Starting phenix.real_space_refine on Sun Mar 24 19:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdg_21635/03_2024/6wdg_21635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdg_21635/03_2024/6wdg_21635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdg_21635/03_2024/6wdg_21635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdg_21635/03_2024/6wdg_21635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdg_21635/03_2024/6wdg_21635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdg_21635/03_2024/6wdg_21635_updated.pdb" } resolution = 3.3 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= 0.117 sd= 0.965 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 4727 5.49 5 S 154 5.16 5 C 74754 2.51 5 N 27663 2.21 5 O 41284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 34": "OE1" <-> "OE2" Residue "b ASP 65": "OD1" <-> "OD2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "b GLU 179": "OE1" <-> "OE2" Residue "b GLU 193": "OE1" <-> "OE2" Residue "b GLU 198": "OE1" <-> "OE2" Residue "b ASP 263": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 74": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 86": "OE1" <-> "OE2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 122": "OE1" <-> "OE2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 100": "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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ASP 136": "OD1" <-> "OD2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g ASP 7": "OD1" <-> "OD2" Residue "g PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 107": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" 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 ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" 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 ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ASP 58": "OD1" <-> "OD2" 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 GLU 114": "OE1" <-> "OE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ASP 2": "OD1" <-> "OD2" 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 ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ASP 81": "OD1" <-> "OD2" 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 GLU 88": "OE1" <-> "OE2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ASP 26": "OD1" <-> "OD2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 45": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s GLU 59": "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 42": "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 ASP 7": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 64": "OD1" <-> "OD2" 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 GLU 38": "OE1" <-> "OE2" 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 GLU 6": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "F GLU 30": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P ASP 71": "OD1" <-> "OD2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 17": "OD1" <-> "OD2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 48": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" 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" Residue "a ASP 183": "OD1" <-> "OD2" Residue "7 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148582 Number of models: 1 Model: "" Number of chains: 57 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': 91, 'rna2p_pyr': 49, 'rna3p_pur': 783, 'rna3p_pyr': 616} Link IDs: {'rna2p': 140, 'rna3p': 1398} 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': 212, 'rna2p_pyr': 96, 'rna3p_pur': 1462, 'rna3p_pyr': 1133} Link IDs: {'rna2p': 308, 'rna3p': 2594} 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': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 63} 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: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1640 Classifications: {'RNA': 76, 'peptide': 2} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'NMTRANS': 1, 'rna2p': 12, 'rna3p': 63, None: 1} Not linked: pdbres=" A 7 76 " pdbres="PHE 7 101 " Chain breaks: 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PHE 7 101 " occ=0.94 ... (9 atoms not shown) pdb=" CZ PHE 7 101 " occ=0.75 Time building chain proxies: 59.35, per 1000 atoms: 0.40 Number of scatterers: 148582 At special positions: 0 Unit cell: (275.931, 262.601, 242.606, 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 4727 15.00 O 41284 8.00 N 27663 7.00 C 74754 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: 64.84 Conformation dependent library (CDL) restraints added in 7.1 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: 11076 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: 183 helices and 72 sheets defined 38.6% alpha, 16.5% beta 1459 base pairs and 2776 stacking pairs defined. Time for finding SS restraints: 78.56 Creating SS restraints... Processing helix chain 'b' and resid 11 through 16 removed outlier: 4.554A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 11 through 16' Processing helix chain 'b' and resid 130 through 135 removed outlier: 4.040A 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 206 through 214 removed outlier: 3.945A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.487A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 removed outlier: 4.268A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.906A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 97 through 104 removed outlier: 3.602A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL c 104 " --> pdb=" O PHE c 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 41 removed outlier: 3.522A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.632A pdb=" N LYS d 106 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 4.127A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN d 136 " --> pdb=" O LYS d 132 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP d 140 " --> pdb=" O GLN d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 4.132A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.884A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.790A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET d 199 " --> pdb=" O GLN d 195 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 4.862A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR e 6 " --> pdb=" O LYS e 2 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP e 9 " --> pdb=" O ASP e 5 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 3.756A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 41 through 46' Processing helix chain 'e' and resid 47 through 60 removed outlier: 3.523A pdb=" N LEU e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 105 removed outlier: 4.131A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.595A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP e 146 " --> pdb=" O TYR e 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 141 through 146' Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.503A pdb=" N LEU e 169 " --> pdb=" O GLY e 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 removed outlier: 3.805A 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 133 through 138 removed outlier: 3.794A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Proline residue: e 138 - end of helix Processing helix chain 'f' and resid 1 through 6 removed outlier: 3.912A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.610A pdb=" N LEU f 71 " --> pdb=" O ALA f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.851A pdb=" N GLY f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU f 147 " --> pdb=" O VAL f 143 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.678A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 4.489A pdb=" N ILE g 44 " --> pdb=" O THR g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 