start: 0.8094 (tttt) cc_final: 0.7647 (tptm) REVERT: z 31 ILE cc_start: 0.7719 (mm) cc_final: 0.7358 (mm) REVERT: z 56 VAL cc_start: 0.9141 (t) cc_final: 0.8317 (t) REVERT: B 19 ASP cc_start: 0.7465 (m-30) cc_final: 0.6792 (p0) REVERT: B 43 THR cc_start: 0.7425 (p) cc_final: 0.6680 (p) REVERT: D 25 LYS cc_start: 0.8427 (ptmm) cc_final: 0.7795 (pttt) REVERT: D 33 ARG cc_start: 0.8003 (ptt180) cc_final: 0.7682 (ptt90) REVERT: E 48 MET cc_start: 0.7673 (pmm) cc_final: 0.7430 (pmm) REVERT: E 49 VAL cc_start: 0.8391 (t) cc_final: 0.8019 (t) REVERT: E 58 ILE cc_start: 0.7998 (mt) cc_final: 0.7784 (pt) REVERT: E 63 TYR cc_start: 0.7084 (m-10) cc_final: 0.6478 (m-80) REVERT: F 8 LYS cc_start: 0.6831 (mtmm) cc_final: 0.6556 (ptpt) REVERT: G 5 MET cc_start: 0.7945 (ptt) cc_final: 0.7052 (ttt) REVERT: G 8 MET cc_start: 0.8356 (mtp) cc_final: 0.7620 (ptp) REVERT: G 34 ARG cc_start: 0.6776 (tpp80) cc_final: 0.6077 (tpp80) REVERT: G 46 VAL cc_start: 0.8697 (t) cc_final: 0.8295 (t) REVERT: G 50 ASN cc_start: 0.8242 (m-40) cc_final: 0.7762 (p0) REVERT: G 56 LEU cc_start: 0.7970 (tt) cc_final: 0.7456 (tt) REVERT: G 76 SER cc_start: 0.7223 (t) cc_final: 0.6986 (m) REVERT: G 89 PHE cc_start: 0.4975 (m-80) cc_final: 0.4393 (m-80) REVERT: G 125 PHE cc_start: 0.7217 (m-80) cc_final: 0.6538 (m-80) REVERT: G 139 GLU cc_start: 0.8538 (pp20) cc_final: 0.8209 (pp20) REVERT: G 185 ILE cc_start: 0.6881 (pt) cc_final: 0.6600 (pt) REVERT: H 87 ARG cc_start: 0.6964 (tmm-80) cc_final: 0.6577 (ttm-80) REVERT: H 135 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7651 (ptp-170) REVERT: H 151 GLU cc_start: 0.7204 (tp30) cc_final: 0.6877 (tp30) REVERT: I 12 ARG cc_start: 0.3374 (mtm180) cc_final: 0.2549 (mtp180) REVERT: I 100 VAL cc_start: 0.6035 (t) cc_final: 0.5776 (t) REVERT: I 123 MET cc_start: 0.8198 (ttp) cc_final: 0.7884 (ttm) REVERT: I 177 MET cc_start: 0.3225 (mpp) cc_final: 0.2862 (mtp) REVERT: J 12 GLU cc_start: 0.8291 (pm20) cc_final: 0.7723 (pp20) REVERT: J 63 MET cc_start: 0.7238 (ppp) cc_final: 0.7018 (ppp) REVERT: J 115 GLU cc_start: 0.8185 (pt0) cc_final: 0.7955 (tp30) REVERT: J 134 ASN cc_start: 0.8804 (m-40) cc_final: 0.8444 (m110) REVERT: J 139 THR cc_start: 0.8844 (p) cc_final: 0.8422 (p) REVERT: J 146 MET cc_start: 0.4504 (tmm) cc_final: 0.4080 (ttp) REVERT: J 151 MET cc_start: 0.8652 (mmp) cc_final: 0.8253 (mmp) REVERT: K 37 HIS cc_start: 0.7840 (m90) cc_final: 0.7454 (m90) REVERT: K 67 PRO cc_start: 0.8227 (Cg_endo) cc_final: 0.7638 (Cg_exo) REVERT: L 67 ASN cc_start: 0.7138 (t0) cc_final: 0.6532 (t0) REVERT: L 95 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7810 (ttm110) REVERT: L 115 MET cc_start: 0.8551 (mtm) cc_final: 0.8348 (mtm) REVERT: L 136 LYS cc_start: 0.8453 (tptm) cc_final: 0.8147 (mmtp) REVERT: M 17 GLN cc_start: 0.8770 (mt0) cc_final: 0.8218 (mt0) REVERT: M 35 ILE cc_start: 0.8495 (mt) cc_final: 0.8164 (mt) REVERT: M 61 THR cc_start: 0.7179 (m) cc_final: 0.6788 (m) REVERT: M 86 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7573 (mmmt) REVERT: M 100 ILE cc_start: 0.7497 (pt) cc_final: 0.7208 (pt) REVERT: M 125 ILE cc_start: 0.8101 (mp) cc_final: 0.7814 (mp) REVERT: M 126 CYS cc_start: 0.8712 (p) cc_final: 0.8209 (p) REVERT: N 4 GLN cc_start: 0.5186 (tt0) cc_final: 0.3950 (tp40) REVERT: N 11 ARG cc_start: 0.7469 (tpt90) cc_final: 0.7055 (tpt90) REVERT: N 30 ASN cc_start: 0.7485 (t0) cc_final: 0.7043 (p0) REVERT: N 45 MET cc_start: 0.8646 (ptp) cc_final: 0.8047 (pmm) REVERT: P 34 THR cc_start: 0.6279 (p) cc_final: 0.5995 (t) REVERT: Q 29 LYS cc_start: 0.7359 (mttt) cc_final: 0.6756 (mttt) REVERT: Q 34 THR cc_start: 0.7735 (p) cc_final: 0.7326 (t) REVERT: Q 35 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7446 (ttm170) REVERT: Q 95 HIS cc_start: 0.6775 (m90) cc_final: 0.6470 (m90) REVERT: Q 113 ARG cc_start: 0.5768 (ptt-90) cc_final: 0.4935 (ptt-90) REVERT: R 76 ILE cc_start: 0.8451 (mt) cc_final: 0.7890 (mt) REVERT: S 82 LYS cc_start: 0.7181 (mmmt) cc_final: 0.6457 (mmmt) REVERT: T 17 ASP cc_start: 0.8760 (p0) cc_final: 0.8214 (p0) REVERT: U 36 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6617 (p) REVERT: V 15 LYS cc_start: 0.3589 (pttp) cc_final: 0.2294 (tptp) REVERT: V 27 PHE cc_start: 0.8685 (t80) cc_final: 0.8232 (t80) REVERT: V 33 TYR cc_start: 0.6763 (m-80) cc_final: 0.6233 (m-80) REVERT: W 43 ILE cc_start: 0.8566 (mp) cc_final: 0.8356 (mm) REVERT: W 53 GLN cc_start: 0.8009 (pt0) cc_final: 0.7622 (pm20) REVERT: W 58 ILE cc_start: 0.8680 (mm) cc_final: 0.8391 (mt) REVERT: X 11 ASP cc_start: 0.7199 (t0) cc_final: 0.6700 (t0) REVERT: X 65 MET cc_start: 0.7478 (ppp) cc_final: 0.7096 (tmm) REVERT: Y 58 ASP cc_start: 0.7248 (t0) cc_final: 0.7035 (t0) REVERT: Y 83 ASN cc_start: 0.9049 (p0) cc_final: 0.8590 (p0) REVERT: Z 38 GLU cc_start: 0.8305 (tp30) cc_final: 0.7891 (tm-30) REVERT: Z 46 ARG cc_start: 0.9245 (mmp80) cc_final: 0.8933 (mmm160) REVERT: Z 54 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8364 (ttt180) outliers start: 23 outliers final: 6 residues processed: 1865 average time/residue: 1.4272 time to fit residues: 4463.1989 Evaluate side-chains 1445 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1437 time to evaluate : 6.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 798 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 961 optimal weight: 9.9990 chunk 1038 optimal weight: 10.0000 chunk 856 optimal weight: 10.0000 chunk 953 optimal weight: 10.0000 chunk 327 optimal weight: 0.8980 chunk 771 optimal weight: 10.0000 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 14 HIS b 24 HIS ** b 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN d 46 GLN d 92 HIS ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 11 GLN j 40 HIS j 80 HIS ** k 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS p 9 GLN q 55 GLN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS u 65 GLN u 73 ASN z 19 HIS z 33 HIS E 42 HIS G 38 HIS ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN J 42 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN T 37 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.7973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.274 163139 Z= 0.444 Angle : 0.885 19.750 244082 Z= 0.447 Chirality : 0.045 0.434 31220 Planarity : 0.009 0.242 13080 Dihedral : 23.456 175.994 81722 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.13 % Favored : 88.65 % Rotamer: Outliers : 0.59 % Allowed : 9.54 % Favored : 89.87 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.44 (0.10), residues: 5919 helix: -1.72 (0.10), residues: 1870 sheet: -2.02 (0.15), residues: 977 loop : -2.78 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.005 TRP b 212 HIS 0.025 0.003 HIS m 13 PHE 0.050 0.004 PHE G 183 TYR 0.039 0.004 TYR L 43 ARG 0.059 0.002 ARG N 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1940 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1911 time to evaluate : 6.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 ASN cc_start: 0.7901 (t0) cc_final: 0.7234 (t0) REVERT: b 25 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7904 (mttm) REVERT: b 29 PHE cc_start: 0.8248 (t80) cc_final: 0.7991 (t80) REVERT: b 34 GLU cc_start: 0.6796 (tp30) cc_final: 0.6512 (tp30) REVERT: b 35 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7709 (tptp) REVERT: b 58 LYS cc_start: 0.8830 (tppp) cc_final: 0.8528 (ttpt) REVERT: b 63 ILE cc_start: 0.8989 (mt) cc_final: 0.8622 (mp) REVERT: b 78 GLU cc_start: 0.8153 (tt0) cc_final: 0.7705 (tt0) REVERT: b 82 TYR cc_start: 0.8359 (t80) cc_final: 0.8086 (t80) REVERT: b 86 ARG cc_start: 0.7508 (mmt-90) cc_final: 0.7201 (mmt-90) REVERT: b 92 LEU cc_start: 0.9311 (tp) cc_final: 0.8950 (tt) REVERT: b 97 ASP cc_start: 0.8427 (p0) cc_final: 0.8086 (t0) REVERT: b 114 GLN cc_start: 0.8741 (pp30) cc_final: 0.8499 (pp30) REVERT: b 115 ILE cc_start: 0.8888 (pt) cc_final: 0.8663 (pt) REVERT: b 138 SER cc_start: 0.8847 (t) cc_final: 0.8511 (t) REVERT: b 146 LYS cc_start: 0.7507 (mttm) cc_final: 0.6985 (mttp) REVERT: c 11 MET cc_start: 0.7875 (ttm) cc_final: 0.6422 (ttm) REVERT: c 30 GLU cc_start: 0.8366 (mp0) cc_final: 0.7951 (mp0) REVERT: c 80 TRP cc_start: 0.7573 (m-90) cc_final: 0.6446 (m-90) REVERT: c 82 PHE cc_start: 0.8211 (m-80) cc_final: 0.7983 (m-10) REVERT: c 84 LEU cc_start: 0.8529 (mm) cc_final: 0.8176 (mm) REVERT: c 96 ILE cc_start: 0.9149 (tp) cc_final: 0.8743 (mt) REVERT: c 128 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7219 (tmt170) REVERT: c 154 LYS cc_start: 0.8737 (pttp) cc_final: 0.8073 (pttt) REVERT: c 175 LEU cc_start: 0.8768 (mm) cc_final: 0.8558 (mt) REVERT: d 1 MET cc_start: 0.8837 (tpt) cc_final: 0.8396 (mmm) REVERT: d 2 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8070 (mm-30) REVERT: d 30 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8911 (tm-30) REVERT: d 43 THR cc_start: 0.7617 (p) cc_final: 0.7270 (p) REVERT: d 111 GLU cc_start: 0.8816 (pp20) cc_final: 0.8305 (tm-30) REVERT: d 117 ARG cc_start: 0.7262 (ptm160) cc_final: 0.7014 (ptm160) REVERT: d 122 GLU cc_start: 0.8998 (tp30) cc_final: 0.8617 (tp30) REVERT: d 145 ASP cc_start: 0.8407 (t0) cc_final: 0.7631 (t0) REVERT: d 152 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8121 (tm-30) REVERT: d 155 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8242 (pm20) REVERT: d 176 ASP cc_start: 0.6667 (p0) cc_final: 0.6344 (p0) REVERT: d 184 ASP cc_start: 0.7569 (m-30) cc_final: 0.7320 (m-30) REVERT: e 5 ASP cc_start: 0.8878 (m-30) cc_final: 0.8484 (t70) REVERT: e 35 LEU cc_start: 0.7834 (mp) cc_final: 0.7622 (mp) REVERT: e 62 GLN cc_start: 0.7334 (pt0) cc_final: 0.7133 (pt0) REVERT: e 79 ARG cc_start: 0.8847 (ptt-90) cc_final: 0.8578 (mmt180) REVERT: e 86 CYS cc_start: 0.5584 (m) cc_final: 0.5094 (m) REVERT: e 95 MET cc_start: 0.9390 (tmm) cc_final: 0.8750 (ttp) REVERT: e 119 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8426 (pttm) REVERT: e 129 MET cc_start: 0.7298 (tmm) cc_final: 0.7089 (tmm) REVERT: f 80 GLU cc_start: 0.8955 (tp30) cc_final: 0.8388 (tm-30) REVERT: f 82 PHE cc_start: 0.6457 (m-80) cc_final: 0.6165 (m-80) REVERT: g 22 LYS cc_start: 0.7865 (mmmm) cc_final: 0.7138 (mttt) REVERT: g 30 LEU cc_start: 0.7940 (mt) cc_final: 0.7454 (mt) REVERT: g 43 ASN cc_start: 0.8991 (m110) cc_final: 0.8786 (m110) REVERT: g 46 PHE cc_start: 0.9113 (m-80) cc_final: 0.8757 (m-80) REVERT: g 55 GLU cc_start: 0.6731 (mp0) cc_final: 0.6244 (tp30) REVERT: h 52 MET cc_start: -0.0022 (mtp) cc_final: -0.1638 (tmm) REVERT: h 86 MET cc_start: 0.1999 (tpt) cc_final: 0.1344 (tpt) REVERT: i 116 MET cc_start: 0.0274 (ttt) cc_final: -0.0136 (ttm) REVERT: j 7 LYS cc_start: 0.7527 (mttt) cc_final: 0.7154 (tttp) REVERT: j 14 ASP cc_start: 0.8626 (p0) cc_final: 0.8335 (p0) REVERT: j 28 LEU cc_start: 0.8187 (pp) cc_final: 0.7913 (pt) REVERT: j 31 GLU cc_start: 0.7991 (pp20) cc_final: 0.7482 (pp20) REVERT: j 32 LEU cc_start: 0.8117 (tt) cc_final: 0.7896 (mt) REVERT: j 36 LEU cc_start: 0.9268 (mt) cc_final: 0.9007 (mp) REVERT: j 93 ILE cc_start: 0.8718 (pt) cc_final: 0.8478 (pt) REVERT: j 99 ARG cc_start: 0.7913 (pmt-80) cc_final: 0.6835 (mtm110) REVERT: j 139 VAL cc_start: 0.7162 (t) cc_final: 0.6949 (t) REVERT: k 3 GLN cc_start: 0.7360 (pt0) cc_final: 0.6946 (pt0) REVERT: k 13 ASN cc_start: 0.7334 (p0) cc_final: 0.7065 (p0) REVERT: k 23 LYS cc_start: 0.7730 (ttpp) cc_final: 0.7247 (tttt) REVERT: k 51 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8952 (mmmm) REVERT: k 53 LYS cc_start: 0.8173 (mppt) cc_final: 0.7940 (mmtm) REVERT: k 56 ASP cc_start: 0.7993 (t0) cc_final: 0.7758 (t0) REVERT: k 67 LYS cc_start: 0.7391 (tptt) cc_final: 0.7039 (tptt) REVERT: k 71 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8360 (mmm160) REVERT: l 38 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8002 (mm-40) REVERT: l 54 GLN cc_start: 0.8492 (tt0) cc_final: 0.8264 (tp-100) REVERT: l 59 ARG cc_start: 0.8134 (ttt180) cc_final: 0.7406 (ttt90) REVERT: l 76 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7616 (mp0) REVERT: l 105 ILE cc_start: 0.8942 (mm) cc_final: 0.8304 (mm) REVERT: l 106 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8215 (tm-30) REVERT: l 136 GLU cc_start: 0.9450 (pt0) cc_final: 0.9175 (pt0) REVERT: m 5 LYS cc_start: 0.7358 (tmtt) cc_final: 0.7151 (tmtt) REVERT: m 41 LEU cc_start: 0.7631 (mt) cc_final: 0.7302 (mt) REVERT: m 58 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8667 (tptp) REVERT: m 84 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8728 (mmpt) REVERT: m 100 LYS cc_start: 0.8541 (tptm) cc_final: 0.8169 (tppt) REVERT: m 104 GLU cc_start: 0.7863 (tt0) cc_final: 0.7152 (tt0) REVERT: m 115 GLU cc_start: 0.8586 (pp20) cc_final: 0.8160 (mp0) REVERT: m 132 THR cc_start: 0.8575 (m) cc_final: 0.8348 (p) REVERT: n 74 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8112 (tm-30) REVERT: n 75 ILE cc_start: 0.8413 (mm) cc_final: 0.8112 (mt) REVERT: n 112 TYR cc_start: 0.7902 (m-80) cc_final: 0.7632 (m-10) REVERT: n 118 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8266 (ttp80) REVERT: o 3 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8096 (mmtt) REVERT: o 4 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8847 (mmtt) REVERT: o 12 THR cc_start: 0.8442 (p) cc_final: 0.8183 (p) REVERT: o 46 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7222 (mt-10) REVERT: o 63 LYS cc_start: 0.9090 (tmmt) cc_final: 0.8784 (tmtt) REVERT: o 64 TYR cc_start: 0.7331 (t80) cc_final: 0.6943 (t80) REVERT: o 92 PHE cc_start: 0.8840 (t80) cc_final: 0.8213 (t80) REVERT: o 95 SER cc_start: 0.8159 (m) cc_final: 0.7716 (m) REVERT: p 108 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8390 (ptt90) REVERT: q 36 GLN cc_start: 0.8518 (pt0) cc_final: 0.8222 (pt0) REVERT: q 61 ILE cc_start: 0.8756 (tp) cc_final: 0.8516 (tp) REVERT: q 78 PHE cc_start: 0.8582 (t80) cc_final: 0.8318 (t80) REVERT: q 100 PHE cc_start: 0.6735 (m-80) cc_final: 0.6332 (m-10) REVERT: q 111 LYS cc_start: 0.9653 (tptm) cc_final: 0.9383 (ttpt) REVERT: r 1 MET cc_start: 0.6589 (tpp) cc_final: 0.6089 (tpp) REVERT: r 6 GLN cc_start: 0.8475 (tt0) cc_final: 0.7570 (tm-30) REVERT: r 18 GLN cc_start: 0.8109 (tt0) cc_final: 0.7839 (mp10) REVERT: r 37 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7267 (mp0) REVERT: r 41 ILE cc_start: 0.8704 (mp) cc_final: 0.8384 (mt) REVERT: r 49 ILE cc_start: 0.7472 (pt) cc_final: 0.7264 (pt) REVERT: r 95 ASP cc_start: 0.7772 (t70) cc_final: 0.7552 (t70) REVERT: s 6 LYS cc_start: 0.8529 (tttm) cc_final: 0.8205 (tttm) REVERT: s 17 VAL cc_start: 0.8744 (t) cc_final: 0.8517 (t) REVERT: s 24 ILE cc_start: 0.8763 (pt) cc_final: 0.8369 (mt) REVERT: s 40 ASN cc_start: 0.8443 (p0) cc_final: 0.8196 (p0) REVERT: s 83 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7192 (mmmm) REVERT: s 86 MET cc_start: 0.8144 (tpt) cc_final: 0.7522 (tpp) REVERT: t 59 ASN cc_start: 0.8943 (m-40) cc_final: 0.8417 (t0) REVERT: u 21 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7541 (mtt-85) REVERT: v 29 ILE cc_start: 0.7570 (pt) cc_final: 0.7268 (pt) REVERT: v 41 GLU cc_start: 0.6740 (tp30) cc_final: 0.6191 (pt0) REVERT: v 46 LYS cc_start: 0.8766 (tppt) cc_final: 0.8531 (tppt) REVERT: v 56 PHE cc_start: 0.8561 (t80) cc_final: 0.7976 (t80) REVERT: v 80 HIS cc_start: 0.8248 (t-170) cc_final: 0.7874 (t-170) REVERT: v 87 GLN cc_start: 0.8721 (mt0) cc_final: 0.8137 (mt0) REVERT: w 20 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8265 (mmtm) REVERT: w 36 GLN cc_start: 0.7758 (pp30) cc_final: 0.6942 (pp30) REVERT: w 46 ASN cc_start: 0.8622 (m-40) cc_final: 0.8150 (t0) REVERT: w 68 LYS cc_start: 0.6440 (mmmt) cc_final: 0.6154 (mmmt) REVERT: w 73 ARG cc_start: 0.7854 (mpp80) cc_final: 0.6122 (mpp80) REVERT: w 77 SER cc_start: 0.8153 (t) cc_final: 0.7817 (m) REVERT: x 13 THR cc_start: 0.8951 (t) cc_final: 0.8253 (m) REVERT: x 39 VAL cc_start: 0.8679 (t) cc_final: 0.7777 (p) REVERT: x 53 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8568 (tttt) REVERT: x 55 MET cc_start: 0.7454 (mtt) cc_final: 0.7084 (mtt) REVERT: y 12 GLU cc_start: 0.8837 (tp30) cc_final: 0.8579 (tp30) REVERT: y 31 GLN cc_start: 0.9349 (tt0) cc_final: 0.8987 (tp-100) REVERT: y 37 LEU cc_start: 0.6584 (tt) cc_final: 0.6148 (tt) REVERT: y 44 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8450 (ttpp) REVERT: y 48 ARG cc_start: 0.8606 (mmt-90) cc_final: 0.8357 (mmt-90) REVERT: z 31 ILE cc_start: 0.7853 (mm) cc_final: 0.7382 (mm) REVERT: z 44 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7702 (ttm110) REVERT: z 53 MET cc_start: 0.6715 (ptt) cc_final: 0.5782 (ptt) REVERT: z 55 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8771 (tmtt) REVERT: z 56 VAL cc_start: 0.8566 (t) cc_final: 0.8246 (t) REVERT: B 30 ASP cc_start: 0.7455 (t0) cc_final: 0.6892 (t0) REVERT: C 18 HIS cc_start: 0.7012 (t-90) cc_final: 0.6790 (t70) REVERT: D 1 MET cc_start: 0.5756 (mmm) cc_final: 0.4655 (mpp) REVERT: D 6 GLN cc_start: 0.8895 (mp10) cc_final: 0.8487 (mp10) REVERT: D 22 MET cc_start: 0.8827 (mmt) cc_final: 0.8418 (mmm) REVERT: D 25 LYS cc_start: 0.8422 (ptmm) cc_final: 0.7787 (pptt) REVERT: D 33 ARG cc_start: 0.7742 (ptt180) cc_final: 0.7385 (ptt180) REVERT: D 41 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8212 (mtp180) REVERT: E 49 VAL cc_start: 0.8004 (t) cc_final: 0.7755 (t) REVERT: E 58 ILE cc_start: 0.8326 (mt) cc_final: 0.7932 (pt) REVERT: F 8 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7452 (ptpt) REVERT: G 5 MET cc_start: 0.8573 (ptt) cc_final: 0.7772 (tpp) REVERT: G 8 MET cc_start: 0.8560 (mtp) cc_final: 0.8085 (mtp) REVERT: G 17 HIS cc_start: 0.7036 (m-70) cc_final: 0.5565 (m-70) REVERT: G 34 ARG cc_start: 0.7472 (tpp80) cc_final: 0.6886 (tpp80) REVERT: G 46 VAL cc_start: 0.8627 (t) cc_final: 0.8031 (t) REVERT: G 50 ASN cc_start: 0.8425 (m-40) cc_final: 0.7686 (p0) REVERT: G 80 LYS cc_start: 0.8963 (tmmt) cc_final: 0.8762 (pttm) REVERT: G 87 ASP cc_start: 0.9018 (p0) cc_final: 0.8705 (p0) REVERT: G 99 MET cc_start: 0.8798 (mmp) cc_final: 0.7803 (mpp) REVERT: G 102 ASN cc_start: 0.8548 (t0) cc_final: 0.8338 (t0) REVERT: G 107 ARG cc_start: 0.9042 (ttm110) cc_final: 0.8697 (ptp-110) REVERT: G 161 PHE cc_start: 0.8370 (t80) cc_final: 0.8094 (t80) REVERT: G 176 ASN cc_start: 0.9185 (m-40) cc_final: 0.8935 (m-40) REVERT: H 10 ARG cc_start: 0.6921 (mtt90) cc_final: 0.6209 (ttm110) REVERT: H 26 LYS cc_start: 0.6257 (ttmt) cc_final: 0.5939 (ttmt) REVERT: H 87 ARG cc_start: 0.7300 (tmm-80) cc_final: 0.6978 (ttm110) REVERT: H 113 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8077 (mppt) REVERT: H 138 GLN cc_start: 0.9138 (mt0) cc_final: 0.8737 (mt0) REVERT: H 163 ARG cc_start: 0.8210 (ptt180) cc_final: 0.7929 (ptt90) REVERT: I 12 ARG cc_start: 0.5057 (mtm180) cc_final: 0.3418 (mtm180) REVERT: I 50 TYR cc_start: 0.7526 (t80) cc_final: 0.7292 (t80) REVERT: I 