72 removed outlier: 5.272A pdb=" N ALA g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA g 59 " --> pdb=" O GLU g 55 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 4.538A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.508A pdb=" N ASP h 7 " --> pdb=" O LEU h 3 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.926A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG h 46 " --> pdb=" O ARG h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.795A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix No H-bonds generated for 'chain 'h' and resid 62 through 68' Processing helix chain 'h' and resid 94 through 106 removed outlier: 4.014A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS h 105 " --> pdb=" O LYS h 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 77 removed outlier: 3.524A pdb=" N ALA h 75 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE h 76 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL h 77 " --> pdb=" O ASP h 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 29 removed outlier: 4.926A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 46 Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.669A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY i 84 " --> pdb=" O LYS i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.655A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.513A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.279A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.961A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 120 removed outlier: 5.580A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU k 118 " --> pdb=" O LYS k 114 " (cutoff:3.500A) Proline residue: k 120 - end of helix Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.516A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 74 removed outlier: 4.304A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.706A 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 78 through 85 removed outlier: 4.002A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 99 removed outlier: 5.001A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.773A pdb=" N ARG l 132 " --> pdb=" O THR l 128 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.569A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.859A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 37 through 58 removed outlier: 3.510A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.584A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.231A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 88 removed outlier: 4.528A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) removed outlier: 5.164A 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 20 removed outlier: 5.384A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 4.309A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.910A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA o 110 " --> pdb=" O LEU o 106 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 12 removed outlier: 3.589A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 98 through 103 removed outlier: 3.731A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 98 through 103' Processing helix chain 'q' and resid 6 through 21 removed outlier: 3.814A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.309A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 36 removed outlier: 4.529A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 72 removed outlier: 3.864A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.522A pdb=" N ALA q 107 " --> pdb=" O VAL q 103 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA q 114 " --> pdb=" O GLU q 110 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.896A pdb=" N VAL s 17 " --> pdb=" O SER s 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 3.858A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR s 39 " --> pdb=" O ILE s 35 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.553A pdb=" N ASN s 57 " --> pdb=" O SER s 53 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 4.327A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.697A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.768A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 4.933A 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: 3.757A pdb=" N SER v 17 " --> pdb=" O GLY v 13 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 3.781A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.206A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.659A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 Processing helix chain 'y' and resid 1 through 9 removed outlier: 3.628A pdb=" N GLU y 5 " --> pdb=" O MET y 1 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS y 9 " --> pdb=" O GLU y 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 1 through 9' Processing helix chain 'y' and resid 10 through 23 removed outlier: 3.764A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU y 18 " --> pdb=" O LEU y 14 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU y 19 " --> pdb=" O ASN y 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN y 20 " --> pdb=" O THR y 16 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) Processing helix chain 'y' and resid 25 through 35 removed outlier: 3.515A pdb=" N ALA y 32 " --> pdb=" O LEU y 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 63 removed outlier: 4.700A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) removed outlier: 4.349A 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: 3.591A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.623A pdb=" N ARG B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.920A pdb=" N HIS D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.577A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.530A pdb=" N GLN D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.731A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.816A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 45 Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.519A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 4 through 12 Processing helix chain 'G' and resid 26 through 31 removed outlier: 3.540A pdb=" N ILE G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 26 through 31' Processing helix chain 'G' and resid 41 through 63 removed outlier: 3.659A pdb=" N THR G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.721A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 removed outlier: 5.132A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.195A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR G 118 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 5.121A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.835A pdb=" N MET G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.810A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 5.017A pdb=" N VAL G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP G 196 " --> pdb=" O PRO G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.636A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.865A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.503A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU H 45 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.782A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 4.201A pdb=" N ASP H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 112' Processing helix chain 'H' and resid 113 through 126 removed outlier: 3.547A pdb=" N SER H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.615A pdb=" N LYS H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 137 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.219A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.502A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.688A