77 GLU cc_start: 0.8715 (tp30) cc_final: 0.7899 (tp30) REVERT: I 81 LEU cc_start: 0.7987 (tp) cc_final: 0.7698 (tp) REVERT: I 92 LEU cc_start: 0.7447 (mt) cc_final: 0.7221 (mt) REVERT: I 118 SER cc_start: 0.7187 (t) cc_final: 0.6669 (p) REVERT: I 177 MET cc_start: 0.2300 (mpp) cc_final: 0.1703 (mtp) REVERT: I 194 ILE cc_start: 0.8389 (mp) cc_final: 0.8156 (mp) REVERT: I 196 GLU cc_start: 0.7836 (pp20) cc_final: 0.6857 (pt0) REVERT: J 63 MET cc_start: 0.7212 (ppp) cc_final: 0.6952 (ppp) REVERT: J 70 MET cc_start: 0.6957 (mtp) cc_final: 0.6459 (mtt) REVERT: J 96 GLN cc_start: 0.7976 (tt0) cc_final: 0.7681 (mt0) REVERT: J 115 GLU cc_start: 0.8304 (pt0) cc_final: 0.7975 (tp30) REVERT: J 155 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8275 (pttm) REVERT: K 4 TYR cc_start: 0.7039 (m-80) cc_final: 0.6502 (m-80) REVERT: K 6 ILE cc_start: 0.9042 (mt) cc_final: 0.8775 (mt) REVERT: K 45 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7368 (mtm-85) REVERT: K 88 MET cc_start: 0.8348 (mtm) cc_final: 0.7988 (mtt) REVERT: L 31 VAL cc_start: 0.7055 (m) cc_final: 0.6750 (m) REVERT: L 66 GLU cc_start: 0.8624 (pp20) cc_final: 0.8263 (pp20) REVERT: L 95 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7565 (ttm110) REVERT: L 115 MET cc_start: 0.8933 (mtm) cc_final: 0.8684 (mtm) REVERT: L 122 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8045 (tp30) REVERT: L 135 LYS cc_start: 0.9124 (ptpt) cc_final: 0.8902 (pptt) REVERT: L 148 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8367 (mtpp) REVERT: M 9 MET cc_start: 0.8474 (tmm) cc_final: 0.8010 (tmm) REVERT: M 17 GLN cc_start: 0.8834 (mt0) cc_final: 0.7689 (tt0) REVERT: M 39 LEU cc_start: 0.8899 (tt) cc_final: 0.8511 (pp) REVERT: M 63 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8336 (ptpt) REVERT: M 71 VAL cc_start: 0.8864 (t) cc_final: 0.8524 (m) REVERT: M 88 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7621 (ptpp) REVERT: M 110 MET cc_start: 0.8407 (ptp) cc_final: 0.8064 (ptt) REVERT: M 112 ASP cc_start: 0.8845 (p0) cc_final: 0.8510 (p0) REVERT: M 123 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7497 (tm-30) REVERT: M 125 ILE cc_start: 0.8808 (mp) cc_final: 0.8350 (mp) REVERT: N 4 GLN cc_start: 0.5492 (tt0) cc_final: 0.4274 (mm-40) REVERT: N 19 PHE cc_start: 0.6013 (m-10) cc_final: 0.5739 (m-10) REVERT: O 5 ARG cc_start: 0.6144 (tpt90) cc_final: 0.5795 (tpp-160) REVERT: P 60 PHE cc_start: 0.8836 (t80) cc_final: 0.8567 (t80) REVERT: P 69 CYS cc_start: 0.8837 (t) cc_final: 0.8560 (t) REVERT: P 97 ARG cc_start: 0.8171 (ptp-110) cc_final: 0.7798 (ptp90) REVERT: Q 34 THR cc_start: 0.8115 (p) cc_final: 0.7654 (p) REVERT: Q 37 TYR cc_start: 0.7897 (p90) cc_final: 0.7670 (p90) REVERT: Q 52 CYS cc_start: 0.7817 (p) cc_final: 0.6893 (t) REVERT: Q 60 PHE cc_start: 0.9074 (m-80) cc_final: 0.8857 (m-80) REVERT: Q 75 GLU cc_start: 0.8244 (mp0) cc_final: 0.7370 (mp0) REVERT: Q 93 ARG cc_start: 0.8817 (ptp-170) cc_final: 0.8318 (mtm-85) REVERT: R 27 THR cc_start: 0.7975 (p) cc_final: 0.7537 (p) REVERT: R 51 GLN cc_start: 0.9166 (mt0) cc_final: 0.8863 (mp10) REVERT: R 94 LEU cc_start: 0.8499 (mp) cc_final: 0.7935 (tt) REVERT: S 75 LYS cc_start: 0.7832 (tptm) cc_final: 0.7381 (tppt) REVERT: S 89 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7200 (ptt180) REVERT: T 47 LYS cc_start: 0.8463 (mttt) cc_final: 0.7172 (tppt) REVERT: T 49 HIS cc_start: 0.9028 (m-70) cc_final: 0.8403 (m-70) REVERT: T 50 HIS cc_start: 0.8336 (m90) cc_final: 0.7712 (m90) REVERT: U 8 ARG cc_start: 0.6963 (tpt-90) cc_final: 0.6570 (tpt-90) REVERT: U 21 VAL cc_start: 0.8714 (p) cc_final: 0.8424 (m) REVERT: U 28 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7858 (ttt180) REVERT: U 53 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6008 (p0) REVERT: V 17 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6562 (tm-30) REVERT: V 18 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7293 (ttpp) REVERT: V 33 TYR cc_start: 0.8467 (m-80) cc_final: 0.7497 (m-80) REVERT: V 36 PHE cc_start: 0.7596 (m-80) cc_final: 0.7336 (m-80) REVERT: V 77 VAL cc_start: 0.9123 (t) cc_final: 0.8855 (t) REVERT: W 42 ARG cc_start: 0.8734 (tmm160) cc_final: 0.8484 (tmm-80) REVERT: W 50 TYR cc_start: 0.6988 (m-80) cc_final: 0.6618 (m-80) REVERT: W 53 GLN cc_start: 0.8114 (pt0) cc_final: 0.7518 (pm20) REVERT: W 69 TYR cc_start: 0.6759 (m-80) cc_final: 0.6354 (m-10) REVERT: X 11 ASP cc_start: 0.7488 (t0) cc_final: 0.7120 (t0) REVERT: X 43 MET cc_start: 0.8526 (mpp) cc_final: 0.7777 (mpp) REVERT: X 46 LEU cc_start: 0.7814 (mm) cc_final: 0.7540 (tp) REVERT: X 72 GLU cc_start: 0.8114 (tt0) cc_final: 0.7656 (tt0) REVERT: X 73 PHE cc_start: 0.7803 (m-80) cc_final: 0.7002 (m-80) REVERT: Y 18 LYS cc_start: 0.8949 (mmpt) cc_final: 0.8690 (mmmt) REVERT: Z 19 LYS cc_start: 0.6038 (pptt) cc_final: 0.5729 (pptt) REVERT: Z 54 ARG cc_start: 0.8481 (ttt180) cc_final: 0.8202 (ttt180) outliers start: 29 outliers final: 6 residues processed: 1923 average time/residue: 1.4677 time to fit residues: 4764.2647 Evaluate side-chains 1562 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1554 time to evaluate : 6.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 50.0000 chunk 722 optimal weight: 10.0000 chunk 499 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 458 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 965 optimal weight: 10.0000 chunk 1021 optimal weight: 10.0000 chunk 504 optimal weight: 6.9990 chunk 914 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 49 GLN ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN d 92 HIS d 97 ASN ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN f 37 ASN f 63 GLN f 142 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 ASN k 82 ASN k 89 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 9 GLN q 55 GLN q 58 GLN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS s 9 HIS ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN B 4 GLN B 18 HIS C 18 HIS G 41 ASN G 88 GLN G 176 ASN I 88 ASN I 135 GLN I 197 HIS ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 GLN O 64 GLN ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN R 13 HIS S 61 ASN T 36 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 163139 Z= 0.303 Angle : 0.699 13.484 244082 Z= 0.359 Chirality : 0.039 0.294 31220 Planarity : 0.006 0.122 13080 Dihedral : 23.368 176.632 81722 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.84 % Favored : 91.03 % Rotamer: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.94 (0.10), residues: 5919 helix: -1.13 (0.11), residues: 1876 sheet: -1.81 (0.15), residues: 1006 loop : -2.57 (0.10), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP b 212 HIS 0.013 0.002 HIS P 21 PHE 0.028 0.002 PHE Z 36 TYR 0.039 0.003 TYR R 22 ARG 0.014 0.001 ARG S 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1891 time to evaluate : 6.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 12 ARG cc_start: 0.7486 (tpm170) cc_final: 0.6923 (tpm170) REVERT: b 20 ASN cc_start: 0.7904 (t0) cc_final: 0.7391 (t0) REVERT: b 25 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8007 (mttm) REVERT: b 34 GLU cc_start: 0.7054 (tp30) cc_final: 0.6782 (tp30) REVERT: b 78 GLU cc_start: 0.8315 (tt0) cc_final: 0.7929 (tt0) REVERT: b 82 TYR cc_start: 0.8371 (t80) cc_final: 0.8161 (t80) REVERT: b 87 SER cc_start: 0.8931 (p) cc_final: 0.8434 (p) REVERT: b 97 ASP cc_start: 0.8464 (p0) cc_final: 0.7877 (t0) REVERT: b 132 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8288 (mmm-85) REVERT: b 134 ILE cc_start: 0.8715 (tt) cc_final: 0.8471 (tt) REVERT: b 184 GLU cc_start: 0.6823 (mp0) cc_final: 0.6245 (pm20) REVERT: c 4 LEU cc_start: 0.7832 (mp) cc_final: 0.7434 (mp) REVERT: c 11 MET cc_start: 0.7806 (ttm) cc_final: 0.6468 (ttm) REVERT: c 30 GLU cc_start: 0.8620 (mp0) cc_final: 0.8143 (mp0) REVERT: c 46 ARG cc_start: 0.8107 (ptm160) cc_final: 0.7178 (ptm-80) REVERT: c 80 TRP cc_start: 0.7772 (m-90) cc_final: 0.6708 (m-90) REVERT: c 96 ILE cc_start: 0.9270 (tp) cc_final: 0.8925 (mt) REVERT: c 126 ASN cc_start: 0.8656 (m110) cc_final: 0.8377 (m110) REVERT: c 128 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.6736 (tmt170) REVERT: c 141 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7895 (mtp85) REVERT: d 1 MET cc_start: 0.8813 (tpt) cc_final: 0.8311 (mmm) REVERT: d 2 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8163 (mm-30) REVERT: d 10 SER cc_start: 0.8751 (m) cc_final: 0.8519 (p) REVERT: d 30 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8573 (tm-30) REVERT: d 43 THR cc_start: 0.7918 (p) cc_final: 0.7566 (p) REVERT: d 94 GLN cc_start: 0.8252 (mt0) cc_final: 0.8030 (mt0) REVERT: d 101 TYR cc_start: 0.8386 (t80) cc_final: 0.7931 (t80) REVERT: d 111 GLU cc_start: 0.8558 (pp20) cc_final: 0.8303 (tm-30) REVERT: d 145 ASP cc_start: 0.8066 (t0) cc_final: 0.7687 (t0) REVERT: d 155 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8361 (pm20) REVERT: d 168 ASP cc_start: 0.8294 (t0) cc_final: 0.7900 (t0) REVERT: d 171 ASP cc_start: 0.9073 (t0) cc_final: 0.8858 (t0) REVERT: d 175 ILE cc_start: 0.7339 (mm) cc_final: 0.7054 (mm) REVERT: d 176 ASP cc_start: 0.7106 (p0) cc_final: 0.6561 (p0) REVERT: e 62 GLN cc_start: 0.7232 (pt0) cc_final: 0.6994 (pt0) REVERT: e 119 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8580 (pttm) REVERT: e 124 ARG cc_start: 0.7974 (tpp-160) cc_final: 0.7549 (mmm-85) REVERT: e 129 MET cc_start: 0.7572 (tmm) cc_final: 0.7275 (tmm) REVERT: e 156 THR cc_start: 0.7777 (m) cc_final: 0.7435 (p) REVERT: e 174 PHE cc_start: 0.7593 (m-80) cc_final: 0.7268 (m-10) REVERT: f 41 GLU cc_start: 0.7777 (pp20) cc_final: 0.7281 (pp20) REVERT: f 68 ARG cc_start: 0.8258 (tmt170) cc_final: 0.7954 (tmm160) REVERT: f 80 GLU cc_start: 0.8980 (tp30) cc_final: 0.8438 (tm-30) REVERT: f 82 PHE cc_start: 0.6919 (m-80) cc_final: 0.6441 (m-80) REVERT: f 152 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.6978 (tpp-160) REVERT: g 22 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7829 (mmmm) REVERT: g 45 GLU cc_start: 0.8970 (pp20) cc_final: 0.8654 (pp20) REVERT: g 46 PHE cc_start: 0.9046 (m-10) cc_final: 0.8799 (m-80) REVERT: g 55 GLU cc_start: 0.6677 (mp0) cc_final: 0.5893 (tp30) REVERT: h 52 MET cc_start: 0.0150 (mtp) cc_final: -0.1587 (tmm) REVERT: h 118 ILE cc_start: 0.3678 (OUTLIER) cc_final: 0.3467 (pt) REVERT: i 116 MET cc_start: -0.0191 (ttt) cc_final: -0.0590 (ttm) REVERT: j 7 LYS cc_start: 0.7765 (mttt) cc_final: 0.7450 (tttp) REVERT: j 14 ASP cc_start: 0.8770 (p0) cc_final: 0.8206 (p0) REVERT: j 21 THR cc_start: 0.9093 (p) cc_final: 0.8566 (p) REVERT: j 75 TYR cc_start: 0.6835 (m-80) cc_final: 0.6603 (m-80) REVERT: j 99 ARG cc_start: 0.7621 (pmt-80) cc_final: 0.6966 (mtp-110) REVERT: j 136 GLN cc_start: 0.9048 (mm110) cc_final: 0.8495 (mm110) REVERT: k 1 MET cc_start: 0.6447 (ttm) cc_final: 0.6191 (ttm) REVERT: k 4 GLU cc_start: 0.7285 (mp0) cc_final: 0.6994 (mp0) REVERT: k 13 ASN cc_start: 0.6704 (p0) cc_final: 0.6470 (p0) REVERT: k 30 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7267 (ttt180) REVERT: k 51 LYS cc_start: 0.9368 (mmmt) cc_final: 0.8856 (mmmt) REVERT: k 53 LYS cc_start: 0.8305 (mppt) cc_final: 0.8034 (mmtm) REVERT: k 71 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8199 (mmm160) REVERT: k 108 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7300 (ttp80) REVERT: k 121 GLU cc_start: 0.8397 (pm20) cc_final: 0.7649 (pm20) REVERT: l 59 ARG cc_start: 0.8243 (ttt180) cc_final: 0.7587 (ttt90) REVERT: l 105 ILE cc_start: 0.8890 (mm) cc_final: 0.8540 (tt) REVERT: l 106 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8175 (tm-30) REVERT: m 41 LEU cc_start: 0.8612 (mt) cc_final: 0.8238 (mt) REVERT: m 104 GLU cc_start: 0.7273 (tt0) cc_final: 0.6998 (tt0) REVERT: m 110 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6941 (tm-30) REVERT: n 9 GLN cc_start: 0.7659 (pp30) cc_final: 0.7096 (pp30) REVERT: n 36 THR cc_start: 0.8414 (p) cc_final: 0.8181 (p) REVERT: n 75 ILE cc_start: 0.8524 (mm) cc_final: 0.8251 (mt) REVERT: n 106 ASP cc_start: 0.8077 (p0) cc_final: 0.7865 (p0) REVERT: n 118 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7959 (ttp80) REVERT: o 4 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8906 (mmtt) REVERT: o 9 ARG cc_start: 0.8924 (pmt-80) cc_final: 0.8543 (pmt-80) REVERT: o 63 LYS cc_start: 0.9030 (tmmt) cc_final: 0.8571 (tmtt) REVERT: o 64 TYR cc_start: 0.7508 (t80) cc_final: 0.6812 (t80) REVERT: o 81 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.7783 (tmm-80) REVERT: o 92 PHE cc_start: 0.8826 (t80) cc_final: 0.8141 (t80) REVERT: o 95 SER cc_start: 0.7523 (m) cc_final: 0.7220 (m) REVERT: p 26 GLU cc_start: 0.6025 (tp30) cc_final: 0.5541 (tp30) REVERT: p 28 LYS cc_start: 0.7694 (mmtp) cc_final: 0.7425 (mmtm) REVERT: q 36 GLN cc_start: 0.8806 (pt0) cc_final: 0.8603 (pt0) REVERT: q 60 TRP cc_start: 0.8350 (m-10) cc_final: 0.7575 (m-10) REVERT: q 78 PHE cc_start: 0.8593 (t80) cc_final: 0.8389 (t80) REVERT: q 100 PHE cc_start: 0.6756 (m-80) cc_final: 0.6500 (m-10) REVERT: q 111 LYS cc_start: 0.9670 (tptm) cc_final: 0.9379 (tttm) REVERT: r 6 GLN cc_start: 0.8429 (tt0) cc_final: 0.7900 (tm-30) REVERT: r 10 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8338 (ptpp) REVERT: r 37 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7335 (mp0) REVERT: r 40 MET cc_start: 0.8231 (tpp) cc_final: 0.7834 (tpp) REVERT: s 6 LYS cc_start: 0.8665 (tttm) cc_final: 0.7468 (tttm) REVERT: s 61 ASN cc_start: 0.7444 (m-40) cc_final: 0.7197 (m110) REVERT: s 86 MET cc_start: 0.8307 (tpt) cc_final: 0.7655 (tpp) REVERT: t 73 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7787 (mtt-85) REVERT: v 41 GLU cc_start: 0.7251 (tp30) cc_final: 0.6154 (pt0) REVERT: v 50 MET cc_start: 0.8345 (mtm) cc_final: 0.7935 (mtm) REVERT: v 55 GLU cc_start: 0.8336 (pp20) cc_final: 0.7921 (tm-30) REVERT: v 56 PHE cc_start: 0.8499 (t80) cc_final: 0.7977 (t80) REVERT: v 73 LYS cc_start: 0.7685 (tptp) cc_final: 0.7384 (ttmm) REVERT: v 87 GLN cc_start: 0.8756 (mt0) cc_final: 0.8195 (mt0) REVERT: w 36 GLN cc_start: 0.7677 (pp30) cc_final: 0.6864 (pp30) REVERT: w 58 LYS cc_start: 0.8583 (mtpt) cc_final: 0.7996 (mmtt) REVERT: w 68 LYS cc_start: 0.6010 (mmmt) cc_final: 0.5700 (mmmt) REVERT: w 73 ARG cc_start: 0.7874 (mpp80) cc_final: 0.6429 (mpp80) REVERT: x 2 ARG cc_start: 0.7329 (tpp80) cc_final: 0.7110 (mtt90) REVERT: x 39 VAL cc_start: 0.8523 (t) cc_final: 0.8207 (p) REVERT: x 44 ARG cc_start: 0.7484 (ptt90) cc_final: 0.7098 (ptt90) REVERT: y 12 GLU cc_start: 0.8864 (tp30) cc_final: 0.8615 (tp30) REVERT: y 31 GLN cc_start: 0.9251 (tt0) cc_final: 0.8780 (tp-100) REVERT: z 8 GLN cc_start: 0.8917 (tt0) cc_final: 0.8686 (tt0) REVERT: z 15 ARG cc_start: 0.7975 (mmt-90) cc_final: 0.7590 (mmt-90) REVERT: z 30 ARG cc_start: 0.8655 (mtm180) cc_final: 0.7332 (mtm-85) REVERT: z 31 ILE cc_start: 0.7842 (mm) cc_final: 0.7414 (mm) REVERT: z 55 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8462 (tptp) REVERT: B 30 ASP cc_start: 0.7552 (t0) cc_final: 0.6686 (t0) REVERT: D 6 GLN cc_start: 0.8740 (mp10) cc_final: 0.8134 (mp10) REVERT: D 12 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8335 (ttm-80) REVERT: D 22 MET cc_start: 0.8802 (mmt) cc_final: 0.8280 (mmm) REVERT: D 25 LYS cc_start: 0.8305 (ptmm) cc_final: 0.7886 (pptt) REVERT: D 39 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7624 (mtp180) REVERT: E 14 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8379 (mptt) REVERT: E 48 MET cc_start: 0.9010 (mmp) cc_final: 0.8492 (mmm) REVERT: E 58 ILE cc_start: 0.8284 (mt) cc_final: 0.7891 (pt) REVERT: F 8 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7516 (ptpt) REVERT: F 26 ILE cc_start: 0.8871 (mm) cc_final: 0.8656 (mm) REVERT: G 5 MET cc_start: 0.8566 (ptt) cc_final: 0.7813 (tpp) REVERT: G 17 HIS cc_start: 0.7440 (m-70) cc_final: 0.6005 (m-70) REVERT: G 34 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7205 (tpp80) REVERT: G 41 ASN cc_start: 0.7838 (t0) cc_final: 0.7219 (t0) REVERT: G 46 VAL cc_start: 0.8595 (t) cc_final: 0.8334 (t) REVERT: G 56 LEU cc_start: 0.7797 (tt) cc_final: 0.7411 (tt) REVERT: G 68 PHE cc_start: 0.9120 (m-10) cc_final: 0.8844 (m-10) REVERT: G 92 ASN cc_start: 0.7887 (p0) cc_final: 0.7585 (p0) REVERT: G 99 MET cc_start: 0.9090 (mmp) cc_final: 0.8159 (mpp) REVERT: G 102 ASN cc_start: 0.8928 (t0) cc_final: 0.8631 (t0) REVERT: G 139 GLU cc_start: 0.8380 (pp20) cc_final: 0.8134 (pp20) REVERT: G 161 PHE cc_start: 0.8154 (t80) cc_final: 0.7899 (t80) REVERT: H 10 ARG cc_start: 0.6982 (mtt90) cc_final: 0.6563 (ttm110) REVERT: H 113 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8200 (mmtm) REVERT: H 138 GLN cc_start: 0.9140 (mt0) cc_final: 0.8844 (mt0) REVERT: H 163 ARG cc_start: 0.8351 (ptt180) cc_final: 0.8085 (ptt90) REVERT: H 187 GLU cc_start: 0.7832 (tp30) cc_final: 0.7388 (tp30) REVERT: I 12 ARG cc_start: 0.4825 (mtm180) cc_final: 0.3109 (mtm180) REVERT: I 177 MET cc_start: 0.3164 (mpp) cc_final: 0.1969 (mtp) REVERT: I 194 ILE cc_start: 0.8361 (mp) cc_final: 0.8053 (mp) REVERT: I 196 GLU cc_start: 0.8079 (pp20) cc_final: 0.7161 (pp20) REVERT: J 11 GLN cc_start: 0.8328 (mp10) cc_final: 0.8086 (mp10) REVERT: J 40 ASP cc_start: 0.7894 (p0) cc_final: 0.7274 (p0) REVERT: J 72 ASN cc_start: 0.8500 (p0) cc_final: 0.8274 (p0) REVERT: J 96 GLN cc_start: 0.8184 (tt0) cc_final: 0.7637 (mt0) REVERT: J 115 GLU cc_start: 0.8299 (pt0) cc_final: 0.8053 (tp30) REVERT: J 155 LYS cc_start: 0.8688 (ptmt) cc_final: 0.8342 (ptpp) REVERT: K 2 ARG cc_start: 0.7026 (mtp180) cc_final: 0.6711 (mtp85) REVERT: K 4 TYR cc_start: 0.6749 (m-80) cc_final: 0.5782 (m-80) REVERT: K 25 TYR cc_start: 0.7858 (m-80) cc_final: 0.7339 (m-80) REVERT: K 47 LEU cc_start: 0.8766 (tp) cc_final: 0.8409 (tp) REVERT: K 61 LEU cc_start: 0.8351 (tt) cc_final: 0.7239 (mp) REVERT: L 78 ARG cc_start: 0.5583 (ptp90) cc_final: 0.5175 (ptp90) REVERT: L 91 ARG cc_start: 0.8861 (mmt180) cc_final: 0.8322 (ttm-80) REVERT: L 136 LYS cc_start: 0.8390 (tttt) cc_final: 0.8090 (mttt) REVERT: L 148 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8347 (mtpp) REVERT: M 17 GLN cc_start: 0.8763 (mt0) cc_final: 0.8284 (mt0) REVERT: M 39 LEU cc_start: 0.8822 (tt) cc_final: 0.8292 (pp) REVERT: M 63 LYS cc_start: 0.8238 (ptpt) cc_final: 0.7947 (ptpp) REVERT: M 107 LYS cc_start: 0.8276 (mmpt) cc_final: 0.8039 (mmtt) REVERT: M 112 ASP cc_start: 0.8937 (p0) cc_final: 0.8516 (p0) REVERT: M 120 LEU cc_start: 0.6532 (mt) cc_final: 0.6226 (mt) REVERT: M 123 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7356 (tm-30) REVERT: M 125 ILE cc_start: 0.8758 (mp) cc_final: 0.8458 (mp) REVERT: N 4 GLN cc_start: 0.6129 (tt0) cc_final: 0.4733 (mm-40) REVERT: N 19 PHE cc_start: 0.6338 (m-10) cc_final: 0.5886 (m-10) REVERT: N 45 MET cc_start: 0.8584 (ptp) cc_final: 0.8260 (pmm) REVERT: N 86 LEU cc_start: 0.7620 (tp) cc_final: 0.7089 (mt) REVERT: O 88 MET cc_start: 0.7948 (ppp) cc_final: 0.7732 (ppp) REVERT: P 34 THR cc_start: 0.7013 (p) cc_final: 0.6569 (p) REVERT: P 41 LEU cc_start: 0.8484 (pt) cc_final: 0.8244 (pt) REVERT: P 45 THR cc_start: 0.8224 (p) cc_final: 0.7957 (p) REVERT: P 49 SER cc_start: 0.6303 (p) cc_final: 0.4926 (p) REVERT: P 63 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7852 (mt0) REVERT: P 68 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8300 (mtp-110) REVERT: P 69 CYS cc_start: 0.8807 (t) cc_final: 0.8567 (t) REVERT: P 79 LYS cc_start: 0.7576 (mmmt) cc_final: 0.7325 (mmmt) REVERT: Q 34 THR cc_start: 0.8630 (p) cc_final: 0.8290 (p) REVERT: Q 52 CYS cc_start: 0.7852 (p) cc_final: 0.6169 (t) REVERT: Q 60 PHE cc_start: 0.9157 (m-80) cc_final: 0.8894 (m-80) REVERT: Q 61 GLU cc_start: 0.7591 (tp30) cc_final: 0.6970 (tp30) REVERT: Q 73 LEU cc_start: 0.7692 (mp) cc_final: 0.7234 (mp) REVERT: Q 75 GLU cc_start: 0.8373 (mp0) cc_final: 0.7710 (mp0) REVERT: R 30 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8347 (ptpt) REVERT: R 76 ILE cc_start: 0.8327 (mt) cc_final: 0.8036 (mt) REVERT: R 80 MET cc_start: 0.6731 (mtp) cc_final: 0.6444 (mtp) REVERT: R 85 TYR cc_start: 0.7969 (t80) cc_final: 0.7718 (t80) REVERT: R 88 LEU cc_start: 0.9143 (pp) cc_final: 0.8914 (tp) REVERT: R 94 LEU cc_start: 0.8562 (mp) cc_final: 0.7929 (tt) REVERT: S 46 LYS cc_start: 0.7122 (mppt) cc_final: 0.6914 (mmtp) REVERT: S 53 ASP cc_start: 0.6871 (m-30) cc_final: 0.6438 (p0) REVERT: S 75 LYS cc_start: 0.7746 (tptm) cc_final: 0.7395 (tppt) REVERT: S 82 LYS cc_start: 0.7348 (mmmt) cc_final: 0.6926 (mmmt) REVERT: T 47 LYS cc_start: 0.8601 (mttt) cc_final: 0.8331 (mttt) REVERT: T 48 ASP cc_start: 0.6720 (t0) cc_final: 0.6286 (t0) REVERT: T 49 HIS cc_start: 0.8908 (m-70) cc_final: 0.8592 (m-70) REVERT: V 7 LEU cc_start: 0.6980 (pt) cc_final: 0.6766 (pt) REVERT: V 27 PHE cc_start: 0.8623 (t80) cc_final: 0.8047 (t80) REVERT: V 33 TYR cc_start: 0.8684 (m-80) cc_final: 0.7925 (m-80) REVERT: W 29 LYS cc_start: 0.9442 (pttm) cc_final: 0.9195 (pttp) REVERT: W 42 ARG cc_start: 0.8676 (tmm160) cc_final: 0.8392 (tmm-80) REVERT: W 50 TYR cc_start: 0.7134 (m-80) cc_final: 0.6735 (m-80) REVERT: W 53 GLN cc_start: 0.8256 (pt0) cc_final: 0.7636 (pm20) REVERT: W 69 TYR cc_start: 0.7163 (m-80) cc_final: 0.6906 (m-10) REVERT: X 11 ASP cc_start: 0.7220 (t0) cc_final: 0.6811 (t0) REVERT: X 43 MET cc_start: 0.8375 (mpp) cc_final: 0.7885 (mpp) REVERT: X 65 MET cc_start: 0.8001 (ppp) cc_final: 0.7752 (ppp) REVERT: X 72 GLU cc_start: 0.8045 (tt0) cc_final: 0.7557 (tt0) REVERT: X 73 PHE cc_start: 0.7787 (m-80) cc_final: 0.6821 (m-80) REVERT: Y 32 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8932 (mmtt) REVERT: Y 79 THR cc_start: 0.8655 (m) cc_final: 0.8416 (m) REVERT: Z 38 GLU cc_start: 0.8332 (pp20) cc_final: 0.7800 (pt0) REVERT: Z 54 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7819 (ttt180) REVERT: a 30 LEU cc_start: 0.3993 (pt) cc_final: 0.3722 (mt) outliers start: 8 outliers final: 2 residues processed: 1893 average time/residue: 1.3946 time to fit residues: 4432.5983 Evaluate side-chains 1593 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1590 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 30.0000 chunk 579 optimal weight: 50.0000 chunk 14 optimal weight: 3.9990 chunk 760 optimal weight: 30.0000 chunk 421 optimal weight: 2.9990 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 521 optimal weight: 4.9990 chunk 917 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 52 HIS ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 173 GLN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 18 GLN g 33 GLN k 9 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 ASN ** o 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 116 GLN p 40 GLN ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 58 GLN s 9 HIS ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS x 5 GLN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS C 18 HIS D 13 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN H 189 HIS I 197 HIS ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS K 68 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN S 61 ASN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN Y 74 HIS Z 63 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.9309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 163139 Z= 0.287 Angle : 0.672 13.472 244082 Z= 0.345 Chirality : 0.038 0.498 31220 Planarity : 0.006 0.102 13080 Dihedral : 23.394 175.698 81722 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.02 % Favored : 89.85 % Rotamer: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 5919 helix: -0.82 (0.11), residues: 1873 sheet: -1.72 (0.15), residues: 1000 loop : -2.41 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP b 212 HIS 0.021 0.002 HIS P 117 PHE 0.035 0.002 PHE p 73 TYR 0.028 0.002 TYR N 37 ARG 0.022 0.001 ARG v 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1866 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1861 time to evaluate : 6.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 20 ASN cc_start: 0.7968 (t0) cc_final: 0.7556 (t0) REVERT: b 25 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8092 (mttm) REVERT: b 78 GLU cc_start: 0.8328 (tt0) cc_final: 0.7960 (tt0) REVERT: b 81 GLU cc_start: 0.7733 (pm20) cc_final: 0.7255 (pm20) REVERT: b 82 TYR cc_start: 0.8294 (t80) cc_final: 0.7731 (t80) REVERT: b 87 SER cc_start: 0.9061 (p) cc_final: 0.8818 (p) REVERT: b 97 ASP cc_start: 0.8336 (p0) cc_final: 0.7875 (t0) REVERT: b 132 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8326 (mmm-85) REVERT: b 183 VAL cc_start: 0.9248 (m) cc_final: 0.8948 (p) REVERT: c 11 MET cc_start: 0.7886 (ttm) cc_final: 0.6831 (ttm) REVERT: c 30 GLU cc_start: 0.8596 (mp0) cc_final: 0.8142 (mp0) REVERT: c 45 TYR cc_start: 0.5441 (p90) cc_final: 0.5092 (p90) REVERT: c 64 GLU cc_start: 0.8035 (mp0) cc_final: 0.7755 (mp0) REVERT: c 84 LEU cc_start: 0.8458 (mm) cc_final: 0.8063 (mp) REVERT: c 96 ILE cc_start: 0.9264 (tp) cc_final: 0.8970 (mt) REVERT: c 128 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.6734 (tmt170) REVERT: d 1 MET cc_start: 0.8819 (tpt) cc_final: 0.8108 (mmp) REVERT: d 2 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8247 (mm-30) REVERT: d 10 SER cc_start: 0.8812 (m) cc_final: 0.8578 (p) REVERT: d 30 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8407 (tm-30) REVERT: d 35 TYR cc_start: 0.8566 (t80) cc_final: 0.8356 (t80) REVERT: d 43 THR cc_start: 0.7918 (p) cc_final: 0.7565 (p) REVERT: d 114 ARG cc_start: 0.9254 (mtm180) cc_final: 0.8816 (ptp-110) REVERT: d 122 GLU cc_start: 0.9035 (tp30) cc_final: 0.8436 (tp30) REVERT: d 124 PHE cc_start: 0.6976 (t80) cc_final: 0.6587 (t80) REVERT: d 145 ASP cc_start: 0.8345 (t0) cc_final: 0.7475 (t0) REVERT: d 155 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8258 (pm20) REVERT: d 168 ASP cc_start: 0.7807 (t0) cc_final: 0.7316 (t0) REVERT: d 175 ILE cc_start: 0.7277 (mm) cc_final: 0.6966 (mm) REVERT: d 184 ASP cc_start: 0.7985 (m-30) cc_final: 0.7731 (m-30) REVERT: d 191 ASP cc_start: 0.9204 (m-30) cc_final: 0.9000 (m-30) REVERT: e 37 MET cc_start: 0.6924 (tmm) cc_final: 0.6676 (tmm) REVERT: e 50 ASP cc_start: 0.9152 (m-30) cc_final: 0.8814 (m-30) REVERT: e 95 MET cc_start: 0.9472 (tmm) cc_final: 0.8751 (ttp) REVERT: e 119 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8500 (pttm) REVERT: e 129 MET cc_start: 0.7563 (tmm) cc_final: 0.7279 (tmm) REVERT: e 135 ILE cc_start: 0.9747 (pt) cc_final: 0.9509 (mm) REVERT: e 137 PHE cc_start: 0.7842 (m-10) cc_final: 0.6890 (m-10) REVERT: e 147 ARG cc_start: 0.8801 (tpm170) cc_final: 0.7861 (tpt-90) REVERT: e 156 THR cc_start: 0.7757 (m) cc_final: 0.7243 (p) REVERT: e 174 PHE cc_start: 0.7570 (m-80) cc_final: 0.7274 (m-10) REVERT: f 22 VAL cc_start: 0.8461 (t) cc_final: 0.8211 (m) REVERT: f 41 GLU cc_start: 0.7574 (pp20) cc_final: 0.7340 (pp20) REVERT: f 54 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7406 (ttm110) REVERT: f 68 ARG cc_start: 0.8448 (tmt170) cc_final: 0.7433 (mmt180) REVERT: f 80 GLU cc_start: 0.9069 (tp30) cc_final: 0.8534 (tm-30) REVERT: f 82 PHE cc_start: 0.6861 (m-80) cc_final: 0.6368 (m-80) REVERT: f 87 GLN cc_start: 0.8352 (tt0) cc_final: 0.7580 (tm-30) REVERT: f 152 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7023 (tpp-160) REVERT: g 25 TYR cc_start: 0.7950 (t80) cc_final: 0.7633 (t80) REVERT: g 45 GLU cc_start: 0.8972 (pp20) cc_final: 0.8584 (pp20) REVERT: g 46 PHE cc_start: 0.8814 (m-10) cc_final: 0.8609 (m-80) REVERT: g 55 GLU cc_start: 0.6765 (mp0) cc_final: 0.6064 (tp30) REVERT: h 52 MET cc_start: 0.0153 (mtp) cc_final: -0.1510 (tmm) REVERT: i 116 MET cc_start: -0.0000 (ttt) cc_final: -0.0411 (ttm) REVERT: j 7 LYS cc_start: 0.7854 (mttt) cc_final: 0.7377 (tttp) REVERT: j 14 ASP cc_start: 0.8795 (p0) cc_final: 0.8156 (p0) REVERT: j 16 TYR cc_start: 0.8232 (m-80) cc_final: 0.7865 (m-80) REVERT: j 31 GLU cc_start: 0.8100 (pp20) cc_final: 0.7731 (pp20) REVERT: j 32 LEU cc_start: 0.8263 (mt) cc_final: 0.8019 (mt) REVERT: j 47 HIS cc_start: 0.8010 (p90) cc_final: 0.7331 (p90) REVERT: j 52 ASP cc_start: 0.8477 (p0) cc_final: 0.8205 (p0) REVERT: j 75 TYR cc_start: 0.7147 (m-80) cc_final: 0.6774 (m-80) REVERT: j 128 ASN cc_start: 0.8221 (t0) cc_final: 0.8007 (t0) REVERT: j 136 GLN cc_start: 0.9072 (mm110) cc_final: 0.8647 (mm110) REVERT: k 1 MET cc_start: 0.6300 (ttm) cc_final: 0.5875 (ttm) REVERT: k 20 MET cc_start: 0.8232 (mmp) cc_final: 0.7424 (mmm) REVERT: k 45 GLU cc_start: 0.7632 (mp0) cc_final: 0.7295 (mp0) REVERT: k 51 LYS cc_start: 0.9424 (mmmt) cc_final: 0.8923 (mmmt) REVERT: k 53 LYS cc_start: 0.8221 (mppt) cc_final: 0.7932 (mmtm) REVERT: k 67 LYS cc_start: 0.7434 (tptt) cc_final: 0.7024 (tptt) REVERT: k 71 ARG cc_start: 0.8804 (mmm160) cc_final: 0.8357 (tpp80) REVERT: k 108 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7467 (ttp80) REVERT: l 59 ARG cc_start: 0.8144 (ttt180) cc_final: 0.7796 (mtp85) REVERT: l 105 ILE cc_start: 0.9049 (mm) cc_final: 0.8665 (tt) REVERT: l 106 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8196 (tm-30) REVERT: m 11 LYS cc_start: 0.7768 (mptt) cc_final: 0.7504 (mptt) REVERT: m 58 LYS cc_start: 0.8266 (tmtt) cc_final: 0.8057 (tptp) REVERT: m 104 GLU cc_start: 0.6171 (tt0) cc_final: 0.5951 (tt0) REVERT: n 9 GLN cc_start: 0.7934 (pp30) cc_final: 0.7224 (pp30) REVERT: n 11 ASN cc_start: 0.7611 (t0) cc_final: 0.7398 (t0) REVERT: n 75 ILE cc_start: 0.8404 (mm) cc_final: 0.7960 (mt) REVERT: n 118 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8007 (ttp80) REVERT: o 13 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.8352 (mtp-110) REVERT: o 63 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8658 (tmtt) REVERT: o 64 TYR cc_start: 0.7521 (t80) cc_final: 0.6600 (t80) REVERT: o 92 PHE cc_start: 0.8732 (t80) cc_final: 0.8415 (t80) REVERT: p 6 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8212 (tm-30) REVERT: p 28 LYS cc_start: 0.7735 (mmtp) cc_final: 0.6919 (mmtm) REVERT: p 38 ARG cc_start: 0.6654 (ttm110) cc_final: 0.6424 (ttm-80) REVERT: p 105 LYS cc_start: 0.8846 (pttm) cc_final: 0.8542 (pttp) REVERT: q 21 LYS cc_start: 0.7163 (tptt) cc_final: 0.6873 (tttm) REVERT: q 36 GLN cc_start: 0.8922 (pt0) cc_final: 0.8637 (pt0) REVERT: q 49 ARG cc_start: 0.7794 (mmt90) cc_final: 0.6921 (mpp80) REVERT: q 55 GLN cc_start: 0.8013 (tt0) cc_final: 0.7749 (tt0) REVERT: q 60 TRP cc_start: 0.8508 (m-10) cc_final: 0.7606 (m-10) REVERT: q 78 PHE cc_start: 0.8625 (t80) cc_final: 0.8365 (t80) REVERT: q 100 PHE cc_start: 0.6799 (m-80) cc_final: 0.6453 (m-10) REVERT: q 102 LYS cc_start: 0.8837 (tppt) cc_final: 0.8597 (tptp) REVERT: q 111 LYS cc_start: 0.9681 (tptm) cc_final: 0.9370 (tttp) REVERT: r 6 GLN cc_start: 0.8658 (tt0) cc_final: 0.7908 (tp-100) REVERT: r 10 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8286 (ptpp) REVERT: s 6 LYS cc_start: 0.8707 (tttm) cc_final: 0.7946 (tttm) REVERT: s 40 ASN cc_start: 0.8210 (p0) cc_final: 0.7871 (p0) REVERT: s 70 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7661 (mptt) REVERT: s 83 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7930 (mmmm) REVERT: s 84 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7667 (mmt-90) REVERT: s 86 MET cc_start: 0.8267 (tpt) cc_final: 0.7674 (tpp) REVERT: t 12 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8319 (tpp-160) REVERT: t 33 LYS cc_start: 0.8135 (mttm) cc_final: 0.7741 (mmtp) REVERT: t 43 ILE cc_start: 0.9445 (mm) cc_final: 0.9176 (mm) REVERT: t 56 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8255 (mp0) REVERT: t 59 ASN cc_start: 0.9000 (m-40) cc_final: 0.8203 (t0) REVERT: u 13 LEU cc_start: 0.7774 (mt) cc_final: 0.7458 (mt) REVERT: v 24 ASN cc_start: 0.6844 (t0) cc_final: 0.6265 (t0) REVERT: v 41 GLU cc_start: 0.7133 (tp30) cc_final: 0.6712 (pt0) REVERT: v 73 LYS cc_start: 0.7905 (tptp) cc_final: 0.7469 (ttmm) REVERT: v 87 GLN cc_start: 0.8509 (mt0) cc_final: 0.7967 (mt0) REVERT: w 58 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8020 (mmtt) REVERT: w 66 GLU cc_start: 0.7793 (mm-30) cc_final: 0.6988 (mt-10) REVERT: w 68 LYS cc_start: 0.5999 (mmmt) cc_final: 0.5694 (mmmt) REVERT: w 73 ARG cc_start: 0.7922 (mpp80) cc_final: 0.7122 (mpp80) REVERT: x 2 ARG cc_start: 0.7478 (tpp80) cc_final: 0.7150 (mtt90) REVERT: x 39 VAL cc_start: 0.8540 (t) cc_final: 0.8263 (p) REVERT: x 44 ARG cc_start: 0.7413 (ptt90) cc_final: 0.7098 (ptt90) REVERT: x 71 ARG cc_start: 0.8838 (mpp80) cc_final: 0.8582 (mpp80) REVERT: y 1 MET cc_start: 0.7256 (ptm) cc_final: 0.7031 (ptm) REVERT: y 12 GLU cc_start: 0.8888 (tp30) cc_final: 0.8634 (tp30) REVERT: y 31 GLN cc_start: 0.9231 (tt0) cc_final: 0.8799 (tp-100) REVERT: z 8 GLN cc_start: 0.8966 (tt0) cc_final: 0.8759 (tt0) REVERT: z 31 ILE cc_start: 0.7925 (mm) cc_final: 0.7453 (mm) REVERT: z 46 MET cc_start: 0.8200 (mmm) cc_final: 0.7451 (mmt) REVERT: z 53 MET cc_start: 0.7573 (ptt) cc_final: 0.7070 (ptt) REVERT: z 55 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8862 (tptp) REVERT: B 30 ASP cc_start: 0.7504 (t0) cc_final: 0.6701 (t0) REVERT: D 1 MET cc_start: 0.5364 (mmm) cc_final: 0.5107 (mtt) REVERT: D 6 GLN cc_start: 0.8706 (mp10) cc_final: 0.8031 (mp10) REVERT: D 12 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8243 (ttm-80) REVERT: D 22 MET cc_start: 0.8708 (mmt) cc_final: 0.8216 (mmm) REVERT: D 24 THR cc_start: 0.8357 (t) cc_final: 0.8139 (t) REVERT: D 25 LYS cc_start: 0.8255 (ptmm) cc_final: 0.7747 (ttpt) REVERT: D 28 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.7628 (mtp180) REVERT: D 37 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8081 (mtpt) REVERT: D 39 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7546 (mtp180) REVERT: E 21 PHE cc_start: 0.8945 (m-80) cc_final: 0.8402 (m-80) REVERT: E 48 MET cc_start: 0.8887 (mmp) cc_final: 0.8249 (mmm) REVERT: E 58 ILE cc_start: 0.8307 (mt) cc_final: 0.7816 (pt) REVERT: F 4 ARG cc_start: 0.7684 (mmp80) cc_final: 0.7354 (mmp80) REVERT: G 5 MET cc_start: 0.8484 (ptt) cc_final: 0.7605 (tpp) REVERT: G 8 MET cc_start: 0.8805 (mtp) cc_final: 0.7764 (mtp) REVERT: G 17 HIS cc_start: 0.7441 (m-70) cc_final: 0.6054 (m-70) REVERT: G 34 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7204 (tpp80) REVERT: G 41 ASN cc_start: 0.7680 (t0) cc_final: 0.7160 (t0) REVERT: G 46 VAL cc_start: 0.8470 (t) cc_final: 0.8103 (t) REVERT: G 48 MET cc_start: 0.8124 (tmm) cc_final: 0.7727 (tmm) REVERT: G 56 LEU cc_start: 0.8136 (tt) cc_final: 0.7825 (tt) REVERT: G 68 PHE cc_start: 0.9190 (m-10) cc_final: 0.8828 (m-10) REVERT: G 92 ASN cc_start: 0.7701 (p0) cc_final: 0.7277 (p0) REVERT: G 99 MET cc_start: 0.8952 (mmp) cc_final: 0.8049 (mpp) REVERT: G 102 ASN cc_start: 0.8651 (t0) cc_final: 0.8307 (t0) REVERT: G 136 ARG cc_start: 0.7770 (ptm-80) cc_final: 0.7202 (ptm-80) REVERT: G 139 GLU cc_start: 0.8521 (pp20) cc_final: 0.8279 (pp20) REVERT: G 161 PHE cc_start: 0.8157 (t80) cc_final: 0.7810 (t80) REVERT: G 195 VAL cc_start: 0.7666 (t) cc_final: 0.7428 (p) REVERT: H 10 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6889 (mtt-85) REVERT: H 26 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7475 (ttmt) REVERT: H 68 HIS cc_start: 0.8806 (m90) cc_final: 0.8399 (m90) REVERT: H 81 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9128 (tm-30) REVERT: H 113 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8087 (mppt) REVERT: H 128 MET cc_start: 0.6413 (ttp) cc_final: 0.6159 (ttt) REVERT: H 138 GLN cc_start: 0.9145 (mt0) cc_final: 0.8833 (mt0) REVERT: H 187 GLU cc_start: 0.8072 (tp30) cc_final: 0.7700 (tp30) REVERT: I 12 ARG cc_start: 0.4924 (mtm180) cc_final: 0.3135 (mtm180) REVERT: I 67 LEU cc_start: 0.9050 (mt) cc_final: 0.8837 (mt) REVERT: I 177 MET cc_start: 0.2832 (mpp) cc_final: 0.1597 (mtp) REVERT: I 190 LEU cc_start: 0.8421 (mp) cc_final: 0.8217 (mp) REVERT: I 196 GLU cc_start: 0.8008 (pp20) cc_final: 0.7233 (pp20) REVERT: J 28 ARG cc_start: 0.7529 (ptp-170) cc_final: 0.6356 (mtt180) REVERT: J 44 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7373 (mmm-85) REVERT: J 60 GLN cc_start: 0.8301 (mp10) cc_final: 0.7869 (tm-30) REVERT: J 69 ASN cc_start: 0.8052 (t0) cc_final: 0.7282 (t0) REVERT: J 96 GLN cc_start: 0.8103 (tt0) cc_final: 0.7656 (mt0) REVERT: J 115 GLU cc_start: 0.8356 (pt0) cc_final: 0.8007 (tp30) REVERT: K 4 TYR cc_start: 0.6939 (m-80) cc_final: 0.6487 (m-80) REVERT: K 25 TYR cc_start: 0.7787 (m-80) cc_final: 0.7518 (m-80) REVERT: K 44 ARG cc_start: 0.7012 (ttp80) cc_final: 0.6620 (ttp80) REVERT: K 45 ARG cc_start: 0.8380 (mtm110) cc_final: 0.8103 (mtm110) REVERT: K 47 LEU cc_start: 0.8980 (tp) cc_final: 0.8612 (tp) REVERT: K 61 LEU cc_start: 0.8324 (tt) cc_final: 0.7299 (mp) REVERT: L 78 ARG cc_start: 0.5922 (ptp90) cc_final: 0.4821 (ptp90) REVERT: L 109 LYS cc_start: 0.8055 (mmpt) cc_final: 0.7499 (mtmm) REVERT: L 136 LYS cc_start: 0.8416 (tttt) cc_final: 0.8114 (mtmm) REVERT: L 148 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8460 (mtpp) REVERT: M 12 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7119 (mmm-85) REVERT: M 60 LEU cc_start: 0.8906 (mt) cc_final: 0.8676 (mm) REVERT: M 63 LYS cc_start: 0.8381 (ptpt) cc_final: 0.7983 (ptpp) REVERT: M 88 LYS cc_start: 0.8228 (ptpt) cc_final: 0.7766 (ptpp) REVERT: M 98 LEU cc_start: 0.9147 (pp) cc_final: 0.8927 (pp) REVERT: M 110 MET cc_start: 0.8654 (ptt) cc_final: 0.8256 (ptt) REVERT: M 112 ASP cc_start: 0.8934 (p0) cc_final: 0.8706 (p0) REVERT: M 116 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8932 (tpp80) REVERT: M 123 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7483 (tm-30) REVERT: M 125 ILE cc_start: 0.8815 (mp) cc_final: 0.8412 (mp) REVERT: N 4 GLN cc_start: 0.6164 (tt0) cc_final: 