pdb=" N GLU I 77 " --> pdb=" O ASN I 73 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.903A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.871A pdb=" N SER I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.692A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 205 removed outlier: 3.655A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.920A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.245A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 3.744A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN J 145 " --> pdb=" O ASP J 141 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.772A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.906A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 removed outlier: 4.282A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.850A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR K 30 " --> pdb=" O THR K 26 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.730A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP K 82 " --> pdb=" O PHE K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.788A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 53 removed outlier: 4.117A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 69 removed outlier: 3.817A pdb=" N ALA L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.845A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.893A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.575A pdb=" N LYS L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.546A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 43 through 53 removed outlier: 4.655A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.266A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.510A pdb=" N ILE N 78 " --> pdb=" O GLN N 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 101 removed outlier: 5.416A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 33 removed outlier: 4.546A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA O 21 " --> pdb=" O LEU O 17 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.743A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.570A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 removed outlier: 4.386A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.397A 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 72 removed outlier: 4.695A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 removed outlier: 6.140A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.949A pdb=" N LEU Q 6 " --> pdb=" O THR Q 2 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.498A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.868A 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 22 removed outlier: 4.315A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.623A pdb=" N SER R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.913A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 4.733A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.522A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.656A pdb=" N LEU R 88 " --> pdb=" O CYS R 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY R 93 " --> pdb=" O ARG R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.648A pdb=" N VAL S 13 " --> pdb=" O GLU S 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.562A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.881A pdb=" N GLN S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 5.497A 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 Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.744A pdb=" N ALA T 8 " --> pdb=" O THR T 4 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 46 removed outlier: 3.519A pdb=" N HIS T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU T 44 " --> pdb=" O GLY T 40 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.930A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR T 68 " --> pdb=" O LYS T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.688A pdb=" N GLY T 85 " --> pdb=" O ILE T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.605A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA U 58 " --> pdb=" O LEU U 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.589A pdb=" N ALA U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 17 removed outlier: 6.370A pdb=" N GLU W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 4.565A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.716A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 65 removed outlier: 3.582A pdb=" N LEU W 64 " --> pdb=" O ARG W 60 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER W 65 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.880A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY X 25 " --> pdb=" O ALA X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.554A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.250A 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 40 removed outlier: 3.807A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.553A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN Y 54 " --> pdb=" O PHE Y 50 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.866A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.192A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.649A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 32 Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix removed outlier: 3.544A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 3.666A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 35 removed outlier: 3.625A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR a 35 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.583A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 3.824A pdb=" N ILE b 90 " --> pdb=" O GLU b 81 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.237A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN b 162 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.989A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 24 through 28 Processing sheet with id= 6, first strand: chain 'c' and resid 36 through 40 removed outlier: 3.613A pdb=" N GLN c 36 " --> pdb=" O GLN c 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU c 40 " --> pdb=" O TYR c 45 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR c 45 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 168 through 173 removed outlier: 4.269A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER c 113 " --> pdb=" O GLU c 168 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 46 through 51 removed outlier: 5.126A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE c 82 " --> pdb=" O ILE c 48 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 107 through 111 Processing sheet with id= 10, first strand: chain 'd' and resid 1 through 5 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'd' and resid 117 through 120 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 146 through 149 current: chain 'd' and resid 167 through 170 Processing sheet with id= 12, first strand: chain 'e' and resid 31 through 37 removed outlier: 4.145A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR e 156 " --> pdb=" O LYS e 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR e 154 " --> pdb=" O THR e 34 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'e' and resid 64 through 68 removed outlier: 4.764A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.502A pdb=" N LYS f 26 " --> pdb=" O ASP f 15 " (cutoff:3.500A) 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: 6.272A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'f' and resid 94 through 97 removed outlier: 3.561A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 2 through 5 removed outlier: 5.815A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA g 39 " --> pdb=" O GLN g 2 