0.4444 (mm-40) REVERT: N 5 TYR cc_start: 0.7001 (m-80) cc_final: 0.6753 (m-80) REVERT: N 19 PHE cc_start: 0.6368 (m-10) cc_final: 0.5933 (m-80) REVERT: N 45 MET cc_start: 0.8594 (ptp) cc_final: 0.8333 (pmm) REVERT: N 61 ASP cc_start: 0.5949 (p0) cc_final: 0.5520 (p0) REVERT: N 74 GLN cc_start: 0.8946 (mt0) cc_final: 0.8675 (mt0) REVERT: N 86 LEU cc_start: 0.7907 (tp) cc_final: 0.7568 (mt) REVERT: N 87 MET cc_start: 0.8013 (pmm) cc_final: 0.7810 (pmm) REVERT: O 7 ARG cc_start: 0.5572 (mtt180) cc_final: 0.3291 (mmt-90) REVERT: P 41 LEU cc_start: 0.8656 (pt) cc_final: 0.8413 (pt) REVERT: P 45 THR cc_start: 0.8064 (p) cc_final: 0.7653 (p) REVERT: P 49 SER cc_start: 0.6300 (p) cc_final: 0.5098 (p) REVERT: P 63 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8004 (mt0) REVERT: P 68 ARG cc_start: 0.8979 (mmm-85) cc_final: 0.8316 (mtp-110) REVERT: P 80 ASN cc_start: 0.8175 (m-40) cc_final: 0.7936 (m-40) REVERT: Q 52 CYS cc_start: 0.8449 (p) cc_final: 0.6370 (t) REVERT: Q 75 GLU cc_start: 0.8496 (mp0) cc_final: 0.7918 (mp0) REVERT: R 30 LYS cc_start: 0.8671 (ptpp) cc_final: 0.8277 (ptpt) REVERT: R 84 CYS cc_start: 0.5094 (p) cc_final: 0.4766 (p) REVERT: R 88 LEU cc_start: 0.9098 (pp) cc_final: 0.8840 (tp) REVERT: R 94 LEU cc_start: 0.8271 (mp) cc_final: 0.8015 (tt) REVERT: S 53 ASP cc_start: 0.7790 (m-30) cc_final: 0.7259 (p0) REVERT: S 75 LYS cc_start: 0.7689 (tptm) cc_final: 0.7207 (tppt) REVERT: S 82 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6939 (mmmt) REVERT: T 47 LYS cc_start: 0.8680 (mttt) cc_final: 0.8366 (mttt) REVERT: T 48 ASP cc_start: 0.6394 (t0) cc_final: 0.6083 (t0) REVERT: T 49 HIS cc_start: 0.8981 (m-70) cc_final: 0.8656 (m-70) REVERT: T 63 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8362 (mmm160) REVERT: T 65 LEU cc_start: 0.8978 (mp) cc_final: 0.8773 (mt) REVERT: T 77 TYR cc_start: 0.8421 (t80) cc_final: 0.7999 (t80) REVERT: U 53 ASP cc_start: 0.7081 (p0) cc_final: 0.6354 (p0) REVERT: V 15 LYS cc_start: 0.4688 (pttp) cc_final: 0.3951 (tptp) REVERT: V 17 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6601 (tm-30) REVERT: V 18 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8143 (mtmm) REVERT: V 27 PHE cc_start: 0.8823 (t80) cc_final: 0.8329 (t80) REVERT: V 32 ILE cc_start: 0.9199 (tp) cc_final: 0.8930 (tp) REVERT: V 33 TYR cc_start: 0.8526 (m-80) cc_final: 0.7877 (m-80) REVERT: V 63 CYS cc_start: 0.6623 (p) cc_final: 0.6309 (p) REVERT: V 71 SER cc_start: 0.7843 (t) cc_final: 0.7606 (t) REVERT: W 29 LYS cc_start: 0.9402 (pttm) cc_final: 0.9158 (pttp) REVERT: W 69 TYR cc_start: 0.7037 (m-80) cc_final: 0.6471 (m-10) REVERT: X 11 ASP cc_start: 0.7505 (t0) cc_final: 0.7223 (t0) REVERT: X 43 MET cc_start: 0.8596 (mpp) cc_final: 0.7575 (mpp) REVERT: X 46 LEU cc_start: 0.8194 (mm) cc_final: 0.7984 (tp) REVERT: X 70 LEU cc_start: 0.7574 (mp) cc_final: 0.7344 (mp) REVERT: X 72 GLU cc_start: 0.8142 (tt0) cc_final: 0.7646 (tt0) REVERT: X 73 PHE cc_start: 0.8015 (m-80) cc_final: 0.7566 (m-80) REVERT: Y 32 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8900 (mmtt) REVERT: Y 39 GLU cc_start: 0.8375 (tp30) cc_final: 0.7204 (tm-30) REVERT: Y 56 ILE cc_start: 0.8586 (mm) cc_final: 0.8384 (mm) REVERT: Z 38 GLU cc_start: 0.8815 (pp20) cc_final: 0.8585 (pt0) REVERT: a 30 LEU cc_start: 0.4007 (pt) cc_final: 0.3670 (mt) outliers start: 5 outliers final: 1 residues processed: 1862 average time/residue: 1.4139 time to fit residues: 4411.1224 Evaluate side-chains 1623 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1622 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 9.9990 chunk 920 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 599 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 1022 optimal weight: 20.0000 chunk 848 optimal weight: 10.0000 chunk 473 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 536 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 142 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN g 33 GLN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 ASN l 38 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 40 GLN q 51 GLN ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 61 ASN t 70 HIS ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS G 88 GLN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS O 15 HIS P 21 HIS ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN R 13 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 163139 Z= 0.250 Angle : 0.637 13.944 244082 Z= 0.328 Chirality : 0.036 0.332 31220 Planarity : 0.005 0.076 13080 Dihedral : 23.396 175.697 81722 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.19 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -2.44 (0.10), residues: 5919 helix: -0.64 (0.12), residues: 1887 sheet: -1.48 (0.16), residues: 960 loop : -2.33 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP b 212 HIS 0.019 0.002 HIS P 117 PHE 0.034 0.002 PHE G 31 TYR 0.029 0.002 TYR b 102 ARG 0.026 0.001 ARG w 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1877 time to evaluate : 5.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 12 ARG cc_start: 0.7833 (tpp-160) cc_final: 0.7502 (tpm170) REVERT: b 20 ASN cc_start: 0.8234 (t0) cc_final: 0.7948 (t0) REVERT: b 34 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6947 (mm-30) REVERT: b 78 GLU cc_start: 0.8425 (tt0) cc_final: 0.8056 (tt0) REVERT: b 81 GLU cc_start: 0.7795 (pm20) cc_final: 0.7293 (pm20) REVERT: b 82 TYR cc_start: 0.8134 (t80) cc_final: 0.7669 (t80) REVERT: b 97 ASP cc_start: 0.8272 (p0) cc_final: 0.7854 (t0) REVERT: b 132 ARG cc_start: 0.8631 (mmm160) cc_final: 0.8382 (mmm-85) REVERT: b 179 GLU cc_start: 0.7909 (tt0) cc_final: 0.7685 (tt0) REVERT: b 184 GLU cc_start: 0.6878 (mp0) cc_final: 0.6386 (mp0) REVERT: c 11 MET cc_start: 0.7972 (ttm) cc_final: 0.7198 (ttm) REVERT: c 45 TYR cc_start: 0.5515 (p90) cc_final: 0.5132 (p90) REVERT: c 80 TRP cc_start: 0.8288 (m-90) cc_final: 0.7050 (m-90) REVERT: c 96 ILE cc_start: 0.9261 (tp) cc_final: 0.9014 (mt) REVERT: c 126 ASN cc_start: 0.8734 (m110) cc_final: 0.8452 (m110) REVERT: c 128 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.6783 (tmt170) REVERT: c 155 VAL cc_start: 0.8607 (t) cc_final: 0.8405 (m) REVERT: d 1 MET cc_start: 0.8684 (tpt) cc_final: 0.8131 (mmm) REVERT: d 2 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8433 (mm-30) REVERT: d 10 SER cc_start: 0.8853 (m) cc_final: 0.8637 (p) REVERT: d 30 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8506 (tm-30) REVERT: d 43 THR cc_start: 0.7885 (p) cc_final: 0.7535 (p) REVERT: d 94 GLN cc_start: 0.8290 (mt0) cc_final: 0.7999 (pt0) REVERT: d 114 ARG cc_start: 0.9216 (mtm180) cc_final: 0.8697 (mtm180) REVERT: d 122 GLU cc_start: 0.8996 (tp30) cc_final: 0.8390 (tp30) REVERT: d 124 PHE cc_start: 0.7092 (t80) cc_final: 0.6649 (t80) REVERT: d 145 ASP cc_start: 0.8055 (t0) cc_final: 0.7228 (t0) REVERT: d 155 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8305 (pm20) REVERT: d 175 ILE cc_start: 0.7222 (mm) cc_final: 0.6941 (mm) REVERT: d 184 ASP cc_start: 0.8188 (m-30) cc_final: 0.7742 (m-30) REVERT: e 19 PHE cc_start: 0.8406 (m-10) cc_final: 0.8055 (m-80) REVERT: e 68 LYS cc_start: 0.9321 (mmtm) cc_final: 0.8997 (mmtp) REVERT: e 95 MET cc_start: 0.9470 (tmm) cc_final: 0.9196 (tmm) REVERT: e 124 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7459 (mmm-85) REVERT: e 129 MET cc_start: 0.7778 (tmm) cc_final: 0.7498 (tmm) REVERT: e 132 ARG cc_start: 0.7306 (mmt90) cc_final: 0.6586 (mpt180) REVERT: e 156 THR cc_start: 0.7790 (m) cc_final: 0.7301 (p) REVERT: e 174 PHE cc_start: 0.7779 (m-80) cc_final: 0.7421 (m-10) REVERT: f 54 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6945 (ttm110) REVERT: f 63 GLN cc_start: 0.9161 (mp10) cc_final: 0.8947 (mp10) REVERT: f 68 ARG cc_start: 0.8554 (tmt170) cc_final: 0.7633 (mmt180) REVERT: f 80 GLU cc_start: 0.9066 (tp30) cc_final: 0.8472 (tm-30) REVERT: f 82 PHE cc_start: 0.6913 (m-80) cc_final: 0.6479 (m-80) REVERT: f 87 GLN cc_start: 0.8210 (tt0) cc_final: 0.7594 (tm-30) REVERT: f 152 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7869 (tpp-160) REVERT: g 20 ASN cc_start: 0.8864 (m-40) cc_final: 0.8631 (m-40) REVERT: g 22 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7974 (mmmm) REVERT: g 25 TYR cc_start: 0.7848 (t80) cc_final: 0.7449 (t80) REVERT: g 45 GLU cc_start: 0.8933 (pp20) cc_final: 0.8557 (pp20) REVERT: g 55 GLU cc_start: 0.6706 (mp0) cc_final: 0.6026 (tp30) REVERT: h 52 MET cc_start: -0.0274 (mtp) cc_final: -0.1701 (tmm) REVERT: j 7 LYS cc_start: 0.7951 (mttt) cc_final: 0.7323 (mmtp) REVERT: j 9 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7371 (pm20) REVERT: j 13 ARG cc_start: 0.7758 (ptp-170) cc_final: 0.6805 (ptm160) REVERT: j 14 ASP cc_start: 0.8900 (p0) cc_final: 0.8200 (p0) REVERT: j 16 TYR cc_start: 0.8022 (m-80) cc_final: 0.7602 (m-80) REVERT: j 47 HIS cc_start: 0.8075 (p90) cc_final: 0.7418 (p90) REVERT: j 49 ASP cc_start: 0.7243 (t70) cc_final: 0.6321 (t70) REVERT: j 52 ASP cc_start: 0.8409 (p0) cc_final: 0.8201 (p0) REVERT: j 75 TYR cc_start: 0.7082 (m-80) cc_final: 0.6586 (m-80) REVERT: j 118 MET cc_start: 0.8141 (tmm) cc_final: 0.7625 (ttm) REVERT: j 136 GLN cc_start: 0.9061 (mm110) cc_final: 0.8580 (mm110) REVERT: k 1 MET cc_start: 0.6022 (ttm) cc_final: 0.5745 (ttm) REVERT: k 6 THR cc_start: 0.8126 (p) cc_final: 0.7820 (p) REVERT: k 44 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7971 (mmtp) REVERT: k 58 LEU cc_start: 0.8460 (mt) cc_final: 0.8169 (mt) REVERT: k 67 LYS cc_start: 0.7539 (tptt) cc_final: 0.7257 (tptt) REVERT: k 71 ARG cc_start: 0.8707 (mmm160) cc_final: 0.8203 (mmm160) REVERT: k 88 ASN cc_start: 0.8777 (t0) cc_final: 0.8557 (t0) REVERT: k 89 ASN cc_start: 0.9297 (t0) cc_final: 0.8878 (m-40) REVERT: k 108 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7217 (ttp80) REVERT: l 21 ARG cc_start: 0.7810 (mmt-90) cc_final: 0.7402 (mmt-90) REVERT: l 59 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7821 (mtp85) REVERT: l 84 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7589 (tppt) REVERT: l 105 ILE cc_start: 0.9188 (mm) cc_final: 0.8840 (tt) REVERT: l 106 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8295 (tm-30) REVERT: m 89 VAL cc_start: 0.7849 (p) cc_final: 0.7365 (p) REVERT: m 110 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7333 (tm-30) REVERT: n 9 GLN cc_start: 0.7880 (pp30) cc_final: 0.7109 (pp30) REVERT: n 11 ASN cc_start: 0.7677 (t0) cc_final: 0.7436 (t0) REVERT: n 52 ILE cc_start: 0.9326 (mm) cc_final: 0.9124 (mm) REVERT: n 75 ILE cc_start: 0.8519 (mm) cc_final: 0.8119 (mt) REVERT: n 118 ARG cc_start: 0.8376 (ttp80) cc_final: 0.7929 (ttp80) REVERT: o 12 THR cc_start: 0.8621 (p) cc_final: 0.8376 (p) REVERT: o 63 LYS cc_start: 0.9123 (tmmt) cc_final: 0.8633 (tmtt) REVERT: o 64 TYR cc_start: 0.7629 (t80) cc_final: 0.6766 (t80) REVERT: o 92 PHE cc_start: 0.8940 (t80) cc_final: 0.8521 (t80) REVERT: p 6 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8323 (tm-30) REVERT: p 28 LYS cc_start: 0.7301 (mmtp) cc_final: 0.6846 (mmtm) REVERT: p 105 LYS cc_start: 0.8866 (pttm) cc_final: 0.8568 (pttp) REVERT: q 49 ARG cc_start: 0.7153 (mpt-90) cc_final: 0.6521 (mpp80) REVERT: q 60 TRP cc_start: 0.8436 (m-10) cc_final: 0.7452 (m-10) REVERT: q 78 PHE cc_start: 0.8639 (t80) cc_final: 0.8268 (t80) REVERT: q 100 PHE cc_start: 0.7077 (m-80) cc_final: 0.6619 (m-10) REVERT: q 102 LYS cc_start: 0.8911 (tppt) cc_final: 0.8611 (tptp) REVERT: q 111 LYS cc_start: 0.9685 (tptm) cc_final: 0.9146 (tptp) REVERT: r 6 GLN cc_start: 0.8637 (tt0) cc_final: 0.7804 (tm-30) REVERT: s 6 LYS cc_start: 0.8746 (tttm) cc_final: 0.7947 (tttm) REVERT: s 12 SER cc_start: 0.8732 (t) cc_final: 0.8496 (t) REVERT: s 13 SER cc_start: 0.8703 (p) cc_final: 0.8492 (p) REVERT: s 40 ASN cc_start: 0.8328 (p0) cc_final: 0.7938 (p0) REVERT: s 83 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7761 (mmmm) REVERT: s 84 ARG cc_start: 0.7934 (mmt-90) cc_final: 0.7432 (mmt-90) REVERT: s 86 MET cc_start: 0.8120 (tpt) cc_final: 0.7757 (tpp) REVERT: t 11 LEU cc_start: 0.8884 (mm) cc_final: 0.8678 (mm) REVERT: t 12 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8300 (tpp-160) REVERT: t 59 ASN cc_start: 0.8920 (m-40) cc_final: 0.8047 (t0) REVERT: t 69 ARG cc_start: 0.8166 (mmt90) cc_final: 0.7952 (mmt90) REVERT: t 89 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8444 (mm-30) REVERT: u 13 LEU cc_start: 0.7800 (mt) cc_final: 0.7407 (mt) REVERT: v 20 LEU cc_start: 0.8409 (pp) cc_final: 0.7972 (pp) REVERT: v 31 TYR cc_start: 0.8564 (p90) cc_final: 0.8165 (p90) REVERT: v 42 LEU cc_start: 0.8680 (pt) cc_final: 0.8453 (pt) REVERT: v 46 LYS cc_start: 0.9182 (tppt) cc_final: 0.8949 (tppt) REVERT: v 47 VAL cc_start: 0.9162 (p) cc_final: 0.8742 (p) REVERT: v 51 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8887 (tm-30) REVERT: v 73 LYS cc_start: 0.7895 (tptp) cc_final: 0.7463 (ttmm) REVERT: v 87 GLN cc_start: 0.8638 (mt0) cc_final: 0.8036 (mt0) REVERT: w 19 VAL cc_start: 0.9183 (t) cc_final: 0.8975 (t) REVERT: w 66 GLU cc_start: 0.7805 (mm-30) cc_final: 0.6923 (mt-10) REVERT: x 2 ARG cc_start: 0.7279 (tpp80) cc_final: 0.7039 (mtt90) REVERT: x 5 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8018 (mt0) REVERT: x 39 VAL cc_start: 0.8636 (t) cc_final: 0.8367 (p) REVERT: x 44 ARG cc_start: 0.7211 (ptt90) cc_final: 0.6885 (ptt90) REVERT: y 1 MET cc_start: 0.7471 (ptm) cc_final: 0.7209 (ptm) REVERT: y 12 GLU cc_start: 0.8903 (tp30) cc_final: 0.8605 (tp30) REVERT: y 18 LEU cc_start: 0.7979 (mm) cc_final: 0.7777 (mm) REVERT: y 31 GLN cc_start: 0.9192 (tt0) cc_final: 0.8796 (tp-100) REVERT: z 15 ARG cc_start: 0.7407 (mmt-90) cc_final: 0.6490 (mmt-90) REVERT: z 31 ILE cc_start: 0.7960 (mm) cc_final: 0.7527 (mm) REVERT: z 46 MET cc_start: 0.7918 (mmm) cc_final: 0.7451 (mmm) REVERT: z 53 MET cc_start: 0.7489 (ptt) cc_final: 0.7108 (ptt) REVERT: z 55 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8351 (tmtt) REVERT: z 56 VAL cc_start: 0.8729 (t) cc_final: 0.8044 (t) REVERT: B 30 ASP cc_start: 0.7362 (t0) cc_final: 0.6690 (t70) REVERT: D 12 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8108 (ttm-80) REVERT: D 22 MET cc_start: 0.8762 (mmt) cc_final: 0.8352 (mmm) REVERT: D 37 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8068 (mtpt) REVERT: E 48 MET cc_start: 0.8934 (mmp) cc_final: 0.8240 (mmm) REVERT: E 58 ILE cc_start: 0.8370 (mt) cc_final: 0.7867 (pt) REVERT: F 4 ARG cc_start: 0.7743 (mmp80) cc_final: 0.7525 (mmp80) REVERT: G 5 MET cc_start: 0.8617 (ptt) cc_final: 0.7847 (tpp) REVERT: G 17 HIS cc_start: 0.7542 (m-70) cc_final: 0.6036 (m-70) REVERT: G 34 ARG cc_start: 0.8081 (tpp80) cc_final: 0.7642 (tpp80) REVERT: G 38 HIS cc_start: 0.7699 (m170) cc_final: 0.7471 (m170) REVERT: G 50 ASN cc_start: 0.8397 (m110) cc_final: 0.8186 (m110) REVERT: G 67 LEU cc_start: 0.8536 (tp) cc_final: 0.8294 (tp) REVERT: G 68 PHE cc_start: 0.9182 (m-10) cc_final: 0.8869 (m-10) REVERT: G 92 ASN cc_start: 0.8069 (p0) cc_final: 0.7693 (p0) REVERT: G 94 ARG cc_start: 0.8020 (ttt90) cc_final: 0.7269 (tpp-160) REVERT: G 99 MET cc_start: 0.8914 (mmp) cc_final: 0.8169 (tpp) REVERT: G 102 ASN cc_start: 0.8792 (t0) cc_final: 0.8467 (t0) REVERT: G 136 ARG cc_start: 0.7831 (ptm-80) cc_final: 0.7056 (ptm160) REVERT: G 139 GLU cc_start: 0.8482 (pp20) cc_final: 0.8195 (pp20) REVERT: G 161 PHE cc_start: 0.8120 (t80) cc_final: 0.7726 (t80) REVERT: G 197 PHE cc_start: 0.7773 (m-10) cc_final: 0.7430 (m-10) REVERT: H 10 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7185 (mtt-85) REVERT: H 68 HIS cc_start: 0.8906 (m90) cc_final: 0.8560 (m90) REVERT: H 81 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9006 (tm-30) REVERT: H 113 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8103 (mppt) REVERT: H 137 VAL cc_start: 0.8831 (t) cc_final: 0.8622 (t) REVERT: H 138 GLN cc_start: 0.9164 (mt0) cc_final: 0.8854 (mt0) REVERT: H 165 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6324 (tt0) REVERT: H 194 VAL cc_start: 0.7992 (t) cc_final: 0.7388 (p) REVERT: I 12 ARG cc_start: 0.4719 (mtm180) cc_final: 0.2944 (mtm180) REVERT: I 71 PHE cc_start: 0.8634 (t80) cc_final: 0.8359 (t80) REVERT: I 74 TYR cc_start: 0.8888 (m-80) cc_final: 0.8686 (m-80) REVERT: I 96 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7805 (tpp-160) REVERT: I 190 LEU cc_start: 0.8469 (mp) cc_final: 0.8257 (mp) REVERT: I 195 ASN cc_start: 0.7788 (t0) cc_final: 0.7118 (t0) REVERT: J 11 GLN cc_start: 0.8083 (mp10) cc_final: 0.7739 (mp10) REVERT: J 28 ARG cc_start: 0.7472 (ptp-170) cc_final: 0.6430 (mtt180) REVERT: J 40 ASP cc_start: 0.8018 (p0) cc_final: 0.7402 (p0) REVERT: J 44 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7344 (mmm-85) REVERT: J 96 GLN cc_start: 0.8095 (tt0) cc_final: 0.7678 (mt0) REVERT: J 115 GLU cc_start: 0.8401 (pt0) cc_final: 0.8042 (tp30) REVERT: J 146 MET cc_start: 0.5127 (ppp) cc_final: 0.4863 (ptt) REVERT: K 4 TYR cc_start: 0.6638 (m-80) cc_final: 0.6100 (m-80) REVERT: K 25 TYR cc_start: 0.7664 (m-80) cc_final: 0.7290 (m-80) REVERT: K 44 ARG cc_start: 0.6909 (ttp80) cc_final: 0.6518 (ttp80) REVERT: K 61 LEU cc_start: 0.8380 (tt) cc_final: 0.7354 (mp) REVERT: K 62 MET cc_start: 0.8422 (mmp) cc_final: 0.8140 (mmm) REVERT: L 30 MET cc_start: 0.8193 (tmm) cc_final: 0.7846 (ttp) REVERT: L 78 ARG cc_start: 0.5996 (ptp90) cc_final: 0.4869 (ptp90) REVERT: L 91 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.8164 (ptp-170) REVERT: L 100 MET cc_start: 0.8374 (ppp) cc_final: 0.8066 (ptm) REVERT: L 122 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7666 (tp30) REVERT: L 128 GLU cc_start: 0.9336 (pm20) cc_final: 0.9129 (pm20) REVERT: L 136 LYS cc_start: 0.8362 (tttt) cc_final: 0.8122 (mtmm) REVERT: L 139 ASP cc_start: 0.8562 (m-30) cc_final: 0.8307 (m-30) REVERT: L 148 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8487 (mtpp) REVERT: M 17 GLN cc_start: 0.8640 (mt0) cc_final: 0.7801 (tt0) REVERT: M 26 MET cc_start: 0.8850 (mpp) cc_final: 0.8603 (mpp) REVERT: M 57 GLU cc_start: 0.8645 (tp30) cc_final: 0.8408 (tp30) REVERT: M 63 LYS cc_start: 0.8250 (ptpt) cc_final: 0.8006 (ptpp) REVERT: M 95 MET cc_start: 0.7901 (mtp) cc_final: 0.7586 (ttm) REVERT: M 98 LEU cc_start: 0.9191 (pp) cc_final: 0.8634 (pp) REVERT: M 107 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7879 (mmtt) REVERT: M 110 MET cc_start: 0.8649 (ptt) cc_final: 0.8235 (ptt) REVERT: M 123 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7526 (tm-30) REVERT: M 125 ILE cc_start: 0.8789 (mp) cc_final: 0.8422 (mp) REVERT: N 4 GLN cc_start: 0.6160 (tt0) cc_final: 0.4470 (mm-40) REVERT: N 5 TYR cc_start: 0.7070 (m-80) cc_final: 0.6781 (m-80) REVERT: N 19 PHE cc_start: 0.6571 (m-10) cc_final: 0.6145 (m-80) REVERT: N 45 MET cc_start: 0.8643 (ptp) cc_final: 0.8361 (pmm) REVERT: N 61 ASP cc_start: 0.6080 (p0) cc_final: 0.5624 (p0) REVERT: O 7 ARG cc_start: 0.5575 (mtt180) cc_final: 0.3311 (mmt-90) REVERT: O 45 ARG cc_start: 0.7022 (ptm-80) cc_final: 0.6690 (ptm160) REVERT: P 41 LEU cc_start: 0.8738 (pt) cc_final: 0.8489 (pt) REVERT: P 63 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8197 (mt0) REVERT: P 68 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8563 (mtp-110) REVERT: P 69 CYS cc_start: 0.8953 (t) cc_final: 0.8719 (t) REVERT: P 80 ASN cc_start: 0.8114 (m-40) cc_final: 0.7896 (m-40) REVERT: P 124 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7380 (mmtm) REVERT: Q 34 THR cc_start: 0.8557 (p) cc_final: 0.8271 (p) REVERT: Q 36 VAL cc_start: 0.8630 (t) cc_final: 0.8270 (t) REVERT: Q 52 CYS cc_start: 0.8137 (p) cc_final: 0.6108 (t) REVERT: Q 54 VAL cc_start: 0.6991 (t) cc_final: 0.6517 (t) REVERT: Q 65 TYR cc_start: 0.8669 (t80) cc_final: 0.8131 (t80) REVERT: Q 66 ILE cc_start: 0.8652 (mm) cc_final: 0.8325 (mp) REVERT: Q 75 GLU cc_start: 0.8785 (mp0) cc_final: 0.8306 (mp0) REVERT: R 30 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8294 (ptpt) REVERT: R 76 ILE cc_start: 0.8336 (mt) cc_final: 0.7898 (tp) REVERT: R 79 LEU cc_start: 0.8106 (mt) cc_final: 0.7598 (mt) REVERT: R 80 MET cc_start: 0.7795 (mtm) cc_final: 0.7166 (mpp) REVERT: R 82 LEU cc_start: 0.8149 (tt) cc_final: 0.7829 (tp) REVERT: R 88 LEU cc_start: 0.9178 (pp) cc_final: 0.8969 (tp) REVERT: S 5 MET cc_start: 0.7952 (mmp) cc_final: 0.7653 (mmp) REVERT: S 60 ARG cc_start: 0.4605 (tpt170) cc_final: 0.4326 (mmm160) REVERT: S 75 LYS cc_start: 0.7648 (tptm) cc_final: 0.7202 (tppt) REVERT: S 82 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7065 (mmmt) REVERT: T 44 GLU cc_start: 0.8024 (pp20) cc_final: 0.7712 (pm20) REVERT: T 47 LYS cc_start: 0.8543 (mttt) cc_final: 0.8130 (mttt) REVERT: T 48 ASP cc_start: 0.6426 (t0) cc_final: 0.6019 (t0) REVERT: T 49 HIS cc_start: 0.8998 (m-70) cc_final: 0.8479 (m90) REVERT: T 52 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8361 (ttm-80) REVERT: T 63 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8487 (mmm160) REVERT: U 4 ILE cc_start: 0.7839 (mt) cc_final: 0.7580 (mm) REVERT: U 53 ASP cc_start: 0.7305 (p0) cc_final: 0.6613 (p0) REVERT: V 18 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8101 (mtmm) REVERT: V 25 GLU cc_start: 0.8575 (mp0) cc_final: 0.8279 (mp0) REVERT: V 32 ILE cc_start: 0.9205 (tp) cc_final: 0.8894 (tp) REVERT: V 33 TYR cc_start: 0.8727 (m-80) cc_final: 0.8105 (m-80) REVERT: V 39 ARG cc_start: 0.8411 (mmt180) cc_final: 0.8150 (mmt180) REVERT: V 73 THR cc_start: 0.6421 (t) cc_final: 0.6015 (t) REVERT: W 29 LYS cc_start: 0.9403 (pttm) cc_final: 0.9177 (pttp) REVERT: W 53 GLN cc_start: 0.8450 (tt0) cc_final: 0.7716 (tp40) REVERT: W 69 TYR cc_start: 0.7219 (m-80) cc_final: 0.6475 (m-10) REVERT: X 13 HIS cc_start: 0.7439 (p-80) cc_final: 0.6955 (p90) REVERT: X 73 PHE cc_start: 0.8037 (m-80) cc_final: 0.7182 (m-80) REVERT: Y 32 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8845 (mmtt) REVERT: Y 39 GLU cc_start: 0.8303 (tp30) cc_final: 0.7272 (tm-30) REVERT: Y 56 ILE cc_start: 0.8712 (mm) cc_final: 0.8478 (mm) REVERT: Y 69 ASN cc_start: 0.8558 (m-40) cc_final: 0.8164 (m110) REVERT: Z 33 ARG cc_start: 0.8330 (ppt170) cc_final: 0.7861 (tmm160) REVERT: Z 36 PHE cc_start: 0.6354 (m-80) cc_final: 0.5977 (m-80) REVERT: Z 54 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7686 (ttt180) REVERT: a 30 LEU cc_start: 0.4375 (pt) cc_final: 0.4044 (mt) outliers start: 0 outliers final: 0 residues processed: 1877 average time/residue: 1.5462 time to fit residues: 4954.2731 Evaluate side-chains 1621 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1621 time to evaluate : 6.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 582 optimal weight: 10.0000 chunk 746 optimal weight: 20.0000 chunk 578 optimal weight: 0.8980 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 0.2980 chunk 1018 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 621 optimal weight: 20.0000 chunk 470 optimal weight: 50.0000 overall best weight: 6.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 133 ASN ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 ASN c 36 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN d 97 ASN d 165 HIS ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 142 GLN g 18 GLN g 33 GLN k 9 ASN l 38 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 40 GLN p 65 ASN q 51 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS x 5 GLN y 20 ASN z 8 GLN B 18 HIS G 88 GLN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 95 HIS T 45 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 1.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 163139 Z= 0.339 Angle : 0.721 12.960 244082 Z= 0.368 Chirality : 0.039 0.360 31220 Planarity : 0.006 0.132 13080 Dihedral : 23.517 174.703 81722 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.71 % Favored : 89.15 % Rotamer: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 5919 helix: -0.64 (0.12), residues: 1878 sheet: -1.51 (0.16), residues: 939 loop : -2.36 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP b 212 HIS 0.024 0.002 HIS P 117 PHE 0.042 0.003 PHE D 18 TYR 0.030 0.003 TYR b 102 ARG 0.019 0.001 ARG v 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1888 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1887 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 12 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.6706 (tpm170) REVERT: b 20 ASN cc_start: 0.8296 (t0) cc_final: 0.8081 (t0) REVERT: b 78 GLU cc_start: 0.8529 (tt0) cc_final: 0.8142 (tt0) REVERT: b 82 TYR cc_start: 0.8259 (t80) cc_final: 0.7687 (t80) REVERT: b 97 ASP cc_start: 0.8267 (p0) cc_final: 0.7992 (p0) REVERT: b 132 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8382 (mmm160) REVERT: b 184 GLU cc_start: 0.6937 (mp0) cc_final: 0.6544 (mp0) REVERT: b 200 MET cc_start: 0.8525 (mtp) cc_final: 0.8228 (mtp) REVERT: c 4 LEU cc_start: 0.8210 (mt) cc_final: 0.7641 (mt) REVERT: c 11 MET cc_start: 0.8049 (ttm) cc_final: 0.7549 (ttm) REVERT: c 42 ASN cc_start: 0.8727 (m-40) cc_final: 0.7951 (t0) REVERT: c 45 TYR cc_start: 0.5715 (p90) cc_final: 0.5428 (p90) REVERT: c 80 TRP cc_start: 0.8431 (m-90) cc_final: 0.7426 (m-90) REVERT: c 96 ILE cc_start: 0.9333 (tp) cc_final: 0.9086 (mt) REVERT: c 126 ASN cc_start: 0.8736 (m110) cc_final: 0.8495 (m110) REVERT: d 1 MET cc_start: 0.8665 (tpt) cc_final: 0.8180 (mmm) REVERT: d 30 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8548 (tm-30) REVERT: d 35 TYR cc_start: 0.8763 (t80) cc_final: 0.8295 (t80) REVERT: d 43 THR cc_start: 0.7858 (p) cc_final: 0.7505 (p) REVERT: d 94 GLN cc_start: 0.8316 (mt0) cc_final: 0.7936 (pt0) REVERT: d 114 ARG cc_start: 0.9198 (mtm180) cc_final: 0.8995 (ptp-110) REVERT: d 117 ARG cc_start: 0.7410 (ptp-170) cc_final: 0.7081 (ptp-170) REVERT: d 145 ASP cc_start: 0.8069 (t0) cc_final: 0.7147 (t0) REVERT: d 155 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8414 (pm20) REVERT: d 168 ASP cc_start: 0.8234 (t0) cc_final: 0.7975 (t0) REVERT: d 175 ILE cc_start: 0.7223 (mm) cc_final: 0.6927 (mm) REVERT: d 184 ASP cc_start: 0.8275 (m-30) cc_final: 0.7628 (m-30) REVERT: d 191 ASP cc_start: 0.9175 (m-30) cc_final: 0.8964 (m-30) REVERT: e 19 PHE cc_start: 0.8476 (m-10) cc_final: 0.8206 (m-80) REVERT: e 24 VAL cc_start: 0.8748 (t) cc_final: 0.8476 (p) REVERT: e 25 MET cc_start: 0.8191 (pmm) cc_final: 0.7670 (pmm) REVERT: e 26 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7516 (mm-40) REVERT: e 37 MET cc_start: 0.6784 (tmm) cc_final: 0.6495 (tmm) REVERT: e 68 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8988 (mmtp) REVERT: e 95 MET cc_start: 0.9559 (tmm) cc_final: 0.9312 (tmm) REVERT: e 129 MET cc_start: 0.7488 (tmm) cc_final: 0.7214 (tmm) REVERT: e 132 ARG cc_start: 0.7240 (mmt90) cc_final: 0.6503 (mpt180) REVERT: e 156 THR cc_start: 0.7910 (m) cc_final: 0.7433 (p) REVERT: e 174 PHE cc_start: 0.7354 (m-80) cc_final: 0.7046 (m-10) REVERT: f 68 ARG cc_start: 0.8663 (tmt170) cc_final: 0.7865 (mmt180) REVERT: f 80 GLU cc_start: 0.9085 (tp30) cc_final: 0.8424 (tm-30) REVERT: f 82 PHE cc_start: 0.7080 (m-80) cc_final: 0.6661 (m-80) REVERT: f 87 GLN cc_start: 0.8242 (tt0) cc_final: 0.7700 (tm-30) REVERT: f 89 VAL cc_start: 0.5047 (t) cc_final: 0.4552 (p) REVERT: f 152 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7469 (tpp-160) REVERT: g 22 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8219 (mmmm) REVERT: g 42 LYS cc_start: 0.8171 (pttp) cc_final: 0.7765 (pptt) REVERT: g 55 GLU cc_start: 0.6552 (mp0) cc_final: 0.5627 (tp30) REVERT: h 52 MET cc_start: 0.0020 (mtp) cc_final: -0.1608 (tmm) REVERT: j 7 LYS cc_start: 0.8064 (mttt) cc_final: 0.7522 (tttp) REVERT: j 12 LYS cc_start: 0.8712 (pttt) cc_final: 0.8331 (pttm) REVERT: j 13 ARG cc_start: 0.7709 (ptp-170) cc_final: 0.7247 (ptm160) REVERT: j 14 ASP cc_start: 0.8723 (p0) cc_final: 0.8227 (p0) REVERT: j 50 THR cc_start: 0.8878 (p) cc_final: 0.8549 (m) REVERT: j 52 ASP cc_start: 0.8534 (p0) cc_final: 0.8217 (p0) REVERT: j 65 THR cc_start: 0.7986 (t) cc_final: 0.7664 (p) REVERT: j 136 GLN cc_start: 0.9080 (mm110) cc_final: 0.8611 (mm110) REVERT: k 3 GLN cc_start: 0.7877 (pt0) cc_final: 0.7662 (pt0) REVERT: k 6 THR cc_start: 0.8073 (p) cc_final: 0.7137 (p) REVERT: k 12 ASP cc_start: 0.7766 (p0) cc_final: 0.7357 (p0) REVERT: k 23 LYS cc_start: 0.7427 (tttt) cc_final: 0.7172 (tttt) REVERT: k 25 LEU cc_start: 0.8591 (mt) cc_final: 0.8249 (mt) REVERT: k 58 LEU cc_start: 0.8485 (mt) cc_final: 0.8185 (mt) REVERT: k 71 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8216 (mmm160) REVERT: k 84 CYS cc_start: 0.8529 (p) cc_final: 0.8016 (p) REVERT: k 88 ASN cc_start: 0.8847 (t0) cc_final: 0.8628 (t0) REVERT: k 89 ASN cc_start: 0.9363 (t0) cc_final: 0.9001 (m-40) REVERT: k 108 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7352 (ttp80) REVERT: l 21 ARG cc_start: 0.7625 (mmt-90) cc_final: 0.7112 (mmt-90) REVERT: l 59 ARG cc_start: 0.8395 (ttt180) cc_final: 0.7908 (mtp85) REVERT: l 73 ILE cc_start: 0.8405 (pt) cc_final: 0.8110 (pt) REVERT: l 84 LYS cc_start: 0.8431 (tmtt) cc_final: 0.8065 (tppt) REVERT: l 91 ASP cc_start: 0.8560 (m-30) cc_final: 0.8308 (p0) REVERT: l 105 ILE cc_start: 0.9275 (mm) cc_final: 0.8979 (tp) REVERT: l 106 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8315 (tm-30) REVERT: m 89 VAL cc_start: 0.7908 (p) cc_final: 0.7462 (p) REVERT: m 100 LYS cc_start: 0.8520 (tptm) cc_final: 0.8314 (tptm) REVERT: m 117 PHE cc_start: 0.7687 (m-10) cc_final: 0.7169 (m-80) REVERT: n 9 GLN cc_start: 0.8024 (pp30) cc_final: 0.7357 (pp30) REVERT: n 11 ASN cc_start: 0.7744 (t0) cc_final: 0.7476 (t0) REVERT: n 74 GLU cc_start: 0.8893 (tp30) cc_final: 0.8478 (tp30) REVERT: n 75 ILE cc_start: 0.8491 (mm) cc_final: 0.8002 (mt) REVERT: n 106 ASP cc_start: 0.8229 (p0) cc_final: 0.7945 (p0) REVERT: n 118 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7937 (ttp80) REVERT: o 12 THR cc_start: 0.8618 (p) cc_final: 0.8401 (p) REVERT: o 19 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8685 (mt0) REVERT: o 63 LYS cc_start: 0.9156 (tmmt) cc_final: 0.8663 (tmtt) REVERT: o 64 TYR cc_start: 0.8014 (t80) cc_final: 0.6504 (t80) REVERT: o 65 THR cc_start: 0.8612 (t) cc_final: 0.8306 (t) REVERT: o 92 PHE cc_start: 0.8993 (t80) cc_final: 0.8601 (t80) REVERT: o 115 LEU cc_start: 0.9015 (mm) cc_final: 0.8756 (mm) REVERT: p 6 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8334 (tm-30) REVERT: p 23 ASP cc_start: 0.8709 (m-30) cc_final: 0.7719 (m-30) REVERT: p 26 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6567 (tm-30) REVERT: p 28 LYS cc_start: 0.7309 (mmtp) cc_final: 0.7108 (mmtp) REVERT: p 51 ASN cc_start: 0.8587 (m110) cc_final: 0.8368 (m110) REVERT: p 62 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7808 (tptt) REVERT: p 63 ILE cc_start: 0.9033 (tp) cc_final: 0.8479 (tp) REVERT: p 64 SER cc_start: 0.9100 (m) cc_final: 0.8554 (m) REVERT: p 105 LYS cc_start: 0.8909 (pttm) cc_final: 0.8632 (pttp) REVERT: q 49 ARG cc_start: 0.7746 (mpt-90) cc_final: 0.6789 (mpp80) REVERT: q 60 TRP cc_start: 0.8505 (m-10) cc_final: 0.7608 (m-10) REVERT: q 71 ASN cc_start: 0.7914 (m-40) cc_final: 0.7620 (m-40) REVERT: r 6 GLN cc_start: 0.8745 (tt0) cc_final: 0.7801 (pp30) REVERT: r 10 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8525 (ptpp) REVERT: s 6 LYS cc_start: 0.8622 (tttm) cc_final: 0.8081 (tttp) REVERT: s 12 SER cc_start: 0.8822 (t) cc_final: 0.8572 (t) REVERT: s 23 LEU cc_start: 0.8950 (mt) cc_final: 0.8607 (mt) REVERT: s 40 ASN cc_start: 0.8410 (p0) cc_final: 0.8038 (p0) REVERT: s 66 ILE cc_start: 0.8602 (tp) cc_final: 0.8252 (mm) REVERT: s 70 LYS cc_start: 0.8552 (ttpp) cc_final: 0.7919 (mptt) REVERT: s 74 ILE cc_start: 0.8854 (tt) cc_final: 0.8650 (tt) REVERT: s 83 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7836 (mmmm) REVERT: s 84 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7596 (mmt-90) REVERT: s 86 MET cc_start: 0.8166 (tpt) cc_final: 0.7526 (tpp) REVERT: t 11 LEU cc_start: 0.9031 (mm) cc_final: 0.8777 (mm) REVERT: t 25 GLU cc_start: 0.8962 (tp30) cc_final: 0.8566 (tp30) REVERT: t 33 LYS cc_start: 0.8231 (mttm) cc_final: 0.7804 (mttp) REVERT: t 59 ASN cc_start: 0.8810 (m-40) cc_final: 0.8095 (m-40) REVERT: t 73 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7874 (ptp90) REVERT: t 89 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8124 (mm-30) REVERT: u 13 LEU cc_start: 0.8011 (mt) cc_final: 0.7531 (mt) REVERT: u 21 ARG cc_start: 0.8395 (ptp-110) cc_final: 0.7945 (ptp-110) REVERT: u 94 PHE cc_start: 0.7724 (p90) cc_final: 0.7169 (p90) REVERT: v 8 VAL cc_start: 0.8478 (t) cc_final: 0.8246 (t) REVERT: v 20 LEU cc_start: 0.8433 (pp) cc_final: 0.8219 (pp) REVERT: v 42 LEU cc_start: 0.8717 (pt) cc_final: 0.8340 (pt) REVERT: v 51 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8604 (tm-30) REVERT: v 73 LYS cc_start: 0.7996 (tptp) cc_final: 0.7557 (ttmm) REVERT: v 87 GLN cc_start: 0.8812 (mt0) cc_final: 0.8144 (mt0) REVERT: w 66 GLU cc_start: 0.7739 (mm-30) cc_final: 0.6989 (mt-10) REVERT: w 77 SER cc_start: 0.8424 (t) cc_final: 0.8087 (m) REVERT: x 39 VAL cc_start: 0.8630 (t) cc_final: 0.8370 (p) REVERT: x 44 ARG cc_start: 0.7153 (ptt90) cc_final: 0.6861 (ptt180) REVERT: y 1 MET cc_start: 0.7468 (ptm) cc_final: 0.7013 (ptm) REVERT: y 12 GLU cc_start: 0.8973 (tp30) cc_final: 0.8635 (tp30) REVERT: y 31 GLN cc_start: 0.9180 (tt0) cc_final: 0.8780 (tp-100) REVERT: z 15 ARG cc_start: 0.7359 (mmt-90) cc_final: 0.7139 (mmt-90) REVERT: z 31 ILE cc_start: 0.8124 (mm) cc_final: 0.7699 (mm) REVERT: z 55 LYS cc_start: 0.9189 (tmtt) cc_final: 0.8545 (tmtt) REVERT: z 56 VAL cc_start: 0.8930 (t) cc_final: 0.8318 (t) REVERT: B 9 ARG cc_start: 0.8564 (ptp90) cc_final: 0.8228 (ptp-110) REVERT: B 30 ASP cc_start: 0.7638 (t0) cc_final: 0.7157 (t70) REVERT: D 6 GLN cc_start: 0.8682 (mp10) cc_final: 0.8444 (mp10) REVERT: D 22 MET cc_start: 0.8774 (mmt) cc_final: 0.8351 (mmm) REVERT: E 48 MET cc_start: 0.8956 (mmp) cc_final: 0.8219 (mmm) REVERT: G 5 MET cc_start: 0.8691 (ptt) cc_final: 0.7853 (tpp) REVERT: G 17 HIS cc_start: 0.7645 (m-70) cc_final: 0.6251 (m90) REVERT: G 34 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7794 (tpp80) REVERT: G 46 VAL cc_start: 0.8308 (t) cc_final: 0.8010 (t) REVERT: G 50 ASN cc_start: 0.8604 (m110) cc_final: 0.8393 (m110) REVERT: G 67 LEU cc_start: 0.8523 (tp) cc_final: 0.8269 (tp) REVERT: G 68 PHE cc_start: 0.9258 (m-10) cc_final: 0.8883 (m-10) REVERT: G 92 ASN cc_start: 0.8124 (p0) cc_final: 0.7769 (p0) REVERT: G 99 MET cc_start: 0.8819 (mmp) cc_final: 0.8158 (tpp) REVERT: G 102 ASN cc_start: 0.8759 (t0) cc_final: 0.8390 (t0) REVERT: G 136 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7156 (ptm160) REVERT: G 139 GLU cc_start: 0.8526 (pp20) cc_final: 0.8228 (pp20) REVERT: G 161 PHE cc_start: 0.8255 (t80) cc_final: 0.8018 (t80) REVERT: G 191 ASP cc_start: 0.8656 (t0) cc_final: 0.8033 (t0) REVERT: G 197 PHE cc_start: 0.7973 (m-10) cc_final: 0.7699 (m-10) REVERT: H 10 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7353 (mtt-85) REVERT: H 68 HIS cc_start: 0.9031 (m90) cc_final: 0.8690 (m90) REVERT: H 81 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9034 (tm-30) REVERT: H 138 GLN cc_start: 0.9153 (mt0) cc_final: 0.8781 (mt0) REVERT: H 151 GLU cc_start: 0.7565 (tp30) cc_final: 0.7241 (tp30) REVERT: H 165 GLU cc_start: 0.6734 (tm-30) cc_final: 0.5988 (tt0) REVERT: H 168 ARG cc_start: 0.7529 (ptt180) cc_final: 0.7306 (ptm160) REVERT: I 12 ARG cc_start: 0.5207 (mtm180) cc_final: 0.3618 (ttm170) REVERT: I 67 LEU cc_start: 0.9077 (mt) cc_final: 0.8855 (mt) REVERT: I 71 PHE cc_start: 0.8706 (t80) cc_final: 0.8503 (t80) REVERT: I 89 LEU cc_start: 0.9384 (mt) cc_final: 0.9178 (mt) REVERT: I 190 LEU cc_start: 0.8315 (mp) cc_final: 0.8098 (mp) REVERT: J 11 GLN cc_start: 0.7926 (mp10) cc_final: 0.7643 (mp10) REVERT: J 28 ARG cc_start: 0.7579 (ptp-170) cc_final: 0.6562 (mtt180) REVERT: J 40 ASP cc_start: 0.8068 (p0) cc_final: 0.7464 (p0) REVERT: J 44 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: J 115 GLU cc_start: 0.8446 (pt0) cc_final: 0.7918 (tp30) REVERT: K 4 TYR cc_start: 0.7022 (m-80) cc_final: 0.6700 (m-80) REVERT: K 22 ILE cc_start: 0.8336 (mt) cc_final: 0.8011 (pt) REVERT: K 25 TYR cc_start: 0.7903 (m-80) cc_final: 0.7578 (m-80) REVERT: K 44 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6551 (ttp80) REVERT: K 45 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8002 (mtm-85) REVERT: K 61 LEU cc_start: 0.8461 (tt) cc_final: 0.7370 (mp) REVERT: K 62 MET cc_start: 0.8485 (mmp) cc_final: 0.8242 (mmm) REVERT: K 90 MET cc_start: 0.8063 (mpp) cc_final: 0.7703 (mpp) REVERT: L 30 MET cc_start: 0.8296 (tmm) cc_final: 0.7715 (ttt) REVERT: L 47 GLU cc_start: 0.7871 (pt0) cc_final: 0.7140 (mm-30) REVERT: L 78 ARG cc_start: 0.5997 (ptp90) cc_final: 0.5046 (ptp90) REVERT: L 91 ARG cc_start: 0.8491 (tpp-160) cc_final: 0.7921 (ptt-90) REVERT: L 122 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7887 (tp30) REVERT: M 2 MET cc_start: 0.8253 (tpt) cc_final: 0.8012 (tpp) REVERT: M 12 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7554 (mmm-85) REVERT: M 17 GLN cc_start: 0.8684 (mt0) cc_final: 0.8115 (mm-40) REVERT: M 57 GLU cc_start: 0.8800 (tp30) cc_final: 0.8539 (tp30) REVERT: M 63 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7890 (ptpp) REVERT: M 98 LEU cc_start: 0.9275 (pp) cc_final: 0.8085 (pp) REVERT: M 110 MET cc_start: 0.8786 (ptt) cc_final: 0.8545 (ptt) REVERT: M 123 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7586 (tm-30) REVERT: N 4 GLN cc_start: 0.6148 (tt0) cc_final: 0.4461 (mm-40) REVERT: N 5 TYR cc_start: 0.7099 (m-80) cc_final: 0.6762 (m-80) REVERT: N 19 PHE cc_start: 0.6891 (m-10) cc_final: 0.6160 (m-80) REVERT: N 61 ASP cc_start: 0.5618 (p0) cc_final: 0.5136 (p0) REVERT: N 106 ASP cc_start: 0.7438 (t70) cc_final: 0.7126 (t0) REVERT: O 7 ARG cc_start: 0.5921 (mtt180) cc_final: 0.3765 (mpt180) REVERT: P 14 GLN cc_start: 0.8337 (mp10) cc_final: 0.8011 (mp10) REVERT: P 28 ASN cc_start: 0.7418 (t0) cc_final: 0.7071 (t0) REVERT: P 41 LEU cc_start: 0.8953 (pt) cc_final: 0.8710 (pt) REVERT: P 45 THR cc_start: 0.8076 (p) cc_final: 0.7452 (p) REVERT: P 68 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8204 (mtp-110) REVERT: P 69 CYS cc_start: 0.8828 (t) cc_final: 0.8570 (t) REVERT: P 80 ASN cc_start: 0.8358 (m-40) cc_final: 0.7210 (p0) REVERT: P 122 PRO cc_start: 0.9222 (Cg_exo) cc_final: 0.9021 (Cg_endo) REVERT: P 124 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7378 (mmtm) REVERT: Q 35 ARG cc_start: 0.8391 (mmm160) cc_final: 0.7790 (tpt170) REVERT: Q 52 CYS cc_start: 0.8199 (p) cc_final: 0.6637 (t) REVERT: Q 65 TYR cc_start: 0.8701 (t80) cc_final: 0.8395 (t80) REVERT: Q 66 ILE cc_start: 0.8860 (mm) cc_final: 0.8368 (mp) REVERT: Q 75 GLU cc_start: 0.8904 (mp0) cc_final: 0.8326 (mp0) REVERT: R 30 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8475 (ptpt) REVERT: R 51 GLN cc_start: 0.8384 (mt0) cc_final: 0.8017 (mp10) REVERT: R 76 ILE cc_start: 0.8467 (mt) cc_final: 0.8165 (tp) REVERT: R 80 MET cc_start: 0.7912 (mtm) cc_final: 0.7229 (mpp) REVERT: R 82 LEU cc_start: 0.8484 (tt) cc_final: 0.8262 (tt) REVERT: R 84 CYS cc_start: 0.6458 (m) cc_final: 0.3939 (m) REVERT: R 106 ARG cc_start: 0.7657 (mmp-170) cc_final: 0.7358 (mmp80) REVERT: R 109 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8249 (mtpt) REVERT: S 53 ASP cc_start: 0.7826 (m-30) cc_final: 0.7261 (p0) REVERT: S 82 LYS cc_start: 0.7336 (mmmt) cc_final: 0.7012 (mmmt) REVERT: T 9 LYS cc_start: 0.9094 (mmtm) cc_final: 0.8837 (mmtm) REVERT: T 48 ASP cc_start: 0.6690 (t0) cc_final: 0.6140 (t0) REVERT: T 49 HIS cc_start: 0.8713 (m-70) cc_final: 0.8486 (m-70) REVERT: T 63 ARG cc_start: 0.8874 (mmm160) cc_final: 0.8647 (mmm160) REVERT: U 4 ILE cc_start: 0.7831 (mt) cc_final: 0.7567 (mm) REVERT: U 17 TYR cc_start: 0.7834 (m-80) cc_final: 0.7480 (m-80) REVERT: V 32 ILE cc_start: 0.9292 (tp) cc_final: 0.8923 (tp) REVERT: V 33 TYR cc_start: 0.8860 (m-80) cc_final: 0.8268 (m-80) REVERT: V 73 THR cc_start: 0.6863 (t) cc_final: 0.6498 (t) REVERT: W 53 GLN cc_start: 0.8651 (tt0) cc_final: 0.7962 (tp40) REVERT: X 11 ASP cc_start: 0.7242 (t0) cc_final: 0.6848 (t70) REVERT: X 72 GLU cc_start: 0.8414 (tt0) cc_final: 0.7813 (tt0) REVERT: Y 32 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8893 (mmtt) REVERT: Y 39 GLU cc_start: 0.8057 (tp30) cc_final: 0.7121 (tm-30) REVERT: Y 56 ILE cc_start: 0.8787 (mm) cc_final: 0.8553 (mm) REVERT: Y 69 ASN cc_start: 0.8532 (m-40) cc_final: 0.8121 (m110) REVERT: Z 33 ARG cc_start: 0.8382 (ppt170) cc_final: 0.7576 (tmm160) REVERT: a 30 LEU cc_start: 0.4278 (pt) cc_final: 0.3932 (mp) outliers start: 1 outliers final: 0 residues processed: 1887 average time/residue: 1.5304 time to fit residues: 4945.8079 Evaluate side-chains 1629 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1629 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 10.0000 chunk 406 optimal weight: 4.9990 chunk 608 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 647 optimal weight: 10.0000 chunk 694 optimal weight: 40.0000 chunk 503 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 800 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 HIS ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 142 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 GLN k 82 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 76 HIS q 19 GLN q 51 GLN ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN D 29 GLN G 88 GLN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS S 3 GLN T 34 GLN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 1.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 163139 Z= 0.323 Angle : 0.698 16.432 244082 Z= 0.356 Chirality : 0.039 0.312 31220 Planarity : 0.006 0.090 13080 Dihedral : 23.552 175.230 81722 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.80 % Favored : 90.08 % Rotamer: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.43 (0.10), residues: 5919 helix: -0.64 (0.12), residues: 1890 sheet: -1.54 (0.16), residues: 955 loop : -2.31 (0.10), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP b 212 HIS 0.021 0.002 HIS P 117 PHE 0.039 0.003 PHE D 18 TYR 0.042 0.002 TYR e 82 ARG 0.023 0.001 ARG e 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1856 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1855 time to evaluate : 8.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: b 12 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.6805 (tpm170) REVERT: b 34 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7505 (mm-30) REVERT: b 78 GLU cc_start: 0.8592 (tt0) cc_final: 0.8252 (tt0) REVERT: b 82 TYR cc_start: 0.8114 (t80) cc_final: 0.7602 (t80) REVERT: b 97 ASP cc_start: 0.8186 (p0) cc_final: 0.7707 (p0) REVERT: b 184 GLU cc_start: 0.7489 (mp0) cc_final: 0.7177 (mp0) REVERT: c 11 MET cc_start: 0.8039 (ttm) cc_final: 0.7641 (ttm) REVERT: c 42 ASN cc_start: 0.8947 (m-40) cc_final: 0.8146 (t0) REVERT: c 80 TRP cc_start: 0.8450 (m-90) cc_final: 0.7417 (m-90) REVERT: c 126 ASN cc_start: 0.8759 (m110) cc_final: 0.8543 (m110) REVERT: d 1 MET cc_start: 0.8886 (tpt) cc_final: 0.8601 (mmp) REVERT: d 16 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8140 (tm-30) REVERT: d 30 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8529 (tm-30) REVERT: d 35 TYR cc_start: 0.8757 (t80) cc_final: 0.8212 (t80) REVERT: d 43 THR cc_start: 0.7893 (p) cc_final: 0.7536 (p) REVERT: d 94 GLN cc_start: 0.8208 (mt0) cc_final: 0.7927 (pt0) REVERT: d 114 ARG cc_start: 0.9239 (mtm180) cc_final: 0.9038 (ptp-110) REVERT: d 145 ASP cc_start: 0.8153 (t0) cc_final: 0.7344 (t0) REVERT: d 155 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8584 (pm20) REVERT: d 168 ASP cc_start: 0.8222 (t0) cc_final: 0.7911 (t0) REVERT: d 175 ILE cc_start: 0.7280 (mm) cc_final: 0.6977 (mm) REVERT: d 184 ASP cc_start: 0.8442 (m-30) cc_final: 0.7966 (m-30) REVERT: d 191 ASP cc_start: 0.9166 (m-30) cc_final: 0.8936 (m-30) REVERT: e 26 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7787 (mm-40) REVERT: e 41 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6986 (tm-30) REVERT: e 68 LYS cc_start: 0.9266 (mmtm) cc_final: 0.9004 (mmtp) REVERT: e 95 MET cc_start: 0.9593 (tmm) cc_final: 0.9327 (tmm) REVERT: e 113 PHE cc_start: 0.6760 (t80) cc_final: 0.6517 (t80) REVERT: e 124 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7250 (tpp80) REVERT: e 129 MET cc_start: 0.7527 (tmm) cc_final: 0.7048 (tmm) REVERT: e 133 GLU cc_start: 0.7632 (tp30) cc_final: 0.7232 (tp30) REVERT: e 156 THR cc_start: 0.7772 (m) cc_final: 0.7276 (p) REVERT: e 174 PHE cc_start: 0.7356 (m-80) cc_final: 0.7077 (m-10) REVERT: f 38 ASP cc_start: 0.9069 (p0) cc_final: 0.8504 (p0) REVERT: f 68 ARG cc_start: 0.8699 (tmt170) cc_final: 0.7946 (mmt180) REVERT: f 80 GLU cc_start: 0.9055 (tp30) cc_final: 0.8374 (tm-30) REVERT: f 82 PHE cc_start: 0.7117 (m-80) cc_final: 0.6752 (m-80) REVERT: f 86 LEU cc_start: 0.7505 (mm) cc_final: 0.7095 (mm) REVERT: f 87 GLN cc_start: 0.8287 (tt0) cc_final: 0.7694 (tm-30) REVERT: f 89 VAL cc_start: 0.4833 (t) cc_final: 0.4299 (p) REVERT: f 152 ARG cc_start: 0.8248 (tpp-160) cc_final: 0.7458 (tpp-160) REVERT: g 22 LYS cc_start: 0.8300 (mmmm) cc_final: 0.8077 (mmmm) REVERT: g 25 TYR cc_start: 0.7622 (t80) cc_final: 0.7383 (t80) REVERT: g 42 LYS cc_start: 0.8228 (pttp) cc_final: 0.7903 (pptt) REVERT: g 147 VAL cc_start: 0.8458 (t) cc_final: 0.8194 (p) REVERT: h 52 MET cc_start: -0.0161 (mtp) cc_final: -0.1497 (tmm) REVERT: h 86 MET cc_start: 0.0960 (tpp) cc_final: 0.0286 (tpp) REVERT: j 7 LYS cc_start: 0.8189 (mttt) cc_final: 0.7585 (tttp) REVERT: j 9 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7953 (mm-30) REVERT: j 12 LYS cc_start: 0.8730 (pttt) cc_final: 0.8372 (pttm) REVERT: j 14 ASP cc_start: 0.8884 (p0) cc_final: 0.8183 (p0) REVERT: j 50 THR cc_start: 0.8909 (p) cc_final: 0.8610 (m) REVERT: j 52 ASP cc_start: 0.8586 (p0) cc_final: 0.8322 (p0) REVERT: j 65 THR cc_start: 0.7936 (t) cc_final: 0.7577 (p) REVERT: j 136 GLN cc_start: 0.9097 (mm110) cc_final: 0.8627 (mm110) REVERT: k 6 THR cc_start: 0.8484 (p) cc_final: 0.8213 (p) REVERT: k 25 LEU cc_start: 0.8664 (mt) cc_final: 0.8312 (mt) REVERT: k 53 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8078 (mmmt) REVERT: k 54 LYS cc_start: 0.9048 (tttp) cc_final: 0.8578 (tptm) REVERT: k 58 LEU cc_start: 0.8487 (mt) cc_final: 0.8117 (mt) REVERT: k 71 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8275 (mmm160) REVERT: k 84 CYS cc_start: 0.8790 (p) cc_final: 0.8363 (p) REVERT: k 88 ASN cc_start: 0.8917 (t0) cc_final: 0.8702 (t0) REVERT: k 89 ASN cc_start: 0.9279 (t0) cc_final: 0.8754 (m-40) REVERT: k 108 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7298 (tmm-80) REVERT: l 21 ARG cc_start: 0.7764 (mmt-90) cc_final: 0.7196 (mmt-90) REVERT: l 59 ARG cc_start: 0.8405 (ttt180) cc_final: 0.7630 (ttt90) REVERT: l 66 PHE cc_start: 0.8611 (p90) cc_final: 0.7532 (p90) REVERT: l 73 ILE cc_start: 0.8386 (pt) cc_final: 0.8082 (pt) REVERT: l 84 LYS cc_start: 0.8521 (tmtt) cc_final: 0.8199 (tppt) REVERT: l 91 ASP cc_start: 0.8760 (m-30) cc_final: 0.8371 (p0) REVERT: l 105 ILE cc_start: 0.9204 (mm) cc_final: 0.8941 (tp) REVERT: m 31 PHE cc_start: 0.8424 (m-10) cc_final: 0.8072 (m-10) REVERT: m 89 VAL cc_start: 0.7893 (p) cc_final: 0.7448 (p) REVERT: m 100 LYS cc_start: 0.8520 (tptm) cc_final: 0.8274 (tptm) REVERT: m 105 MET cc_start: 0.7353 (mtm) cc_final: 0.7139 (ptp) REVERT: n 9 GLN cc_start: 0.7984 (pp30) cc_final: 0.7319 (pp30) REVERT: n 11 ASN cc_start: 0.7815 (t0) cc_final: 0.7589 (t0) REVERT: n 74 GLU cc_start: 0.8858 (tp30) cc_final: 0.8493 (tp30) REVERT: n 75 ILE cc_start: 0.8473 (mm) cc_final: 0.7993 (mt) REVERT: n 106 ASP cc_start: 0.8182 (p0) cc_final: 0.7860 (p0) REVERT: n 118 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7910 (ttp80) REVERT: o 12 THR cc_start: 0.8846 (p) cc_final: 0.8642 (p) REVERT: o 64 TYR cc_start: 0.8102 (t80) cc_final: 0.6633 (t80) REVERT: o 65 THR cc_start: 0.8619 (t) cc_final: 0.8332 (t) REVERT: o 76 LYS cc_start: 0.9457 (ptpp) cc_final: 0.9233 (ptpp) REVERT: o 92 PHE cc_start: 0.8950 (t80) cc_final: 0.8598 (t80) REVERT: o 95 SER cc_start: 0.8145 (m) cc_final: 0.7581 (p) REVERT: o 112 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8671 (mt-10) REVERT: o 115 LEU cc_start: 0.9019 (mm) cc_final: 0.8811 (mm) REVERT: p 23 ASP cc_start: 0.8582 (m-30) cc_final: 0.7242 (m-30) REVERT: p 51 ASN cc_start: 0.8629 (m110) cc_final: 0.8398 (m110) REVERT: p 73 PHE cc_start: 0.8886 (m-10) cc_final: 0.8643 (m-10) REVERT: p 91 VAL cc_start: 0.9194 (m) cc_final: 0.8971 (p) REVERT: p 105 LYS cc_start: 0.8878 (pttm) cc_final: 0.8576 (pttp) REVERT: q 27 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8375 (mtp85) REVERT: q 49 ARG cc_start: 0.7778 (mpt-90) cc_final: 0.6980 (mpp80) REVERT: q 60 TRP cc_start: 0.8660 (m-10) cc_final: 0.7796 (m-10) REVERT: r 6 GLN cc_start: 0.8801 (tt0) cc_final: 0.7875 (pp30) REVERT: r 18 GLN cc_start: 0.9013 (tp40) cc_final: 0.8743 (tp-100) REVERT: r 24 LYS cc_start: 0.7494 (tppt) cc_final: 0.6925 (tptm) REVERT: s 3 THR cc_start: 0.8770 (m) cc_final: 0.7662 (m) REVERT: s 6 LYS cc_start: 0.8627 (tttm) cc_final: 0.8359 (tttm) REVERT: s 12 SER cc_start: 0.8841 (t) cc_final: 0.8609 (t) REVERT: s 23 LEU cc_start: 0.8980 (mt) cc_final: 0.8533 (mt) REVERT: s 40 ASN cc_start: 0.8427 (p0) cc_final: 0.8071 (p0) REVERT: s 66 ILE cc_start: 0.8663 (tp) cc_final: 0.8295 (mm) REVERT: s 70 LYS cc_start: 0.8611 (ttpp) cc_final: 0.7932 (mptt) REVERT: s 86 MET cc_start: 0.8100 (tpt) cc_final: 0.7469 (tpp) REVERT: t 11 LEU cc_start: 0.9051 (mm) cc_final: 0.8822 (mm) REVERT: t 12 ARG cc_start: 0.8850 (tpp-160) cc_final: 0.8456 (tpp80) REVERT: t 25 GLU cc_start: 0.8977 (tp30) cc_final: 0.8599 (tp30) REVERT: t 59 ASN cc_start: 0.8754 (m-40) cc_final: 0.8018 (m-40) REVERT: t 73 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7873 (ptp90) REVERT: u 13 LEU cc_start: 0.7879 (mt) cc_final: 0.7349 (mt) REVERT: u 21 ARG cc_start: 0.8462 (ptp-110) cc_final: 0.7951 (ptp-110) REVERT: u 94 PHE cc_start: 0.7811 (p90) cc_final: 0.7198 (p90) REVERT: v 51 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8454 (tm-30) REVERT: v 73 LYS cc_start: 0.8072 (tptp) cc_final: 0.7610 (ttmm) REVERT: v 87 GLN cc_start: 0.8807 (mt0) cc_final: 0.8123 (mt0) REVERT: w 19 VAL cc_start: 0.9109 (t) cc_final: 0.8884 (t) REVERT: w 66 GLU cc_start: 0.7819 (mm-30) cc_final: 0.6951 (mt-10) REVERT: w 77 SER cc_start: 0.8318 (t) cc_final: 0.8088 (m) REVERT: x 5 GLN cc_start: 0.8754 (mm110) cc_final: 0.8092 (mp10) REVERT: x 17 ARG cc_start: 0.8320 (mmt-90) cc_final: 0.8117 (mmt-90) REVERT: x 39 VAL cc_start: 0.8673 (t) cc_final: 0.8409 (p) REVERT: x 44 ARG cc_start: 0.7150 (ptt90) cc_final: 0.6886 (ptt180) REVERT: y 12 GLU cc_start: 0.8959 (tp30) cc_final: 0.8618 (tp30) REVERT: y 31 GLN cc_start: 0.9111 (tt0) cc_final: 0.8746 (tp-100) REVERT: z 3 THR cc_start: 0.9109 (p) cc_final: 0.8907 (p) REVERT: z 31 ILE cc_start: 0.8274 (mm) cc_final: 0.7753 (mm) REVERT: z 46 MET cc_start: 0.8074 (mmm) cc_final: 0.7550 (mmm) REVERT: z 55 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8441 (tmtt) REVERT: z 56 VAL cc_start: 0.8755 (t) cc_final: 0.8153 (t) REVERT: B 9 ARG cc_start: 0.8574 (ptp90) cc_final: 0.8270 (ptp-110) REVERT: B 16 ARG cc_start: 0.7395 (mtt-85) cc_final: 0.7129 (mtt-85) REVERT: B 30 ASP cc_start: 0.7424 (t0) cc_final: 0.6947 (t70) REVERT: D 22 MET cc_start: 0.8765 (mmt) cc_final: 0.8097 (mmm) REVERT: E 48 MET cc_start: 0.8929 (mmp) cc_final: 0.8191 (mmm) REVERT: E 58 ILE cc_start: 0.8499 (mt) cc_final: 0.8081 (pt) REVERT: F 4 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7472 (mmp80) REVERT: G 5 MET cc_start: 0.8776 (ptt) cc_final: 0.7875 (tpp) REVERT: G 6 ARG cc_start: 0.9338 (mmm160) cc_final: 0.8647 (tpm170) REVERT: G 9 LEU cc_start: 0.9035 (tp) cc_final: 0.8487 (tp) REVERT: G 17 HIS cc_start: 0.7702 (m-70) cc_final: 0.6393 (m-70) REVERT: G 34 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7594 (tpp80) REVERT: G 46 VAL cc_start: 0.8316 (t) cc_final: 0.7986 (t) REVERT: G 50 ASN cc_start: 0.8637 (m110) cc_final: 0.8406 (m110) REVERT: G 55 GLU cc_start: 0.8796 (pp20) cc_final: 0.8480 (pp20) REVERT: G 67 LEU cc_start: 0.8550 (tp) cc_final: 0.8332 (tp) REVERT: G 68 PHE cc_start: 0.9292 (m-10) cc_final: 0.9064 (m-10) REVERT: G 92 ASN cc_start: 0.8139 (p0) cc_final: 0.7740 (p0) REVERT: G 99 MET cc_start: 0.8614 (mmp) cc_final: 0.7912 (tpp) REVERT: G 136 ARG cc_start: 0.7952 (ptm-80) cc_final: 0.7239 (ptm160) REVERT: G 139 GLU cc_start: 0.8543 (pp20) cc_final: 0.8235 (pp20) REVERT: G 161 PHE cc_start: 0.8255 (t80) cc_final: 0.7936 (t80) REVERT: H 10 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7243 (mtt-85) REVERT: H 68 HIS cc_start: 0.9021 (m90) cc_final: 0.8747 (m90) REVERT: H 138 GLN cc_start: 0.9145 (mt0) cc_final: 0.8790 (mt0) REVERT: H 151 GLU cc_start: 0.7464 (tp30) cc_final: 0.7207 (tp30) REVERT: I 50 TYR cc_start: 0.7213 (t80) cc_final: 0.6973 (t80) REVERT: I 67 LEU cc_start: 0.9063 (mt) cc_final: 0.8853 (mt) REVERT: I 71 PHE cc_start: 0.8824 (t80) cc_final: 0.8549 (t80) REVERT: I 96 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7650 (mtt90) REVERT: I 194 ILE cc_start: 0.8192 (mm) cc_final: 0.7824 (pt) REVERT: I 195 ASN cc_start: 0.7591 (t0) cc_final: 0.7355 (t0) REVERT: J 11 GLN cc_start: 0.7889 (mp10) cc_final: 0.7649 (mp10) REVERT: J 28 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.6600 (mtt180) REVERT: J 40 ASP cc_start: 0.8026 (p0) cc_final: 0.7455 (p0) REVERT: K 25 TYR cc_start: 0.8011 (m-80) cc_final: 0.7582 (m-80) REVERT: K 44 ARG cc_start: 0.7384 (ttp80) cc_final: 0.7105 (ttp80) REVERT: K 47 LEU cc_start: 0.8913 (tp) cc_final: 0.8412 (tp) REVERT: K 61 LEU cc_start: 0.8496 (tt) cc_final: 0.7451 (mp) REVERT: K 62 MET cc_start: 0.8408 (mmp) cc_final: 0.8040 (mmm) REVERT: L 29 LEU cc_start: 0.8269 (mm) cc_final: 0.8061 (mm) REVERT: L 71 THR cc_start: 0.9042 (p) cc_final: 0.7894 (p) REVERT: L 89 GLU cc_start: 0.9054 (pm20) cc_final: 0.8736 (tp30) REVERT: L 91 ARG cc_start: 0.8389 (tpp-160) cc_final: 0.7863 (ptt-90) REVERT: L 132 THR cc_start: 0.8016 (p) cc_final: 0.7639 (p) REVERT: L 135 LYS cc_start: 0.9307 (ptmm) cc_final: 0.8867 (pptt) REVERT: L 136 LYS cc_start: 0.8620 (tttt) cc_final: 0.8283 (mptt) REVERT: L 145 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8562 (mp0) REVERT: M 17 GLN cc_start: 0.8697 (mt0) cc_final: 0.8014 (mm-40) REVERT: M 63 LYS cc_start: 0.8187 (ptmt) cc_final: 0.7829 (ptpp) REVERT: M 123 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7512 (tm-30) REVERT: N 5 TYR cc_start: 0.7252 (m-80) cc_final: 0.7044 (m-80) REVERT: N 14 SER cc_start: 0.4009 (t) cc_final: 0.2844 (t) REVERT: N 19 PHE cc_start: 0.6785 (m-10) cc_final: 0.6280 (m-10) REVERT: N 61 ASP cc_start: 0.4589 (p0) cc_final: 0.4304 (p0) REVERT: N 74 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8116 (tp40) REVERT: N 106 ASP cc_start: 0.7685 (t70) cc_final: 0.7460 (t70) REVERT: O 7 ARG cc_start: 0.5891 (mtt180) cc_final: 0.3835 (mmt90) REVERT: O 42 LEU cc_start: 0.8439 (tp) cc_final: 0.7987 (mm) REVERT: O 45 ARG cc_start: 0.6539 (ptm-80) cc_final: 0.6198 (ptm160) REVERT: P 14 GLN cc_start: 0.8441 (mp10) cc_final: 0.8111 (mp10) REVERT: P 28 ASN cc_start: 0.7588 (t0) cc_final: 0.7272 (t0) REVERT: P 41 LEU cc_start: 0.9073 (pt) cc_final: 0.8861 (pt) REVERT: P 45 THR cc_start: 0.7976 (p) cc_final: 0.7385 (p) REVERT: P 51 PHE cc_start: 0.6554 (m-80) cc_final: 0.6287 (m-80) REVERT: P 63 GLN cc_start: 0.8635 (pt0) cc_final: 0.7955 (pm20) REVERT: P 68 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8223 (mtp-110) REVERT: P 69 CYS cc_start: 0.8907 (t) cc_final: 0.8705 (t) REVERT: P 78 ILE cc_start: 0.7885 (tt) cc_final: 0.7342 (tt) REVERT: P 80 ASN cc_start: 0.8246 (m-40) cc_final: 0.7172 (p0) REVERT: Q 35 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7899 (tpt170) REVERT: Q 37 TYR cc_start: 0.8282 (p90) cc_final: 0.7762 (p90) REVERT: Q 55 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: Q 60 PHE cc_start: 0.9093 (m-80) cc_final: 0.8745 (m-80) REVERT: Q 65 TYR cc_start: 0.8618 (t80) cc_final: 0.8369 (t80) REVERT: R 30 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8570 (ptpt) REVERT: R 79 LEU cc_start: 0.8034 (mt) cc_final: 0.7804 (mt) REVERT: R 80 MET cc_start: 0.8171 (mtm) cc_final: 0.7685 (mtm) REVERT: R 106 ARG cc_start: 0.7509 (mmp-170) cc_final: 0.7237 (mmp80) REVERT: S 46 LYS cc_start: 0.7370 (mppt) cc_final: 0.7155 (mmtp) REVERT: S 89 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.7373 (ptt-90) REVERT: T 48 ASP cc_start: 0.6688 (t0) cc_final: 0.6375 (t0) REVERT: T 49 HIS cc_start: 0.8486 (m-70) cc_final: 0.8234 (m-70) REVERT: T 63 ARG cc_start: 0.8917 (mmm160) cc_final: 0.8700 (mmm160) REVERT: T 77 TYR cc_start: 0.8362 (t80) cc_final: 0.8147 (t80) REVERT: U 4 ILE cc_start: 0.7993 (mt) cc_final: 0.7749 (mm) REVERT: U 17 TYR cc_start: 0.7865 (m-80) cc_final: 0.7523 (m-80) REVERT: U 53 ASP cc_start: 0.7245 (p0) cc_final: 0.6988 (p0) REVERT: V 32 ILE cc_start: 0.9289 (tp) cc_final: 0.8937 (tp) REVERT: V 33 TYR cc_start: 0.8937 (m-80) cc_final: 0.8325 (m-80) REVERT: V 73 THR cc_start: 0.6963 (t) cc_final: 0.6585 (t) REVERT: W 53 GLN cc_start: 0.8772 (tt0) cc_final: 0.8166 (tp40) REVERT: W 63 TYR cc_start: 0.9109 (t80) cc_final: 0.8510 (t80) REVERT: W 67 LEU cc_start: 0.8936 (mt) cc_final: 0.8726 (mt) REVERT: X 43 MET cc_start: 0.8902 (mpp) cc_final: 0.8512 (mpp) REVERT: X 72 GLU cc_start: 0.8399 (tt0) cc_final: 0.7860 (tt0) REVERT: Y 39 GLU cc_start: 0.8326 (tp30) cc_final: 0.7522 (tm-30) REVERT: Y 69 ASN cc_start: 0.8564 (m110) cc_final: 0.8211 (m110) REVERT: Z 33 ARG cc_start: 0.8395 (ppt170) cc_final: 0.7694 (tmm160) REVERT: a 30 LEU cc_start: 0.4570 (pt) cc_final: 0.4294 (mt) outliers start: 1 outliers final: 0 residues processed: 1855 average time/residue: 1.3514 time to fit residues: 4248.9664 Evaluate side-chains 1630 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1630 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 10.0000 chunk 976 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 949 optimal weight: 50.0000 chunk 975 optimal weight: 10.0000 chunk 571 optimal weight: 20.0000 chunk 413 optimal weight: 7.9990 chunk 745 optimal weight: 10.0000 chunk 291 optimal weight: 0.0670 chunk 857 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 overall best weight: 7.