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'g' and resid 76 through 81 removed outlier: 6.600A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'h' and resid 22 through 28 removed outlier: 4.517A pdb=" N LEU h 23 " --> pdb=" O GLU h 87 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU h 87 " --> pdb=" O LEU h 23 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA h 25 " --> pdb=" O SER h 85 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'i' and resid 56 through 61 removed outlier: 3.813A pdb=" N VAL i 57 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL i 69 " --> pdb=" O VAL i 57 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'j' and resid 52 through 57 removed outlier: 3.512A pdb=" N VAL j 17 " --> pdb=" O GLN j 138 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'j' and resid 74 through 77 removed outlier: 3.619A pdb=" N ALA j 87 " --> pdb=" O TYR j 74 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'k' and resid 18 through 21 removed outlier: 3.798A pdb=" N VAL k 19 " --> pdb=" O LEU k 8 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'k' and resid 68 through 71 removed outlier: 4.240A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'm' and resid 62 through 65 removed outlier: 3.585A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 3.947A 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 36 removed outlier: 7.363A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'n' and resid 33 through 36 removed outlier: 7.120A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.715A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'p' and resid 36 through 44 Processing sheet with id= 32, first strand: chain 'p' and resid 48 through 52 removed outlier: 3.814A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'r' and resid 2 through 6 removed outlier: 4.173A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 32 through 36 removed outlier: 6.565A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'r' and resid 57 through 60 removed outlier: 3.716A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 's' and resid 2 through 8 removed outlier: 4.557A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL s 105 " --> pdb=" O ALA s 5 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 's' and resid 73 through 79 removed outlier: 4.749A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 't' and resid 12 through 15 removed outlier: 5.472A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'u' and resid 39 through 44 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'u' and resid 82 through 85 Processing sheet with id= 41, first strand: chain 'v' and resid 69 through 72 removed outlier: 3.717A pdb=" N ILE v 70 " --> pdb=" O ILE v 63 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA v 39 " --> pdb=" O ARG v 9 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'w' and resid 47 through 50 removed outlier: 3.598A pdb=" N GLY w 50 " --> pdb=" O THR w 54 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'w' and resid 63 through 67 Processing sheet with id= 44, first strand: chain 'x' and resid 11 through 15 Processing sheet with id= 45, first strand: chain 'x' and resid 34 through 40 removed outlier: 3.544A pdb=" N ARG x 44 " --> pdb=" O VAL x 39 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'z' and resid 32 through 38 removed outlier: 4.303A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN z 8 " --> pdb=" O HIS z 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.599A pdb=" N SER B 28 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS B 36 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP B 30 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.672A pdb=" N THR C 22 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 33 through 39 removed outlier: 7.040A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 50 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'F' and resid 13 through 18 removed outlier: 8.694A pdb=" N ASN F 13 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER F 28 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.649A pdb=" N PHE G 183 " --> pdb=" O LEU G 160 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'H' and resid 63 through 69 Processing sheet with id= 53, first strand: chain 'H' and resid 147 through 152 removed outlier: 3.821A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'I' and resid 140 through 143 removed outlier: 6.260A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'J' and resid 11 through 15 removed outlier: 3.662A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY J 39 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS J 13 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.363A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 84 " --> pdb=" O MET J 95 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET J 95 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE J 94 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS J 125 " --> pdb=" O PHE J 94 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'J' and resid 32 through 35 removed outlier: 4.523A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.546A pdb=" N HIS K 37 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR K 92 " --> pdb=" O HIS K 3 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'K' and resid 38 through 43 removed outlier: 3.756A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'L' and resid 73 through 76 Processing sheet with id= 61, first strand: chain 'M' and resid 22 through 27 removed outlier: 6.420A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'M' and resid 73 through 76 removed outlier: 7.121A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.606A pdb=" N ILE N 20 " --> pdb=" O TYR N 5 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA N 16 " --> pdb=" O GLY N 9 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS N 26 " --> pdb=" O LEU N 60 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'O' and resid 44 through 52 removed outlier: 3.957A pdb=" N VAL O 74 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE O 76 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE O 6 " --> pdb=" O ILE O 76 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'P' and resid 29 through 34 removed outlier: 4.628A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL P 112 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 28 through 31 removed outlier: 4.997A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Q' and resid 36 through 40 removed outlier: 3.717A pdb=" N LEU Q 56 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.878A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'V' and resid 6 through 10 removed outlier: 6.893A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'V' and resid 18 through 27 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'X' and resid 47 through 51 removed outlier: 4.097A pdb=" N ILE X 48 " --> pdb=" O VAL X 59 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 169 through 176 removed outlier: 5.458A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER a 213 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) 1586 hydrogen bonds defined for protein. 4662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3628 hydrogen bonds 5862 hydrogen bond angles 0 basepair planarities 1459 basepair parallelities 2776 stacking parallelities Total time for adding SS restraints: 266.14 Time building geometry restraints manager: 70.