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 229 HIS c 49 GLN c 140 HIS d 165 HIS ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 142 GLN g 33 GLN ** k 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN p 65 ASN q 19 GLN ** q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS y 20 ASN z 19 HIS ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 1.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 163139 Z= 0.394 Angle : 0.771 16.294 244082 Z= 0.391 Chirality : 0.042 0.338 31220 Planarity : 0.007 0.124 13080 Dihedral : 23.657 175.008 81722 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.32 % Favored : 88.53 % Rotamer: Outliers : 0.02 % Allowed : 1.37 % Favored : 98.61 % 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: -2.56 (0.10), residues: 5919 helix: -0.74 (0.12), residues: 1881 sheet: -1.66 (0.16), residues: 960 loop : -2.36 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.003 TRP b 212 HIS 0.041 0.002 HIS J 82 PHE 0.035 0.003 PHE L 150 TYR 0.038 0.003 TYR T 77 ARG 0.031 0.001 ARG P 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1868 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1867 time to evaluate : 6.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 12 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.6655 (tpm170) REVERT: b 22 GLU cc_start: 0.8997 (pt0) cc_final: 0.8546 (pt0) REVERT: b 34 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8009 (mm-30) REVERT: b 78 GLU cc_start: 0.8543 (tt0) cc_final: 0.8254 (tt0) REVERT: b 92 LEU cc_start: 0.9321 (tp) cc_final: 0.9055 (tt) REVERT: b 97 ASP cc_start: 0.8086 (p0) cc_final: 0.7676 (p0) REVERT: b 132 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8413 (mmm160) REVERT: c 11 MET cc_start: 0.8214 (ttm) cc_final: 0.7858 (ttm) REVERT: c 42 ASN cc_start: 0.8806 (m-40) cc_final: 0.8096 (t0) REVERT: c 80 TRP cc_start: 0.8453 (m-90) cc_final: 0.7399 (m-90) REVERT: d 1 MET cc_start: 0.8926 (tpt) cc_final: 0.8653 (mmp) REVERT: d 22 ASP cc_start: 0.8114 (p0) cc_final: 0.7863 (p0) REVERT: d 30 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8527 (tm-30) REVERT: d 43 THR cc_start: 0.7761 (p) cc_final: 0.7378 (p) REVERT: d 94 GLN cc_start: 0.8265 (mt0) cc_final: 0.7915 (pt0) REVERT: d 145 ASP cc_start: 0.7904 (t0) cc_final: 0.6917 (t0) REVERT: d 155 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8710 (pm20) REVERT: d 168 ASP cc_start: 0.8312 (t0) cc_final: 0.8004 (t0) REVERT: d 175 ILE cc_start: 0.7320 (mm) cc_final: 0.7058 (mm) REVERT: d 184 ASP cc_start: 0.8072 (m-30) cc_final: 0.7497 (m-30) REVERT: e 26 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8032 (mm-40) REVERT: e 37 MET cc_start: 0.6710 (tmm) cc_final: 0.6306 (tmm) REVERT: e 41 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7330 (tm-30) REVERT: e 46 LYS cc_start: 0.9423 (mmpt) cc_final: 0.9107 (mmpt) REVERT: e 68 LYS cc_start: 0.9325 (mmtm) cc_final: 0.9087 (mmtp) REVERT: e 95 MET cc_start: 0.9620 (tmm) cc_final: 0.9356 (tmm) REVERT: e 113 PHE cc_start: 0.6843 (t80) cc_final: 0.6635 (t80) REVERT: e 129 MET cc_start: 0.7781 (tmm) cc_final: 0.7520 (tmm) REVERT: e 132 ARG cc_start: 0.7550 (mmt180) cc_final: 0.7256 (mmt180) REVERT: e 141 ASP cc_start: 0.9025 (p0) cc_final: 0.8798 (p0) REVERT: e 174 PHE cc_start: 0.7388 (m-80) cc_final: 0.7118 (m-10) REVERT: f 54 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7403 (mtp-110) REVERT: f 57 TYR cc_start: 0.7526 (m-80) cc_final: 0.7293 (m-80) REVERT: f 68 ARG cc_start: 0.8619 (tmt170) cc_final: 0.8371 (tmm160) REVERT: f 80 GLU cc_start: 0.9141 (tp30) cc_final: 0.8524 (tm-30) REVERT: f 82 PHE cc_start: 0.7228 (m-80) cc_final: 0.6851 (m-80) REVERT: f 86 LEU cc_start: 0.7663 (mm) cc_final: 0.7405 (mm) REVERT: f 87 GLN cc_start: 0.8348 (tt0) cc_final: 0.7659 (tm-30) REVERT: f 106 LEU cc_start: 0.8455 (mp) cc_final: 0.8227 (mp) REVERT: f 138 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8555 (tt0) REVERT: f 152 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7966 (tpp-160) REVERT: g 22 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7425 (mttt) REVERT: g 45 GLU cc_start: 0.9172 (pp20) cc_final: 0.8902 (pp20) REVERT: g 147 VAL cc_start: 0.8536 (t) cc_final: 0.8304 (p) REVERT: h 52 MET cc_start: 0.0120 (mtp) cc_final: -0.1338 (tmm) REVERT: i 16 MET cc_start: 0.2008 (tmm) cc_final: 0.1778 (tmm) REVERT: j 9 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8207 (mm-30) REVERT: j 12 LYS cc_start: 0.8754 (pttt) cc_final: 0.8386 (pttm) REVERT: j 14 ASP cc_start: 0.8749 (p0) cc_final: 0.7909 (p0) REVERT: j 52 ASP cc_start: 0.8625 (p0) cc_final: 0.8281 (p0) REVERT: j 65 THR cc_start: 0.7977 (t) cc_final: 0.7588 (p) REVERT: j 136 GLN cc_start: 0.9044 (mm110) cc_final: 0.8604 (mm110) REVERT: k 6 THR cc_start: 0.8649 (p) cc_final: 0.8212 (p) REVERT: k 12 ASP cc_start: 0.7643 (p0) cc_final: 0.7396 (p0) REVERT: k 25 LEU cc_start: 0.8679 (mt) cc_final: 0.8452 (mt) REVERT: k 30 ARG cc_start: 0.7496 (ttt180) cc_final: 0.7001 (tpt-90) REVERT: k 53 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8011 (mmmt) REVERT: k 54 LYS cc_start: 0.9029 (tttp) cc_final: 0.8726 (tptm) REVERT: k 58 LEU cc_start: 0.8555 (mt) cc_final: 0.8132 (mt) REVERT: k 71 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8232 (mmm160) REVERT: k 84 CYS cc_start: 0.8461 (p) cc_final: 0.7957 (p) REVERT: k 88 ASN cc_start: 0.8946 (t0) cc_final: 0.8668 (t0) REVERT: k 89 ASN cc_start: 0.9263 (t0) cc_final: 0.8792 (m-40) REVERT: k 108 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7352 (tmm-80) REVERT: l 21 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7098 (mmt-90) REVERT: l 59 ARG cc_start: 0.8549 (ttt180) cc_final: 0.7791 (ttt90) REVERT: l 73 ILE cc_start: 0.8431 (pt) cc_final: 0.8125 (pt) REVERT: l 84 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8329 (tppt) REVERT: l 91 ASP cc_start: 0.8974 (m-30) cc_final: 0.8532 (p0) REVERT: l 105 ILE cc_start: 0.9238 (mm) cc_final: 0.8999 (tp) REVERT: l 106 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8128 (tm-30) REVERT: m 89 VAL cc_start: 0.7817 (p) cc_final: 0.7403 (p) REVERT: m 100 LYS cc_start: 0.8501 (tptm) cc_final: 0.8287 (tptm) REVERT: m 117 PHE cc_start: 0.7749 (m-80) cc_final: 0.6912 (m-80) REVERT: n 9 GLN cc_start: 0.8110 (pp30) cc_final: 0.7381 (pp30) REVERT: n 11 ASN cc_start: 0.7795 (t0) cc_final: 0.7576 (t0) REVERT: n 72 ASP cc_start: 0.8149 (t0) cc_final: 0.7888 (t0) REVERT: n 74 GLU cc_start: 0.8898 (tp30) cc_final: 0.8502 (tp30) REVERT: n 75 ILE cc_start: 0.8262 (mm) cc_final: 0.7824 (mt) REVERT: n 106 ASP cc_start: 0.8314 (p0) cc_final: 0.8028 (p0) REVERT: n 107 ASN cc_start: 0.8584 (t0) cc_final: 0.8140 (t0) REVERT: n 118 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7873 (ttp80) REVERT: o 12 THR cc_start: 0.8957 (p) cc_final: 0.8750 (p) REVERT: o 63 LYS cc_start: 0.8916 (tmmt) cc_final: 0.8690 (tmtt) REVERT: o 64 TYR cc_start: 0.8122 (t80) cc_final: 0.6487 (t80) REVERT: o 65 THR cc_start: 0.8531 (t) cc_final: 0.8143 (t) REVERT: o 76 LYS cc_start: 0.9455 (ptpp) cc_final: 0.9251 (pttm) REVERT: o 92 PHE cc_start: 0.8958 (t80) cc_final: 0.8646 (t80) REVERT: o 95 SER cc_start: 0.8173 (m) cc_final: 0.7672 (p) REVERT: o 102 ARG cc_start: 0.8314 (mtm180) cc_final: 0.7773 (mtm-85) REVERT: o 112 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8464 (mt-10) REVERT: p 23 ASP cc_start: 0.8608 (m-30) cc_final: 0.7594 (m-30) REVERT: p 62 LYS cc_start: 0.8345 (tmtt) cc_final: 0.7914 (tptt) REVERT: p 63 ILE cc_start: 0.9119 (tp) cc_final: 0.8512 (tp) REVERT: p 64 SER cc_start: 0.9012 (m) cc_final: 0.8414 (m) REVERT: p 73 PHE cc_start: 0.8901 (m-10) cc_final: 0.8648 (m-10) REVERT: p 105 LYS cc_start: 0.8723 (pttm) cc_final: 0.8394 (pttp) REVERT: q 49 ARG cc_start: 0.7843 (mpt-90) cc_final: 0.6941 (mpp80) REVERT: q 60 TRP cc_start: 0.8684 (m-10) cc_final: 0.8103 (m-10) REVERT: r 6 GLN cc_start: 0.8583 (tt0) cc_final: 0.7740 (pp30) REVERT: r 18 GLN cc_start: 0.9040 (tp40) cc_final: 0.8776 (tp40) REVERT: r 37 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7263 (mp0) REVERT: s 3 THR cc_start: 0.8830 (m) cc_final: 0.7970 (m) REVERT: s 6 LYS cc_start: 0.8600 (tttm) cc_final: 0.8322 (tttm) REVERT: s 12 SER cc_start: 0.8836 (t) cc_final: 0.8573 (t) REVERT: s 23 LEU cc_start: 0.8997 (mt) cc_final: 0.8688 (mt) REVERT: s 39 THR cc_start: 0.7858 (p) cc_final: 0.7617 (p) REVERT: s 70 LYS cc_start: 0.8623 (ttpp) cc_final: 0.7962 (mptt) REVERT: t 11 LEU cc_start: 0.9083 (mm) cc_final: 0.8882 (mm) REVERT: t 12 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8193 (tpp80) REVERT: t 25 GLU cc_start: 0.9031 (tp30) cc_final: 0.8681 (tp30) REVERT: t 28 ASN cc_start: 0.8407 (t0) cc_final: 0.7805 (t0) REVERT: t 59 ASN cc_start: 0.8793 (m-40) cc_final: 0.7951 (m-40) REVERT: t 69 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8558 (tpp80) REVERT: u 13 LEU cc_start: 0.8170 (mt) cc_final: 0.7655 (mt) REVERT: u 21 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8142 (ptp-110) REVERT: u 94 PHE cc_start: 0.7936 (p90) cc_final: 0.7653 (p90) REVERT: v 20 LEU cc_start: 0.8392 (pp) cc_final: 0.8068 (pp) REVERT: v 51 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8400 (tm-30) REVERT: v 73 LYS cc_start: 0.8127 (tptp) cc_final: 0.7585 (ttmm) REVERT: v 87 GLN cc_start: 0.8721 (mt0) cc_final: 0.7909 (mt0) REVERT: w 66 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6962 (mt-10) REVERT: w 77 SER cc_start: 0.8330 (t) cc_final: 0.8043 (m) REVERT: w 79 GLU cc_start: 0.8291 (pp20) cc_final: 0.8024 (pp20) REVERT: x 17 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.8115 (mmt-90) REVERT: x 39 VAL cc_start: 0.8655 (t) cc_final: 0.8424 (p) REVERT: y 12 GLU cc_start: 0.8991 (tp30) cc_final: 0.8670 (tp30) REVERT: y 31 GLN cc_start: 0.9143 (tt0) cc_final: 0.8787 (tp-100) REVERT: z 15 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7992 (mmt-90) REVERT: z 30 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7379 (ptt90) REVERT: z 31 ILE cc_start: 0.8344 (mm) cc_final: 0.7929 (mm) REVERT: z 33 HIS cc_start: 0.7421 (t-90) cc_final: 0.7035 (t70) REVERT: z 55 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8319 (tmtt) REVERT: z 56 VAL cc_start: 0.8813 (t) cc_final: 0.8219 (t) REVERT: B 9 ARG cc_start: 0.8565 (ptp90) cc_final: 0.8265 (ptp-110) REVERT: B 30 ASP cc_start: 0.7406 (t0) cc_final: 0.6919 (t70) REVERT: D 6 GLN cc_start: 0.8725 (mp10) cc_final: 0.8385 (mp10) REVERT: D 22 MET cc_start: 0.8562 (mmt) cc_final: 0.8205 (mmm) REVERT: E 48 MET cc_start: 0.8835 (mmp) cc_final: 0.8622 (mmm) REVERT: E 58 ILE cc_start: 0.8514 (mt) cc_final: 0.8063 (pt) REVERT: G 5 MET cc_start: 0.8841 (ptt) cc_final: 0.7878 (tpp) REVERT: G 6 ARG cc_start: 0.9367 (mmm160) cc_final: 0.9150 (tpp80) REVERT: G 17 HIS cc_start: 0.7794 (m-70) cc_final: 0.6515 (m90) REVERT: G 34 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7536 (tpp80) REVERT: G 46 VAL cc_start: 0.8389 (t) cc_final: 0.8080 (t) REVERT: G 55 GLU cc_start: 0.8937 (pp20) cc_final: 0.8636 (pp20) REVERT: G 77 GLU cc_start: 0.8232 (pp20) cc_final: 0.7981 (pm20) REVERT: G 92 ASN cc_start: 0.8214 (p0) cc_final: 0.7822 (p0) REVERT: G 99 MET cc_start: 0.8567 (mmp) cc_final: 0.7999 (tpp) REVERT: G 136 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.7274 (ptm160) REVERT: G 139 GLU cc_start: 0.8501 (pp20) cc_final: 0.8275 (pp20) REVERT: G 161 PHE cc_start: 0.8268 (t80) cc_final: 0.7913 (t80) REVERT: H 10 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7432 (mtt-85) REVERT: H 26 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7825 (tppt) REVERT: H 68 HIS cc_start: 0.9028 (m90) cc_final: 0.8752 (m90) REVERT: H 138 GLN cc_start: 0.9132 (mt0) cc_final: 0.8802 (mt0) REVERT: I 67 LEU cc_start: 0.9021 (mt) cc_final: 0.8769 (mt) REVERT: I 71 PHE cc_start: 0.8822 (t80) cc_final: 0.8546 (t80) REVERT: I 89 LEU cc_start: 0.9281 (mt) cc_final: 0.9071 (mt) REVERT: I 96 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7722 (mtt90) REVERT: I 194 ILE cc_start: 0.8176 (mm) cc_final: 0.7739 (pt) REVERT: I 196 GLU cc_start: 0.7762 (pp20) cc_final: 0.7227 (pp20) REVERT: J 11 GLN cc_start: 0.7345 (mp10) cc_final: 0.7088 (mp10) REVERT: J 40 ASP cc_start: 0.7936 (p0) cc_final: 0.7449 (p0) REVERT: J 44 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7851 (mmm-85) REVERT: J 156 ARG cc_start: 0.6789 (ttp80) cc_final: 0.6431 (ttp80) REVERT: K 25 TYR cc_start: 0.7989 (m-80) cc_final: 0.7727 (m-80) REVERT: K 44 ARG cc_start: 0.7335 (ttp80) cc_final: 0.7081 (ttp80) REVERT: K 45 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8046 (mtm-85) REVERT: K 47 LEU cc_start: 0.8663 (tp) cc_final: 0.8258 (tp) REVERT: K 61 LEU cc_start: 0.8048 (tt) cc_final: 0.7772 (tt) REVERT: K 90 MET cc_start: 0.7748 (mpp) cc_final: 0.7423 (mpp) REVERT: L 30 MET cc_start: 0.7587 (ttt) cc_final: 0.7336 (ttt) REVERT: L 91 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7896 (ptt-90) REVERT: L 135 LYS cc_start: 0.9329 (ptmm) cc_final: 0.8841 (mptt) REVERT: L 145 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8689 (mp0) REVERT: M 17 GLN cc_start: 0.8752 (mt0) cc_final: 0.8093 (mt0) REVERT: M 42 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6799 (tm-30) REVERT: M 57 GLU cc_start: 0.8704 (tp30) cc_final: 0.8344 (tp30) REVERT: M 63 LYS cc_start: 0.8472 (ptmt) cc_final: 0.8102 (ptpp) REVERT: M 75 GLN cc_start: 0.7147 (mp10) cc_final: 0.6545 (mp10) REVERT: M 95 MET cc_start: 0.8012 (tpt) cc_final: 0.7753 (tpp) REVERT: M 123 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7343 (tm-30) REVERT: N 5 TYR cc_start: 0.6941 (m-80) cc_final: 0.6681 (m-80) REVERT: N 14 SER cc_start: 0.5212 (t) cc_final: 0.4437 (m) REVERT: N 19 PHE cc_start: 0.7100 (m-10) cc_final: 0.6435 (m-80) REVERT: N 61 ASP cc_start: 0.4447 (p0) cc_final: 0.4051 (p0) REVERT: N 106 ASP cc_start: 0.7967 (t70) cc_final: 0.7489 (t0) REVERT: N 118 ARG cc_start: 0.5421 (mtt180) cc_final: 0.5204 (mtt180) REVERT: O 7 ARG cc_start: 0.5976 (mtt180) cc_final: 0.3944 (mmt90) REVERT: O 42 LEU cc_start: 0.8477 (tp) cc_final: 0.8053 (mm) REVERT: O 45 ARG cc_start: 0.6644 (ptm-80) cc_final: 0.6328 (ptm-80) REVERT: P 14 GLN cc_start: 0.8412 (mp10) cc_final: 0.8093 (mp10) REVERT: P 28 ASN cc_start: 0.7556 (t0) cc_final: 0.7195 (t0) REVERT: P 41 LEU cc_start: 0.9093 (pt) cc_final: 0.8840 (pt) REVERT: P 45 THR cc_start: 0.8035 (p) cc_final: 0.7445 (p) REVERT: P 68 ARG cc_start: 0.9038 (mmm-85) cc_final: 0.8191 (mtp-110) REVERT: P 78 ILE cc_start: 0.7850 (tt) cc_final: 0.7380 (tt) REVERT: Q 33 CYS cc_start: 0.8258 (t) cc_final: 0.8025 (t) REVERT: Q 35 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7697 (tpt170) REVERT: Q 37 TYR cc_start: 0.8144 (p90) cc_final: 0.7774 (p90) REVERT: R 30 LYS cc_start: 0.9018 (ptpp) cc_final: 0.8666 (ptpt) REVERT: R 51 GLN cc_start: 0.8125 (mt0) cc_final: 0.7812 (mp10) REVERT: R 76 ILE cc_start: 0.8059 (tp) cc_final: 0.7838 (tp) REVERT: R 80 MET cc_start: 0.8436 (mtm) cc_final: 0.8122 (mtp) REVERT: R 82 LEU cc_start: 0.8219 (tt) cc_final: 0.7938 (tt) REVERT: R 106 ARG cc_start: 0.7560 (mmp-170) cc_final: 0.7244 (mmp80) REVERT: S 46 LYS cc_start: 0.7238 (mppt) cc_final: 0.7026 (mmtp) REVERT: S 53 ASP cc_start: 0.7886 (m-30) cc_final: 0.7273 (p0) REVERT: T 49 HIS cc_start: 0.8422 (m-70) cc_final: 0.8052 (m-70) REVERT: U 4 ILE cc_start: 0.7922 (mt) cc_final: 0.7694 (mm) REVERT: U 16 PHE cc_start: 0.7091 (t80) cc_final: 0.6551 (t80) REVERT: U 17 TYR cc_start: 0.7828 (m-80) cc_final: 0.7052 (m-80) REVERT: U 53 ASP cc_start: 0.7359 (p0) cc_final: 0.7086 (p0) REVERT: V 32 ILE cc_start: 0.9289 (tp) cc_final: 0.8900 (tp) REVERT: V 33 TYR cc_start: 0.8983 (m-80) cc_final: 0.8452 (m-80) REVERT: V 56 ASP cc_start: 0.8681 (p0) cc_final: 0.8457 (p0) REVERT: V 73 THR cc_start: 0.6959 (t) cc_final: 0.6522 (t) REVERT: W 50 TYR cc_start: 0.7252 (m-80) cc_final: 0.6950 (m-10) REVERT: W 53 GLN cc_start: 0.8900 (tt0) cc_final: 0.8259 (tp40) REVERT: W 63 TYR cc_start: 0.9052 (t80) cc_final: 0.8681 (t80) REVERT: W 65 SER cc_start: 0.8407 (t) cc_final: 0.8111 (t) REVERT: W 67 LEU cc_start: 0.8665 (mt) cc_final: 0.8451 (mt) REVERT: X 43 MET cc_start: 0.9042 (mpp) cc_final: 0.8695 (mpp) REVERT: X 72 GLU cc_start: 0.8367 (tt0) cc_final: 0.7973 (tt0) REVERT: Y 39 GLU cc_start: 0.8553 (tp30) cc_final: 0.7752 (tm-30) REVERT: Y 69 ASN cc_start: 0.8444 (m110) cc_final: 0.8105 (m-40) REVERT: Y 70 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8655 (tmtt) REVERT: Z 33 ARG cc_start: 0.8429 (ppt170) cc_final: 0.7809 (tmm160) REVERT: a 218 MET cc_start: -0.2278 (ttt) cc_final: -0.3956 (mmt) outliers start: 1 outliers final: 0 residues processed: 1868 average time/residue: 1.3724 time to fit residues: 4341.0484 Evaluate side-chains 1612 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1612 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 50.0000 chunk 623 optimal weight: 30.0000 chunk 1003 optimal weight: 10.0000 chunk 612 optimal weight: 10.0000 chunk 476 optimal weight: 5.9990 chunk 697 optimal weight: 20.0000 chunk 1053 optimal weight: 40.0000 chunk 969 optimal weight: 10.0000 chunk 838 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 647 optimal weight: 10.