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13672 1.31 - 1.44: 67277 1.44 - 1.56: 70702 1.56 - 1.69: 9458 1.69 - 1.82: 278 Bond restraints: 161387 Sorted by residual: bond pdb=" N FME 7 102 " pdb=" CN FME 7 102 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" O5' U 7 12 " pdb=" C5' U 7 12 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.55e+00 bond pdb=" O5' G 7 71 " pdb=" C5' G 7 71 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.32e+00 bond pdb=" C PHE 7 101 " pdb=" O PHE 7 101 " ideal model delta sigma weight residual 1.231 1.181 0.050 2.00e-02 2.50e+03 6.19e+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 6.15e+00 ... (remaining 161382 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.22: 22228 105.22 - 112.41: 90303 112.41 - 119.59: 56131 119.59 - 126.77: 59837 126.77 - 133.96: 12848 Bond angle restraints: 241347 Sorted by residual: angle pdb=" N ALA g 10 " pdb=" CA ALA g 10 " pdb=" C ALA g 10 " ideal model delta sigma weight residual 111.07 121.43 -10.36 1.07e+00 8.73e-01 9.37e+01 angle pdb=" C LEU E 61 " pdb=" N PRO E 62 " pdb=" CA PRO E 62 " ideal model delta sigma weight residual 118.97 128.76 -9.79 1.04e+00 9.25e-01 8.86e+01 angle pdb=" N ILE R 3 " pdb=" CA ILE R 3 " pdb=" C ILE R 3 " ideal model delta sigma weight residual 108.11 121.28 -13.17 1.40e+00 5.10e-01 8.85e+01 angle pdb=" N LYS j 121 " pdb=" CA LYS j 121 " pdb=" C LYS j 121 " ideal model delta sigma weight residual 113.23 101.93 11.30 1.24e+00 6.50e-01 8.31e+01 angle pdb=" N ARG b 213 " pdb=" CA ARG b 213 " pdb=" C ARG b 213 " ideal model delta sigma weight residual 112.23 101.67 10.56 1.26e+00 6.30e-01 7.02e+01 ... (remaining 241342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 92330 35.80 - 71.60: 9816 71.60 - 107.40: 1251 107.40 - 143.21: 12 143.21 - 179.01: 18 Dihedral angle restraints: 103427 sinusoidal: 86265 harmonic: 17162 Sorted by residual: dihedral pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" C2' U 11130 " pdb=" C1' U 11130 " ideal model delta sinusoidal sigma weight residual -35.00 31.98 -66.98 1 8.00e+00 1.56e-02 9.14e+01 dihedral pdb=" C5' U 11130 " pdb=" C4' U 11130 " pdb=" C3' U 11130 " pdb=" O3' U 11130 " ideal model delta sinusoidal sigma weight residual 147.00 81.02 65.98 1 8.00e+00 1.56e-02 8.89e+01 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 35.91 164.09 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 103424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 22335 0.088 - 0.175: 7721 0.175 - 0.263: 702 0.263 - 0.350: 84 0.350 - 0.438: 10 Chirality restraints: 30852 Sorted by residual: chirality pdb=" C3' U 11130 " pdb=" C4' U 11130 " pdb=" O3' U 11130 " pdb=" C2' U 11130 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA PRO k 72 " pdb=" N PRO k 72 " pdb=" C PRO k 72 " pdb=" CB PRO k 72 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA GLN i 11 " pdb=" N GLN i 11 " pdb=" C GLN i 11 " pdb=" CB GLN i 11 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 30849 not shown) Planarity restraints: 13007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 12629 " 0.086 2.00e-02 2.50e+03 4.54e-02 4.64e+01 pdb=" N1 U 12629 " -0.006 2.00e-02 2.50e+03 pdb=" C2 U 12629 " -0.017 2.00e-02 2.50e+03 pdb=" O2 U 12629 " -0.034 2.00e-02 2.50e+03 pdb=" N3 U 12629 " -0.010 2.00e-02 2.50e+03 pdb=" C4 U 12629 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U 12629 " 0.076 2.00e-02 2.50e+03 pdb=" C5 U 12629 " -0.042 2.00e-02 2.50e+03 pdb=" C6 U 12629 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " -0.081 2.00e-02 2.50e+03 3.47e-02 3.32e+01 pdb=" N9 A 11328 " 0.007 2.00e-02 2.50e+03 pdb=" C8 A 11328 " 0.034 2.00e-02 2.50e+03 pdb=" N7 A 11328 " 0.026 2.00e-02 2.50e+03 pdb=" C5 A 11328 " 0.012 2.00e-02 2.50e+03 pdb=" C6 A 11328 " -0.013 2.00e-02 2.50e+03 pdb=" N6 A 11328 " -0.051 2.00e-02 2.50e+03 pdb=" N1 A 11328 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A 11328 " 0.016 2.00e-02 2.50e+03 pdb=" N3 A 11328 " 0.030 2.00e-02 2.50e+03 pdb=" C4 A 11328 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 775 " 0.079 2.00e-02 2.50e+03 3.26e-02 3.19e+01 pdb=" N9 G 1 775 " -0.004 2.00e-02 2.50e+03 pdb=" C8 G 1 775 " -0.032 2.00e-02 2.50e+03 pdb=" N7 G 1 775 " -0.029 2.00e-02 2.50e+03 pdb=" C5 G 1 775 " -0.017 2.00e-02 2.50e+03 pdb=" C6 G 1 775 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G 1 775 " 0.050 2.00e-02 2.50e+03 pdb=" N1 G 1 775 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G 1 775 " -0.008 2.00e-02 2.50e+03 pdb=" N2 G 1 775 " -0.010 2.00e-02 2.50e+03 pdb=" N3 G 1 775 " -0.026 2.00e-02 2.50e+03 pdb=" C4 G 1 775 " -0.027 2.00e-02 2.50e+03 ... (remaining 13004 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 1 2.02 - 2.74: 15584 2.74 - 3.46: 194860 3.46 - 4.18: 472163 4.18 - 4.90: 645996 Nonbonded interactions: 1328604 Sorted by model distance: nonbonded pdb=" O3' A 7 76 " pdb=" C PHE 7 101 " model vdw 1.303 3.270 nonbonded pdb=" O3' A 7 76 " pdb=" O PHE 7 101 " model vdw 2.174 3.040 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR h 58 " pdb=" O GLY h 78 " model vdw 2.251 2.440 nonbonded pdb=" OG SER k 28 " pdb=" N1 A 12566 " model vdw 2.269 2.520 ... (remaining 1328599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.120 Extract box with map and model: 11.650 Check model and map are aligned: 1.670 Set scattering table: 1.050 Process input model: 580.810 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.380 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 603.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.116 161387 Z= 0.359 Angle : 0.960 13.170 241347 Z= 0.639 Chirality : 0.080 0.438 30852 Planarity : 0.007 0.084 13007 Dihedral : 22.171 179.008 92351 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 2.04 % Allowed : 12.16 % Favored : 85.79 % Rotamer: Outliers : 1.02 % Allowed : 7.92 % Favored : 91.06 % 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: -4.96 (0.08), residues: 5919 helix: -3.76 (0.08), residues: 1722 sheet: -2.79 (0.15), residues: 916 loop : -3.24 (0.09), residues: 3281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.006 TRP x 38 HIS 0.002 0.000 HIS J 88 PHE 0.052 0.005 PHE G 89 TYR 0.052 0.007 TYR W 69 ARG 0.007 0.001 ARG k 108 *********************** 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 1930 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1880 time to evaluate : 6.622 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: b 65 ASP cc_start: 0.7734 (t0) cc_final: 0.7283 (t0) REVERT: b 78 GLU cc_start: 0.8121 (tt0) cc_final: 0.7706 (mt-10) REVERT: b 83 ASP cc_start: 0.8132 (t0) cc_final: 0.7830 (t0) REVERT: b 94 LEU cc_start: 0.8871 (tp) cc_final: 0.8586 (tp) REVERT: b 100 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7452 (mtt90) REVERT: b 113 ASP cc_start: 0.8077 (m-30) cc_final: 0.7835 (m-30) REVERT: b 123 ILE cc_start: 0.8892 (mm) cc_final: 0.8683 (mt) REVERT: b 173 LEU cc_start: 0.8868 (mt) cc_final: 0.8360 (mp) REVERT: b 238 ASN cc_start: 0.8343 (p0) cc_final: 0.8141 (p0) REVERT: c 128 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7935 (mtp180) REVERT: c 160 LYS cc_start: 0.9176 (mttp) cc_final: 0.8906 (mttt) REVERT: d 40 ARG cc_start: 0.8911 (mtp180) cc_final: 0.8704 (mtp180) REVERT: d 94 GLN cc_start: 0.8352 (mt0) cc_final: 0.7985 (mt0) REVERT: d 115 GLN cc_start: 0.8683 (mt0) cc_final: 0.7972 (mt0) REVERT: d 168 ASP cc_start: 0.8231 (t0) cc_final: 0.7888 (t0) REVERT: d 194 LYS cc_start: 0.8718 (tptt) cc_final: 0.8480 (tppt) REVERT: d 195 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7702 (tm-30) REVERT: e 7 TYR cc_start: 0.8646 (t80) cc_final: 0.8316 (t80) REVERT: e 39 VAL cc_start: 0.7888 (p) cc_final: 0.7293 (p) REVERT: e 41 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: e 64 PRO cc_start: 0.8762 (Cg_endo) cc_final: 0.8464 (Cg_exo) REVERT: e 98 PHE cc_start: 0.8022 (t80) cc_final: 0.7347 (t80) REVERT: e 99 PHE cc_start: 0.8246 (t80) cc_final: 0.7976 (t80) REVERT: e 126 ASN cc_start: 0.7559 (m-40) cc_final: 0.6972 (m-40) REVERT: e 142 TYR cc_start: 0.6962 (t80) cc_final: 0.6741 (t80) REVERT: e 146 ASP cc_start: 0.8422 (p0) cc_final: 0.8158 (p0) REVERT: e 152 ASP cc_start: 0.7026 (p0) cc_final: 0.6673 (p0) REVERT: e 156 THR cc_start: 0.7733 (t) cc_final: 0.7042 (t) REVERT: e 177 ARG cc_start: 0.7023 (ttp80) cc_final: 0.6530 (ttm110) REVERT: f 63 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8309 (mt0) REVERT: f 76 ILE cc_start: 0.9682 (mm) cc_final: 0.9391 (mm) REVERT: f 87 GLN cc_start: 0.7865 (tt0) cc_final: 0.7286 (tt0) REVERT: f 129 GLU cc_start: 0.8097 (tt0) cc_final: 0.7756 (tt0) REVERT: f 156 TYR cc_start: 0.8760 (m-80) cc_final: 0.8362 (m-80) REVERT: f 162 ARG cc_start: 0.8685 (ptp-170) cc_final: 0.7934 (ptp-170) REVERT: g 25 TYR cc_start: 0.8805 (t80) cc_final: 0.8582 (t80) REVERT: h 38 MET cc_start: 0.5859 (mtt) cc_final: 0.5315 (mpp) REVERT: h 71 CYS cc_start: 0.6660 (m) cc_final: 0.6050 (m) REVERT: j 44 TYR cc_start: 0.8589 (t80) cc_final: 0.7702 (t80) REVERT: j 95 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.6975 (ttp80) REVERT: j 106 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8383 (tttt) REVERT: j 108 MET cc_start: 0.9220 (mtt) cc_final: 0.8626 (mtt) REVERT: j 109 LEU cc_start: 0.9501 (mt) cc_final: 0.9208 (mt) REVERT: j 116 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8136 (mtm-85) REVERT: j 118 MET cc_start: 0.8371 (ptp) cc_final: 0.7698 (ptp) REVERT: j 136 GLN cc_start: 0.8175 (mt0) cc_final: 0.7461 (mp10) REVERT: k 23 LYS cc_start: 0.7749 (tppt) cc_final: 0.7525 (ttmm) REVERT: k 25 LEU cc_start: 0.8679 (mp) cc_final: 0.8476 (mp) REVERT: k 38 ILE cc_start: 0.9320 (mm) cc_final: 0.8832 (mm) REVERT: k 95 ILE cc_start: 0.8617 (mt) cc_final: 0.8317 (mt) REVERT: l 4 ASN cc_start: 0.8836 (p0) cc_final: 0.8447 (p0) REVERT: l 91 ASP cc_start: 0.7965 (t70) cc_final: 0.7754 (t70) REVERT: l 105 ILE cc_start: 0.9238 (mm) cc_final: 0.8732 (mm) REVERT: l 112 LEU cc_start: 0.8754 (tp) cc_final: 0.8470 (tp) REVERT: l 121 THR cc_start: 0.8603 (m) cc_final: 0.8356 (t) REVERT: l 143 GLU cc_start: 0.8154 (pm20) cc_final: 0.7862 (pm20) REVERT: m 82 MET cc_start: 0.8987 (mmp) cc_final: 0.8619 (mmt) REVERT: n 13 ASN cc_start: 0.9218 (p0) cc_final: 0.8921 (p0) REVERT: n 49 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7834 (mt-10) REVERT: n 78 LYS cc_start: 0.9196 (tppp) cc_final: 0.8761 (tppt) REVERT: o 16 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.8474 (tpp80) REVERT: o 38 GLN cc_start: 0.7671 (pt0) cc_final: 0.7468 (pm20) REVERT: o 76 LYS cc_start: 0.8103 (tttt) cc_final: 0.7663 (tppt) REVERT: p 54 LEU cc_start: 0.9177 (tp) cc_final: 0.8795 (tp) REVERT: p 87 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7268 (ttp-170) REVERT: p 105 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7412 (mmmt) REVERT: p 111 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6976 (mp0) REVERT: q 46 TYR cc_start: 0.8939 (t80) cc_final: 0.8655 (t80) REVERT: q 51 GLN cc_start: 0.8207 (tt0) cc_final: 0.7972 (tt0) REVERT: q 75 TYR cc_start: 0.8652 (t80) cc_final: 0.7948 (t80) REVERT: q 83 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8151 (mmtp) REVERT: r 13 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8412 (ttt90) REVERT: r 64 VAL cc_start: 0.9107 (t) cc_final: 0.8782 (t) REVERT: s 106 VAL cc_start: 0.9125 (t) cc_final: 0.8896 (p) REVERT: s 109 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7594 (p0) REVERT: t 12 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7804 (mmm-85) REVERT: t 32 LEU cc_start: 0.9415 (pp) cc_final: 0.9153 (pp) REVERT: t 48 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8368 (mm-40) REVERT: t 74 ILE cc_start: 0.8565 (pt) cc_final: 0.8342 (pt) REVERT: t 91 GLN cc_start: 0.8076 (pp30) cc_final: 0.7774 (pp30) REVERT: u 6 ARG cc_start: 0.8680 (ttt180) cc_final: 0.8348 (ttm110) REVERT: u 23 LYS cc_start: 0.8610 (tttp) cc_final: 0.7786 (tptt) REVERT: v 5 ASN cc_start: 0.8776 (m-40) cc_final: 0.8081 (p0) REVERT: v 34 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8828 (mmmt) REVERT: v 40 ILE cc_start: 0.8979 (mm) cc_final: 0.8545 (pt) REVERT: v 53 LYS cc_start: 0.9151 (mttt) cc_final: 0.8873 (mmtp) REVERT: v 69 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5676 (tm-30) REVERT: w 17 LEU cc_start: 0.9021 (mt) cc_final: 0.8713 (mt) REVERT: w 35 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7229 (ttt-90) REVERT: w 52 ASP cc_start: 0.8407 (t70) cc_final: 0.8172 (t70) REVERT: x 16 ASN cc_start: 0.8385 (t0) cc_final: 0.8007 (t0) REVERT: y 1 MET cc_start: 0.6977 (ttm) cc_final: 0.6318 (ttt) REVERT: y 25 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8735 (tp40) REVERT: y 27 ASN cc_start: 0.8754 (m110) cc_final: 0.8409 (m-40) REVERT: y 29 ARG cc_start: 0.8993 (ttp-170) cc_final: 0.8584 (ttp-170) REVERT: y 41 HIS cc_start: 0.8824 (p-80) cc_final: 0.8309 (p-80) REVERT: y 45 GLN cc_start: 0.8801 (pp30) cc_final: 0.8582 (pp30) REVERT: y 49 ASP cc_start: 0.8622 (m-30) cc_final: 0.8255 (m-30) REVERT: z 31 ILE cc_start: 0.8631 (pt) cc_final: 0.8207 (mt) REVERT: z 36 GLU cc_start: 0.8132 (tt0) cc_final: 0.7528 (pp20) REVERT: z 37 ARG cc_start: 0.8450 (mmp80) cc_final: 0.8209 (mmp80) REVERT: z 39 ASP cc_start: 0.7483 (t70) cc_final: 0.7282 (t0) REVERT: z 57 GLU cc_start: 0.7940 (tp30) cc_final: 0.7576 (tp30) REVERT: D 19 ARG cc_start: 0.9174 (mtp85) cc_final: 0.8908 (mmm-85) REVERT: F 8 LYS cc_start: 0.8515 (mttp) cc_final: 0.8213 (mttm) REVERT: F 37 GLN cc_start: 0.7313 (tp40) cc_final: 0.7012 (tp40) REVERT: G 6 ARG cc_start: 0.8584 (ttp80) cc_final: 0.7996 (mmp-170) REVERT: G 25 LYS cc_start: 0.8683 (mmtm) cc_final: 0.7721 (tptt) REVERT: G 29 PHE cc_start: 0.9014 (m-80) cc_final: 0.8132 (m-80) REVERT: G 89 PHE cc_start: 0.6253 (m-80) cc_final: 0.5958 (m-80) REVERT: G 96 LEU cc_start: 0.9505 (tp) cc_final: 0.9267 (tp) REVERT: G 101 THR cc_start: 0.8752 (p) cc_final: 0.8500 (t) REVERT: G 108 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8398 (mm110) REVERT: G 135 MET cc_start: 0.8612 (ppp) cc_final: 0.8149 (ppp) REVERT: G 147 LEU cc_start: 0.8770 (tt) cc_final: 0.8417 (tt) REVERT: G 150 ILE cc_start: 0.9304 (pt) cc_final: 0.8870 (tp) REVERT: G 176 ASN cc_start: 0.9213 (m110) cc_final: 0.8872 (m110) REVERT: G 185 ILE cc_start: 0.8600 (mm) cc_final: 0.8371 (mm) REVERT: G 224 ARG cc_start: 0.8961 (mmm160) cc_final: 0.8655 (mtm-85) REVERT: H 178 ARG cc_start: 0.7534 (ptm160) cc_final: 0.7191 (ptm-80) REVERT: I 54 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8806 (mt) REVERT: I 69 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7815 (tpp80) REVERT: I 71 PHE cc_start: 0.9344 (t80) cc_final: 0.9141 (t80) REVERT: I 72 ARG cc_start: 0.9385 (ttp80) cc_final: 0.8791 (ttp80) REVERT: I 73 ASN cc_start: 0.8992 (t0) cc_final: 0.8732 (t0) REVERT: I 90 LEU cc_start: 0.9259 (mt) cc_final: 0.8992 (pp) REVERT: I 97 LEU cc_start: 0.9221 (pt) cc_final: 0.8771 (pt) REVERT: I 115 GLN cc_start: 0.7581 (tp40) cc_final: 0.6333 (tp-100) REVERT: I 165 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7894 (tm-30) REVERT: I 169 TRP cc_start: 0.8166 (p90) cc_final: 0.7560 (p90) REVERT: I 183 ARG cc_start: 0.7374 (ppt170) cc_final: 0.7094 (ppt170) REVERT: J 30 PHE cc_start: 0.8426 (m-80) cc_final: 0.7729 (m-10) REVERT: J 61 LYS cc_start: 0.8312 (tttp) cc_final: 0.7946 (tttp) REVERT: J 64 GLU cc_start: 0.8635 (tp30) cc_final: 0.8434 (pm20) REVERT: J 96 GLN cc_start: 0.8545 (tp40) cc_final: 0.8311 (tp40) REVERT: J 100 GLU cc_start: 0.8344 (tp30) cc_final: 0.7927 (tp30) REVERT: J 140 ILE cc_start: 0.9272 (tt) cc_final: 0.9037 (tt) REVERT: K 11 HIS cc_start: 0.8375 (t70) cc_final: 0.7887 (t-90) REVERT: K 78 PHE cc_start: 0.8905 (m-80) cc_final: 0.8283 (m-80) REVERT: K 81 ASN cc_start: 0.8897 (t0) cc_final: 0.8505 (t0) REVERT: K 88 MET cc_start: 0.8022 (ptm) cc_final: 0.6844 (ptm) REVERT: K 90 MET cc_start: 0.8692 (mmt) cc_final: 0.8060 (mmt) REVERT: L 22 LEU cc_start: 