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 142 GLN ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN l 38 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN q 19 GLN q 51 GLN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN G 57 ASN G 88 GLN G 93 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS K 63 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 1.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 163139 Z= 0.428 Angle : 0.804 15.777 244082 Z= 0.406 Chirality : 0.043 0.365 31220 Planarity : 0.007 0.147 13080 Dihedral : 23.790 175.480 81722 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.29 % Favored : 88.60 % Rotamer: Outliers : 0.02 % Allowed : 0.65 % Favored : 99.33 % 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: -2.71 (0.10), residues: 5919 helix: -0.96 (0.11), residues: 1881 sheet: -1.62 (0.16), residues: 961 loop : -2.44 (0.10), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP b 212 HIS 0.014 0.002 HIS b 52 PHE 0.037 0.003 PHE D 18 TYR 0.063 0.003 TYR n 94 ARG 0.018 0.001 ARG B 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1849 time to evaluate : 6.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 4 LYS cc_start: 0.8542 (pttm) cc_final: 0.8305 (pttt) REVERT: b 20 ASN cc_start: 0.8293 (t0) cc_final: 0.8035 (t0) REVERT: b 78 GLU cc_start: 0.8780 (tt0) cc_final: 0.8404 (tt0) REVERT: b 81 GLU cc_start: 0.8747 (pm20) cc_final: 0.8447 (pm20) REVERT: b 97 ASP cc_start: 0.8131 (p0) cc_final: 0.7621 (p0) REVERT: b 132 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8140 (mmm-85) REVERT: b 212 TRP cc_start: 0.6659 (p90) cc_final: 0.5901 (p90) REVERT: c 11 MET cc_start: 0.8212 (ttm) cc_final: 0.7872 (ttm) REVERT: c 14 ILE cc_start: 0.8553 (tt) cc_final: 0.8326 (mt) REVERT: c 42 ASN cc_start: 0.8871 (m-40) cc_final: 0.8075 (t0) REVERT: c 80 TRP cc_start: 0.8686 (m-90) cc_final: 0.7541 (m-90) REVERT: c 94 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7754 (tm-30) REVERT: c 126 ASN cc_start: 0.8821 (m110) cc_final: 0.8614 (m110) REVERT: c 200 ASP cc_start: 0.8712 (m-30) cc_final: 0.8458 (m-30) REVERT: d 1 MET cc_start: 0.8893 (tpt) cc_final: 0.8276 (mmm) REVERT: d 30 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8598 (tm-30) REVERT: d 43 THR cc_start: 0.7768 (p) cc_final: 0.7386 (p) REVERT: d 94 GLN cc_start: 0.8309 (mt0) cc_final: 0.7964 (pt0) REVERT: d 124 PHE cc_start: 0.8012 (t80) cc_final: 0.7469 (t80) REVERT: d 145 ASP cc_start: 0.7900 (t0) cc_final: 0.6726 (t0) REVERT: d 155 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8746 (pm20) REVERT: d 168 ASP cc_start: 0.8417 (t0) cc_final: 0.8101 (t0) REVERT: d 175 ILE cc_start: 0.7380 (mm) cc_final: 0.7048 (mm) REVERT: d 181 ILE cc_start: 0.9242 (mm) cc_final: 0.8941 (tp) REVERT: d 184 ASP cc_start: 0.8235 (m-30) cc_final: 0.7827 (m-30) REVERT: d 191 ASP cc_start: 0.9227 (m-30) cc_final: 0.9021 (m-30) REVERT: e 37 MET cc_start: 0.7004 (tmm) cc_final: 0.6762 (tmm) REVERT: e 41 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7011 (tm-30) REVERT: e 95 MET cc_start: 0.9652 (tmm) cc_final: 0.9360 (tmm) REVERT: e 129 MET cc_start: 0.8058 (tmm) cc_final: 0.7719 (tmm) REVERT: e 132 ARG cc_start: 0.7607 (mmt180) cc_final: 0.6851 (mmm160) REVERT: e 141 ASP cc_start: 0.9057 (p0) cc_final: 0.8791 (p0) REVERT: e 174 PHE cc_start: 0.7044 (m-80) cc_final: 0.6746 (m-10) REVERT: f 54 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.7213 (mtp-110) REVERT: f 76 ILE cc_start: 0.9132 (mm) cc_final: 0.8912 (mm) REVERT: f 80 GLU cc_start: 0.9201 (tp30) cc_final: 0.8590 (tm-30) REVERT: f 82 PHE cc_start: 0.7313 (m-80) cc_final: 0.6787 (m-80) REVERT: f 86 LEU cc_start: 0.7699 (mm) cc_final: 0.7057 (mm) REVERT: f 87 GLN cc_start: 0.8249 (tt0) cc_final: 0.7724 (tm-30) REVERT: f 93 TYR cc_start: 0.8137 (m-80) cc_final: 0.7675 (m-80) REVERT: f 138 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8614 (tt0) REVERT: f 152 ARG cc_start: 0.8195 (tpp-160) cc_final: 0.7759 (tpp-160) REVERT: g 147 VAL cc_start: 0.8515 (t) cc_final: 0.8284 (p) REVERT: h 52 MET cc_start: 0.0446 (mtp) cc_final: -0.1442 (tmm) REVERT: j 7 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7071 (tttp) REVERT: j 9 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8063 (mm-30) REVERT: j 12 LYS cc_start: 0.8792 (pttt) cc_final: 0.8443 (pttm) REVERT: j 14 ASP cc_start: 0.8613 (p0) cc_final: 0.7756 (p0) REVERT: j 19 ASP cc_start: 0.8026 (t70) cc_final: 0.7809 (t0) REVERT: j 21 THR cc_start: 0.9207 (p) cc_final: 0.8778 (p) REVERT: j 52 ASP cc_start: 0.8722 (p0) cc_final: 0.8233 (p0) REVERT: j 61 LYS cc_start: 0.9394 (ttmm) cc_final: 0.9009 (ttpt) REVERT: j 65 THR cc_start: 0.8014 (t) cc_final: 0.7647 (p) REVERT: k 6 THR cc_start: 0.8143 (p) cc_final: 0.6775 (p) REVERT: k 53 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8130 (mmmt) REVERT: k 54 LYS cc_start: 0.9078 (tttp) cc_final: 0.8817 (tptm) REVERT: k 58 LEU cc_start: 0.8555 (mt) cc_final: 0.8144 (mt) REVERT: k 71 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8162 (mmm160) REVERT: k 84 CYS cc_start: 0.8550 (p) cc_final: 0.8337 (p) REVERT: k 89 ASN cc_start: 0.9286 (t0) cc_final: 0.8820 (m-40) REVERT: k 98 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7858 (mmp-170) REVERT: k 99 ILE cc_start: 0.9056 (mm) cc_final: 0.8715 (mt) REVERT: k 108 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7483 (tmm-80) REVERT: l 21 ARG cc_start: 0.7715 (mmt-90) cc_final: 0.7161 (mmt-90) REVERT: l 59 ARG cc_start: 0.8498 (ttt180) cc_final: 0.7743 (ttt90) REVERT: l 73 ILE cc_start: 0.8485 (pt) cc_final: 0.8201 (pt) REVERT: l 84 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8449 (tppt) REVERT: l 91 ASP cc_start: 0.9044 (m-30) cc_final: 0.8502 (p0) REVERT: l 106 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8114 (tm-30) REVERT: m 11 LYS cc_start: 0.7707 (mptt) cc_final: 0.7459 (mttp) REVERT: m 88 ASN cc_start: 0.7793 (t0) cc_final: 0.7522 (t0) REVERT: m 100 LYS cc_start: 0.8526 (tptm) cc_final: 0.8312 (tptm) REVERT: m 117 PHE cc_start: 0.7863 (m-80) cc_final: 0.6942 (m-80) REVERT: n 9 GLN cc_start: 0.8186 (pp30) cc_final: 0.7448 (pp30) REVERT: n 11 ASN cc_start: 0.7959 (t0) cc_final: 0.7611 (t0) REVERT: n 74 GLU cc_start: 0.8789 (tp30) cc_final: 0.8385 (tp30) REVERT: n 75 ILE cc_start: 0.8380 (mm) cc_final: 0.7889 (mt) REVERT: n 107 ASN cc_start: 0.8593 (t0) cc_final: 0.8344 (t0) REVERT: n 115 LEU cc_start: 0.8443 (mp) cc_final: 0.8184 (mp) REVERT: n 118 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7817 (ttp80) REVERT: o 47 VAL cc_start: 0.8968 (m) cc_final: 0.8623 (t) REVERT: o 63 LYS cc_start: 0.8882 (tmmt) cc_final: 0.8637 (tmtt) REVERT: o 64 TYR cc_start: 0.8162 (t80) cc_final: 0.6358 (t80) REVERT: o 65 THR cc_start: 0.8485 (t) cc_final: 0.8140 (t) REVERT: o 76 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9146 (pttm) REVERT: o 92 PHE cc_start: 0.9006 (t80) cc_final: 0.8699 (t80) REVERT: o 95 SER cc_start: 0.8054 (m) cc_final: 0.7608 (p) REVERT: o 112 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8475 (mt-10) REVERT: p 26 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7452 (tm-30) REVERT: p 49 ILE cc_start: 0.8962 (mt) cc_final: 0.8645 (pt) REVERT: p 51 ASN cc_start: 0.8562 (m110) cc_final: 0.8339 (m110) REVERT: p 62 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7783 (tptt) REVERT: p 63 ILE cc_start: 0.9164 (tp) cc_final: 0.8630 (tp) REVERT: p 64 SER cc_start: 0.8980 (m) cc_final: 0.8437 (m) REVERT: p 73 PHE cc_start: 0.8806 (m-10) cc_final: 0.8600 (m-10) REVERT: q 49 ARG cc_start: 0.7923 (mpt-90) cc_final: 0.7615 (mpp80) REVERT: q 60 TRP cc_start: 0.8691 (m-10) cc_final: 0.7821 (m-10) REVERT: q 110 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8605 (mm-30) REVERT: r 2 TYR cc_start: 0.7486 (p90) cc_final: 0.7177 (p90) REVERT: r 6 GLN cc_start: 0.8781 (tt0) cc_final: 0.7614 (pp30) REVERT: r 18 GLN cc_start: 0.9069 (tp40) cc_final: 0.8855 (tp40) REVERT: r 37 GLU cc_start: 0.7799 (mm-30) cc_final: 0.6991 (mp0) REVERT: r 95 ASP cc_start: 0.8479 (t70) cc_final: 0.8254 (t70) REVERT: s 3 THR cc_start: 0.8930 (m) cc_final: 0.8134 (m) REVERT: s 12 SER cc_start: 0.8918 (t) cc_final: 0.8677 (t) REVERT: s 23 LEU cc_start: 0.9102 (mt) cc_final: 0.8743 (mt) REVERT: s 39 THR cc_start: 0.7396 (p) cc_final: 0.7173 (p) REVERT: s 86 MET cc_start: 0.7997 (tpt) cc_final: 0.7396 (tpp) REVERT: t 12 ARG cc_start: 0.8728 (tpp-160) cc_final: 0.8220 (tpp80) REVERT: t 25 GLU cc_start: 0.8980 (tp30) cc_final: 0.8678 (tp30) REVERT: t 28 ASN cc_start: 0.8256 (t0) cc_final: 0.7568 (t0) REVERT: t 44 LYS cc_start: 0.9362 (mmtt) cc_final: 0.9012 (tptt) REVERT: t 59 ASN cc_start: 0.8785 (m-40) cc_final: 0.7948 (m-40) REVERT: u 67 SER cc_start: 0.7943 (m) cc_final: 0.7674 (m) REVERT: u 100 GLU cc_start: 0.8265 (mp0) cc_final: 0.7983 (mp0) REVERT: v 1 MET cc_start: 0.8114 (pmm) cc_final: 0.7369 (pmm) REVERT: v 34 LYS cc_start: 0.8733 (mppt) cc_final: 0.8429 (mmmm) REVERT: v 43 ASP cc_start: 0.8629 (m-30) cc_final: 0.8402 (m-30) REVERT: v 51 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8781 (tp40) REVERT: v 73 LYS cc_start: 0.8122 (tptp) cc_final: 0.7604 (ttmm) REVERT: v 87 GLN cc_start: 0.8690 (mt0) cc_final: 0.8118 (mt0) REVERT: w 66 GLU cc_start: 0.7843 (mm-30) cc_final: 0.6926 (mt-10) REVERT: w 77 SER cc_start: 0.8349 (t) cc_final: 0.7996 (m) REVERT: w 79 GLU cc_start: 0.8480 (pp20) cc_final: 0.8180 (pp20) REVERT: x 5 GLN cc_start: 0.8753 (mm110) cc_final: 0.8135 (mp10) REVERT: x 39 VAL cc_start: 0.8561 (t) cc_final: 0.8256 (p) REVERT: x 40 GLU cc_start: 0.7492 (tp30) cc_final: 0.7277 (tp30) REVERT: x 42 GLU cc_start: 0.7978 (mp0) cc_final: 0.7661 (mp0) REVERT: y 12 GLU cc_start: 0.9027 (tp30) cc_final: 0.8641 (tp30) REVERT: y 31 GLN cc_start: 0.9122 (tt0) cc_final: 0.8920 (tp-100) REVERT: y 56 LEU cc_start: 0.8648 (mt) cc_final: 0.8175 (mt) REVERT: y 59 GLU cc_start: 0.7981 (tt0) cc_final: 0.7640 (mt-10) REVERT: z 31 ILE cc_start: 0.8557 (mm) cc_final: 0.8236 (mm) REVERT: z 46 MET cc_start: 0.8124 (mmm) cc_final: 0.7746 (mmm) REVERT: z 55 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8439 (tmtt) REVERT: z 56 VAL cc_start: 0.8975 (t) cc_final: 0.8403 (t) REVERT: B 9 ARG cc_start: 0.8600 (ptp90) cc_final: 0.8347 (ptp-110) REVERT: B 30 ASP cc_start: 0.7229 (t0) cc_final: 0.6753 (t70) REVERT: B 47 TYR cc_start: 0.7468 (m-80) cc_final: 0.6970 (m-80) REVERT: D 3 ARG cc_start: 0.7550 (tpt170) cc_final: 0.7142 (tpt170) REVERT: D 22 MET cc_start: 0.8692 (mmt) cc_final: 0.8264 (mmm) REVERT: D 25 LYS cc_start: 0.8475 (pptt) cc_final: 0.7997 (pptt) REVERT: E 48 MET cc_start: 0.8887 (mmp) cc_final: 0.8656 (mmm) REVERT: E 58 ILE cc_start: 0.8587 (mt) cc_final: 0.8175 (pt) REVERT: F 12 ARG cc_start: 0.6140 (mtt90) cc_final: 0.5086 (mtt180) REVERT: G 5 MET cc_start: 0.8936 (ptt) cc_final: 0.8017 (tpp) REVERT: G 6 ARG cc_start: 0.9299 (mmm160) cc_final: 0.9053 (tpp80) REVERT: G 17 HIS cc_start: 0.7735 (m-70) cc_final: 0.6583 (m-70) REVERT: G 34 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7514 (tpp80) REVERT: G 67 LEU cc_start: 0.8436 (tp) cc_final: 0.8235 (tp) REVERT: G 68 PHE cc_start: 0.9237 (m-10) cc_final: 0.8858 (m-10) REVERT: G 99 MET cc_start: 0.8325 (mmp) cc_final: 0.7911 (tpp) REVERT: G 136 ARG cc_start: 0.7940 (ptm-80) cc_final: 0.7096 (ptm160) REVERT: G 139 GLU cc_start: 0.8531 (pp20) cc_final: 0.8308 (pp20) REVERT: G 161 PHE cc_start: 0.8288 (t80) cc_final: 0.7890 (t80) REVERT: G 197 PHE cc_start: 0.7919 (m-10) cc_final: 0.7671 (m-10) REVERT: H 10 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7540 (mtt-85) REVERT: H 68 HIS cc_start: 0.9051 (m90) cc_final: 0.8728 (m90) REVERT: H 71 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8168 (mmm160) REVERT: H 85 LYS cc_start: 0.8604 (tttt) cc_final: 0.8398 (ptmt) REVERT: H 135 ARG cc_start: 0.8501 (ptm160) cc_final: 0.7026 (mtm180) REVERT: H 138 GLN cc_start: 0.9119 (mt0) cc_final: 0.8741 (mt0) REVERT: H 165 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6591 (tm-30) REVERT: I 67 LEU cc_start: 0.8961 (mt) cc_final: 0.8720 (mt) REVERT: I 71 PHE cc_start: 0.8859 (t80) cc_final: 0.8525 (t80) REVERT: I 89 LEU cc_start: 0.9265 (mt) cc_final: 0.9058 (mt) REVERT: I 96 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7868 (mtt90) REVERT: I 140 ASP cc_start: 0.7354 (m-30) cc_final: 0.7126 (m-30) REVERT: I 194 ILE cc_start: 0.8005 (mm) cc_final: 0.7560 (pt) REVERT: I 195 ASN cc_start: 0.7776 (t0) cc_final: 0.7542 (t0) REVERT: I 196 GLU cc_start: 0.7728 (pp20) cc_final: 0.7285 (pp20) REVERT: I 201 GLU cc_start: 0.8470 (mp0) cc_final: 0.8257 (mp0) REVERT: J 11 GLN cc_start: 0.7163 (mp10) cc_final: 0.6768 (mp10) REVERT: J 19 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7951 (ttm170) REVERT: J 40 ASP cc_start: 0.7811 (p0) cc_final: 0.7153 (p0) REVERT: J 54 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7802 (tp30) REVERT: J 156 ARG cc_start: 0.6786 (ttp80) cc_final: 0.5856 (ttp-170) REVERT: K 24 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.7114 (mtm-85) REVERT: K 25 TYR cc_start: 0.8080 (m-80) cc_final: 0.7681 (m-80) REVERT: K 45 ARG cc_start: 0.8787 (mtm110) cc_final: 0.8030 (mtm-85) REVERT: K 47 LEU cc_start: 0.8669 (tp) cc_final: 0.8199 (tp) REVERT: K 61 LEU cc_start: 0.8235 (tt) cc_final: 0.7456 (mp) REVERT: K 62 MET cc_start: 0.8440 (mmp) cc_final: 0.7950 (mmm) REVERT: L 30 MET cc_start: 0.7877 (ttt) cc_final: 0.7441 (ttt) REVERT: L 135 LYS cc_start: 0.9348 (ptmm) cc_final: 0.8889 (mptt) REVERT: L 145 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8815 (mp0) REVERT: M 45 ILE cc_start: 0.8893 (mp) cc_final: 0.8664 (mp) REVERT: M 57 GLU cc_start: 0.8448 (tp30) cc_final: 0.8196 (tp30) REVERT: M 60 LEU cc_start: 0.8655 (mt) cc_final: 0.8454 (mt) REVERT: M 63 LYS cc_start: 0.8522 (ptmt) cc_final: 0.8113 (ptpp) REVERT: M 98 LEU cc_start: 0.8850 (pp) cc_final: 0.8617 (pt) REVERT: M 123 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7427 (tm-30) REVERT: N 19 PHE cc_start: 0.7222 (m-10) cc_final: 0.6525 (m-80) REVERT: N 45 MET cc_start: 0.8857 (pmm) cc_final: 0.8646 (pmm) REVERT: N 61 ASP cc_start: 0.4592 (p0) cc_final: 0.4284 (p0) REVERT: N 106 ASP cc_start: 0.8063 (t70) cc_final: 0.7859 (t0) REVERT: O 42 LEU cc_start: 0.8514 (tp) cc_final: 0.8046 (mm) REVERT: P 14 GLN cc_start: 0.8489 (mp10) cc_final: 0.8192 (mp10) REVERT: P 28 ASN cc_start: 0.7689 (t0) cc_final: 0.7337 (t0) REVERT: P 45 THR cc_start: 0.8236 (p) cc_final: 0.7654 (p) REVERT: P 68 ARG cc_start: 0.9065 (mmm-85) cc_final: 0.8189 (mtp-110) REVERT: P 111 ASP cc_start: 0.9000 (t70) cc_final: 0.8719 (t0) REVERT: Q 33 CYS cc_start: 0.8314 (t) cc_final: 0.7927 (t) REVERT: Q 37 TYR cc_start: 0.8058 (p90) cc_final: 0.7691 (p90) REVERT: R 30 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8730 (ptpt) REVERT: R 51 GLN cc_start: 0.8206 (mt0) cc_final: 0.7843 (mp10) REVERT: R 96 VAL cc_start: 0.8803 (p) cc_final: 0.8487 (m) REVERT: R 97 ARG cc_start: 0.6501 (mpt90) cc_final: 0.6242 (mmt-90) REVERT: S 46 LYS cc_start: 0.7181 (mppt) cc_final: 0.6969 (mmtp) REVERT: T 49 HIS cc_start: 0.8296 (m-70) cc_final: 0.8014 (m90) REVERT: T 84 LEU cc_start: 0.8417 (tp) cc_final: 0.7486 (tt) REVERT: U 4 ILE cc_start: 0.8002 (mt) cc_final: 0.7794 (mm) REVERT: U 12 LYS cc_start: 0.8398 (mmpt) cc_final: 0.7980 (mtmt) REVERT: U 16 PHE cc_start: 0.7226 (t80) cc_final: 0.6776 (t80) REVERT: U 17 TYR cc_start: 0.7889 (m-80) cc_final: 0.7503 (m-80) REVERT: V 25 GLU cc_start: 0.7926 (mp0) cc_final: 0.7566 (mp0) REVERT: V 32 ILE cc_start: 0.9276 (tp) cc_final: 0.8867 (tp) REVERT: V 33 TYR cc_start: 0.8970 (m-80) cc_final: 0.8420 (m-80) REVERT: V 61 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8671 (ttp-110) REVERT: V 73 THR cc_start: 0.6975 (t) cc_final: 0.6527 (t) REVERT: W 29 LYS cc_start: 0.9052 (ptpp) cc_final: 0.8778 (pttt) REVERT: W 50 TYR cc_start: 0.7265 (m-80) cc_final: 0.7009 (m-10) REVERT: W 53 GLN cc_start: 0.8949 (tt0) cc_final: 0.8225 (tp40) REVERT: W 65 SER cc_start: 0.8496 (t) cc_final: 0.8260 (t) REVERT: W 67 LEU cc_start: 0.8898 (mt) cc_final: 0.8643 (mt) REVERT: X 11 ASP cc_start: 0.7964 (p0) cc_final: 0.7255 (p0) REVERT: X 43 MET cc_start: 0.8996 (mpp) cc_final: 0.8693 (mpp) REVERT: X 72 GLU cc_start: 0.8369 (tt0) cc_final: 0.7958 (tt0) REVERT: Y 39 GLU cc_start: 0.8387 (tp30) cc_final: 0.7714 (tm-30) REVERT: Y 70 LYS cc_start: 0.8914 (tmtt) cc_final: 0.8530 (tmtt) REVERT: Z 33 ARG cc_start: 0.8468 (ppt170) cc_final: 0.7812 (tmm160) REVERT: a 214 ILE cc_start: 0.5464 (tt) cc_final: 0.5211 (mt) REVERT: a 218 MET cc_start: -0.1720 (ttt) cc_final: -0.3529 (mmt) outliers start: 1 outliers final: 0 residues processed: 1849 average time/residue: 1.3762 time to fit residues: 4312.2513 Evaluate side-chains 1600 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1600 time to evaluate : 6.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 9.9990 chunk 666 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 773 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 839 optimal weight: 40.0000 chunk 351 optimal weight: 9.9990 chunk 862 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 GLN ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 100 ASN f 142 GLN ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN q 19 GLN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 33 HIS ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 HIS ** P 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 ASN T 34 GLN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083134 restraints weight = 446394.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085209 restraints weight = 188676.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085094 restraints weight = 97384.482| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 1.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 163139 Z= 0.302 Angle : 0.703 14.575 244082 Z= 0.358 Chirality : 0.039 0.321 31220 Planarity : 0.006 0.084 13080 Dihedral : 23.743 175.403 81722 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.73 % Favored : 89.14 % Rotamer: Outliers : 0.04 % Allowed : 0.59 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.55 (0.10), residues: 5919 helix: -0.79 (0.12), residues: 1896 sheet: -1.58 (0.16), residues: 998 loop : -2.36 (0.11), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP b 212 HIS 0.017 0.002 HIS P 117 PHE 0.029 0.002 PHE n 80 TYR 0.024 0.002 TYR n 94 ARG 0.047 0.001 ARG e 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54961.32 seconds wall clock time: 953 minutes 56.17 seconds (57236.17 seconds total)