0.9424 (mt) cc_final: 0.9208 (mp) REVERT: L 29 LEU cc_start: 0.8389 (mm) cc_final: 0.8086 (mm) REVERT: L 98 LEU cc_start: 0.9222 (mt) cc_final: 0.8918 (mt) REVERT: L 109 LYS cc_start: 0.8311 (pptt) cc_final: 0.8023 (mmtm) REVERT: L 125 ASP cc_start: 0.9193 (m-30) cc_final: 0.8685 (t0) REVERT: L 139 ASP cc_start: 0.8013 (m-30) cc_final: 0.7751 (m-30) REVERT: M 12 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7880 (mtt-85) REVERT: M 30 LYS cc_start: 0.9274 (ttpp) cc_final: 0.8787 (tttt) REVERT: M 40 LYS cc_start: 0.9337 (tmtt) cc_final: 0.9016 (ttpt) REVERT: M 44 PHE cc_start: 0.7403 (m-80) cc_final: 0.6623 (m-80) REVERT: M 48 PHE cc_start: 0.8401 (p90) cc_final: 0.7965 (p90) REVERT: M 61 THR cc_start: 0.8451 (p) cc_final: 0.7661 (p) REVERT: M 79 ARG cc_start: 0.8429 (ptt180) cc_final: 0.7884 (ptm-80) REVERT: M 93 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8103 (ttmm) REVERT: M 117 GLN cc_start: 0.9264 (mt0) cc_final: 0.8981 (mt0) REVERT: M 125 ILE cc_start: 0.8940 (mm) cc_final: 0.8296 (mp) REVERT: M 126 CYS cc_start: 0.9481 (p) cc_final: 0.9115 (p) REVERT: N 38 PHE cc_start: 0.8722 (p90) cc_final: 0.8343 (p90) REVERT: N 49 GLN cc_start: 0.5802 (OUTLIER) cc_final: 0.5312 (pt0) REVERT: P 55 ARG cc_start: 0.8905 (mpp-170) cc_final: 0.8475 (mmm160) REVERT: P 63 GLN cc_start: 0.8479 (mm110) cc_final: 0.8272 (mm110) REVERT: P 96 ILE cc_start: 0.8858 (pt) cc_final: 0.8634 (mp) REVERT: Q 75 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8122 (mm-30) REVERT: Q 98 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.6063 (mmm-85) REVERT: Q 107 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8143 (mmtm) REVERT: R 2 ARG cc_start: 0.8267 (ttm170) cc_final: 0.7804 (tpt90) REVERT: R 74 MET cc_start: 0.8854 (ttp) cc_final: 0.8474 (tmm) REVERT: R 79 LEU cc_start: 0.9781 (tp) cc_final: 0.9452 (tp) REVERT: R 88 LEU cc_start: 0.8946 (mt) cc_final: 0.8723 (mt) REVERT: S 62 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.5481 (mtm-85) REVERT: S 64 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7822 (mmm-85) REVERT: T 41 HIS cc_start: 0.8827 (t70) cc_final: 0.8425 (t70) REVERT: T 61 GLN cc_start: 0.8616 (tp40) cc_final: 0.8226 (tp40) REVERT: U 31 ARG cc_start: 0.5525 (ttp-110) cc_final: 0.5204 (ttp-170) REVERT: U 52 LEU cc_start: 0.8424 (mp) cc_final: 0.7760 (tt) REVERT: V 11 VAL cc_start: 0.7532 (t) cc_final: 0.7235 (t) REVERT: V 17 GLU cc_start: 0.8778 (mp0) cc_final: 0.8416 (mp0) REVERT: V 58 VAL cc_start: 0.8457 (p) cc_final: 0.8191 (t) REVERT: V 66 LEU cc_start: 0.7805 (mt) cc_final: 0.7565 (mt) REVERT: W 22 TYR cc_start: 0.7802 (p90) cc_final: 0.7501 (p90) REVERT: W 56 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7590 (mtt180) REVERT: W 64 LEU cc_start: 0.9003 (mt) cc_final: 0.8718 (mp) REVERT: X 65 MET cc_start: 0.7978 (mtt) cc_final: 0.7111 (mmm) REVERT: X 68 HIS cc_start: 0.8235 (m90) cc_final: 0.7941 (m-70) REVERT: Y 9 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8245 (tpt-90) REVERT: Y 14 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8477 (tm-30) REVERT: Y 17 ARG cc_start: 0.8123 (ppt170) cc_final: 0.7658 (tmm160) REVERT: Y 18 LYS cc_start: 0.9712 (mtpp) cc_final: 0.9062 (mmtm) REVERT: Y 23 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.7959 (mmm-85) REVERT: Y 47 GLN cc_start: 0.9445 (tp-100) cc_final: 0.9193 (tp-100) REVERT: Z 39 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8131 (mmmt) REVERT: Z 43 GLU cc_start: 0.8739 (mp0) cc_final: 0.8520 (mp0) REVERT: a 8 MET cc_start: 0.5245 (ttm) cc_final: 0.4744 (tmm) REVERT: 7 101 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6875 (m-80) outliers start: 50 outliers final: 28 residues processed: 1911 average time/residue: 1.3754 time to fit residues: 4407.4930 Evaluate side-chains 1583 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1550 time to evaluate : 7.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain h residue 119 PRO Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 83 ILE Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 886 optimal weight: 30.0000 chunk 795 optimal weight: 10.0000 chunk 441 optimal weight: 0.0770 chunk 271 optimal weight: 7.9990 chunk 536 optimal weight: 8.9990 chunk 425 optimal weight: 30.0000 chunk 822 optimal weight: 50.0000 chunk 318 optimal weight: 0.0970 chunk 500 optimal weight: 7.9990 chunk 612 optimal weight: 20.0000 chunk 953 optimal weight: 10.0000 overall best weight: 5.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN b 162 GLN c 150 GLN d 92 HIS d 97 ASN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 ASN f 63 GLN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN h 103 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 135 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN l 104 GLN n 3 HIS n 23 ASN n 107 ASN o 38 GLN o 100 HIS p 2 ASN ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN r 66 HIS r 82 HIS s 15 GLN t 59 ASN u 73 ASN v 12 GLN v 78 GLN w 8 ASN y 39 GLN z 48 ASN E 42 HIS F 13 ASN F 35 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN G 38 HIS G 50 ASN ** G 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 169 HIS H 18 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN J 11 GLN J 72 ASN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN K 3 HIS ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN K 55 HIS L 67 ASN M 3 GLN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN ** N 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 GLN Q 5 GLN Q 45 ASN Q 58 ASN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN S 3 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 GLN ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN W 73 HIS ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS Z 63 ASN a 24 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 161387 Z= 0.283 Angle : 0.685 12.975 241347 Z= 0.355 Chirality : 0.038 0.347 30852 Planarity : 0.006 0.073 13007 Dihedral : 22.926 177.944 80605 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.53 % Favored : 90.32 % Rotamer: Outliers : 4.87 % Allowed : 17.25 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.09), residues: 5919 helix: -2.13 (0.10), residues: 1887 sheet: -2.26 (0.15), residues: 943 loop : -2.83 (0.10), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 102 HIS 0.013 0.002 HIS j 80 PHE 0.023 0.002 PHE G 183 TYR 0.035 0.002 TYR L 43 ARG 0.009 0.001 ARG e 111 *********************** 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 1911 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1672 time to evaluate : 6.562 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: b 65 ASP cc_start: 0.7449 (t0) cc_final: 0.7248 (t0) REVERT: b 78 GLU cc_start: 0.8124 (tt0) cc_final: 0.7567 (mt-10) REVERT: b 113 ASP cc_start: 0.8129 (m-30) cc_final: 0.7895 (m-30) REVERT: b 123 ILE cc_start: 0.8966 (mm) cc_final: 0.8716 (mt) REVERT: b 238 ASN cc_start: 0.8650 (p0) cc_final: 0.8213 (p0) REVERT: b 241 LYS cc_start: 0.8362 (mttp) cc_final: 0.8109 (mttp) REVERT: c 128 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7756 (mtp180) REVERT: d 94 GLN cc_start: 0.8368 (mt0) cc_final: 0.7861 (mt0) REVERT: d 115 GLN cc_start: 0.8487 (mt0) cc_final: 0.7839 (mt0) REVERT: d 144 GLU cc_start: 0.7725 (tt0) cc_final: 0.7290 (mp0) REVERT: d 194 LYS cc_start: 0.8769 (tptt) cc_final: 0.8565 (tppt) REVERT: d 195 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7670 (tm-30) REVERT: e 39 VAL cc_start: 0.8063 (p) cc_final: 0.7608 (p) REVERT: e 41 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: e 56 LEU cc_start: 0.8817 (mt) cc_final: 0.8491 (mt) REVERT: e 64 PRO cc_start: 0.8796 (Cg_endo) cc_final: 0.8493 (Cg_exo) REVERT: e 124 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8381 (mmm-85) REVERT: e 137 PHE cc_start: 0.7980 (m-80) cc_final: 0.7708 (m-80) REVERT: e 142 TYR cc_start: 0.7249 (t80) cc_final: 0.7024 (t80) REVERT: e 156 THR cc_start: 0.7737 (t) cc_final: 0.7469 (t) REVERT: e 161 SER cc_start: 0.8730 (t) cc_final: 0.8396 (t) REVERT: e 177 ARG cc_start: 0.6892 (ttp80) cc_final: 0.6611 (ttp80) REVERT: f 63 GLN cc_start: 0.8976 (mm110) cc_final: 0.8326 (mt0) REVERT: f 76 ILE cc_start: 0.9598 (mm) cc_final: 0.9310 (mm) REVERT: f 82 PHE cc_start: 0.8249 (m-80) cc_final: 0.7935 (m-10) REVERT: f 87 GLN cc_start: 0.8079 (tt0) cc_final: 0.7680 (pt0) REVERT: f 129 GLU cc_start: 0.7917 (tt0) cc_final: 0.7606 (tt0) REVERT: g 127 GLU cc_start: 0.7529 (pp20) cc_final: 0.7216 (pp20) REVERT: g 129 GLU cc_start: 0.5421 (tt0) cc_final: 0.4827 (tm-30) REVERT: h 54 VAL cc_start: 0.3615 (p) cc_final: 0.3356 (m) REVERT: i 116 MET cc_start: -0.0214 (mmt) cc_final: -0.1075 (mmm) REVERT: j 44 TYR cc_start: 0.8731 (t80) cc_final: 0.7961 (t80) REVERT: j 95 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7088 (ttp80) REVERT: j 106 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8422 (tttt) REVERT: j 118 MET cc_start: 0.8462 (ptp) cc_final: 0.7980 (ptp) REVERT: j 136 GLN cc_start: 0.8341 (mt0) cc_final: 0.7793 (mp10) REVERT: k 38 ILE cc_start: 0.9296 (mm) cc_final: 0.8872 (mm) REVERT: k 73 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8119 (p0) REVERT: l 2 ARG cc_start: 0.7320 (tpp80) cc_final: 0.6892 (tpp80) REVERT: l 4 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8483 (p0) REVERT: l 91 ASP cc_start: 0.7974 (t70) cc_final: 0.7648 (t0) REVERT: l 112 LEU cc_start: 0.8743 (tp) cc_final: 0.8512 (tp) REVERT: l 135 ILE cc_start: 0.9371 (mt) cc_final: 0.9138 (tt) REVERT: l 142 ILE cc_start: 0.8709 (mt) cc_final: 0.8461 (mm) REVERT: l 143 GLU cc_start: 0.8227 (pm20) cc_final: 0.7719 (pm20) REVERT: m 6 ARG cc_start: 0.8404 (tmt170) cc_final: 0.8195 (tmt170) REVERT: m 82 MET cc_start: 0.9121 (mmp) cc_final: 0.8808 (mmt) REVERT: m 97 GLN cc_start: 0.8285 (mp10) cc_final: 0.8057 (mp10) REVERT: m 101 VAL cc_start: 0.9292 (t) cc_final: 0.8877 (m) REVERT: m 105 MET cc_start: 0.7351 (ttm) cc_final: 0.7057 (mtm) REVERT: n 49 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7718 (mt-10) REVERT: n 54 LEU cc_start: 0.8721 (tp) cc_final: 0.8282 (tp) REVERT: n 72 ASP cc_start: 0.8535 (t0) cc_final: 0.8323 (t0) REVERT: n 78 LYS cc_start: 0.8990 (tppp) cc_final: 0.8702 (tppp) REVERT: o 16 ARG cc_start: 0.8710 (mmt-90) cc_final: 0.8462 (tpp80) REVERT: o 38 GLN cc_start: 0.7753 (pt0) cc_final: 0.7433 (pm20) REVERT: o 65 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7828 (t) REVERT: o 76 LYS cc_start: 0.7804 (tttt) cc_final: 0.7411 (tppt) REVERT: p 87 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7222 (ttp-170) REVERT: p 105 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8163 (mmmt) REVERT: p 111 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6578 (mm-30) REVERT: q 51 GLN cc_start: 0.8200 (tt0) cc_final: 0.7919 (tt0) REVERT: q 75 TYR cc_start: 0.8809 (t80) cc_final: 0.7850 (t80) REVERT: q 83 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7930 (mmtm) REVERT: r 6 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8244 (tm-30) REVERT: r 13 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8457 (ttt90) REVERT: r 94 THR cc_start: 0.8396 (m) cc_final: 0.8135 (m) REVERT: s 8 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.8086 (mtp-110) REVERT: s 82 MET cc_start: 0.7645 (mpp) cc_final: 0.7302 (mtm) REVERT: t 12 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7862 (mmm-85) REVERT: t 32 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8969 (pp) REVERT: t 48 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7949 (mm-40) REVERT: t 91 GLN cc_start: 0.7862 (pp30) cc_final: 0.7620 (pp30) REVERT: u 6 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8319 (ttm110) REVERT: u 17 ASP cc_start: 0.6751 (t0) cc_final: 0.6488 (t0) REVERT: v 5 ASN cc_start: 0.8706 (m-40) cc_final: 0.7904 (p0) REVERT: v 7 GLU cc_start: 0.8242 (tp30) cc_final: 0.8026 (mp0) REVERT: v 42 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7894 (pp) REVERT: v 53 LYS cc_start: 0.9179 (mttt) cc_final: 0.8884 (mmtp) REVERT: w 16 ARG cc_start: 0.8622 (mpt180) cc_final: 0.8399 (mpt180) REVERT: w 35 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.7108 (ttt-90) REVERT: w 36 GLN cc_start: 0.8662 (pt0) cc_final: 0.8366 (pt0) REVERT: x 9 LYS cc_start: 0.9250 (mttm) cc_final: 0.8640 (mtpp) REVERT: x 16 ASN cc_start: 0.8281 (t0) cc_final: 0.7870 (t0) REVERT: x 55 MET cc_start: 0.8305 (mtp) cc_final: 0.7512 (mtp) REVERT: x 61 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8375 (mttp) REVERT: x 69 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7461 (tm-30) REVERT: y 5 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6933 (mm-30) REVERT: y 17 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8939 (tm-30) REVERT: y 29 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8592 (ttm170) REVERT: y 31 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: y 41 HIS cc_start: 0.8836 (p-80) cc_final: 0.8253 (p-80) REVERT: y 49 ASP cc_start: 0.8445 (m-30) cc_final: 0.8243 (m-30) REVERT: y 54 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8666 (mtpt) REVERT: z 36 GLU cc_start: 0.8095 (tt0) cc_final: 0.7829 (tt0) REVERT: z 37 ARG cc_start: 0.8485 (mmp80) cc_final: 0.8176 (mmp80) REVERT: z 54 VAL cc_start: 0.9276 (t) cc_final: 0.9060 (p) REVERT: z 55 LYS cc_start: 0.9123 (tppt) cc_final: 0.8636 (tmtt) REVERT: z 57 GLU cc_start: 0.7991 (tp30) cc_final: 0.7602 (tp30) REVERT: D 19 ARG cc_start: 0.9158 (mtp85) cc_final: 0.8794 (mmm-85) REVERT: D 26 ASN cc_start: 0.8210 (m110) cc_final: 0.8008 (m-40) REVERT: F 37 GLN cc_start: 0.7384 (tp40) cc_final: 0.7074 (tp40) REVERT: G 6 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8140 (mmp-170) REVERT: G 26 MET cc_start: 0.8756 (tpt) cc_final: 0.8274 (mmm) REVERT: G 29 PHE cc_start: 0.9019 (m-80) cc_final: 0.8739 (m-80) REVERT: G 38 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7597 (m-70) REVERT: G 113 LEU cc_start: 0.9104 (tp) cc_final: 0.8453 (pp) REVERT: G 135 MET cc_start: 0.8982 (ppp) cc_final: 0.8569 (ppp) REVERT: G 147 LEU cc_start: 0.8632 (tt) cc_final: 0.7947 (tt) REVERT: G 150 ILE cc_start: 0.9106 (pt) cc_final: 0.8864 (tp) REVERT: G 153 MET cc_start: 0.6255 (tpp) cc_final: 0.5973 (tpp) REVERT: G 176 ASN cc_start: 0.8839 (m110) cc_final: 0.8406 (m110) REVERT: H 15 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7881 (pttp) REVERT: H 177 LEU cc_start: 0.9117 (mt) cc_final: 0.8889 (mp) REVERT: I 13 ARG cc_start: 0.6429 (tpt170) cc_final: 0.5527 (tpt170) REVERT: I 54 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8998 (mp) REVERT: I 81 LEU cc_start: 0.8997 (mt) cc_final: 0.8684 (mt) REVERT: I 165 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7951 (tm-30) REVERT: I 169 TRP cc_start: 0.8256 (p90) cc_final: 0.7480 (p90) REVERT: I 183 ARG cc_start: 0.7541 (ppt170) cc_final: 0.6812 (ppt170) REVERT: J 30 PHE cc_start: 0.8575 (m-80) cc_final: 0.7873 (m-10) REVERT: J 100 GLU cc_start: 0.8437 (tp30) cc_final: 0.8090 (tp30) REVERT: J 120 HIS cc_start: 0.4411 (OUTLIER) cc_final: 0.3777 (p-80) REVERT: K 45 ARG cc_start: 0.7302 (ptp-170) cc_final: 0.6964 (ptp-170) REVERT: K 70 VAL cc_start: 0.7873 (m) cc_final: 0.7475 (p) REVERT: K 81 ASN cc_start: 0.8815 (t0) cc_final: 0.8267 (t0) REVERT: L 22 LEU cc_start: 0.9385 (mt) cc_final: 0.9079 (mp) REVERT: L 109 LYS cc_start: 0.8282 (pptt) cc_final: 0.7864 (mppt) REVERT: L 125 ASP cc_start: 0.9201 (m-30) cc_final: 0.8589 (t0) REVERT: M 40 LYS cc_start: 0.9263 (tmtt) cc_final: 0.8624 (ptmm) REVERT: M 48 PHE cc_start: 0.8361 (p90) cc_final: 0.7803 (p90) REVERT: M 62 LEU cc_start: 0.9270 (mt) cc_final: 0.8890 (tt) REVERT: M 79 ARG cc_start: 0.8553 (ptt180) cc_final: 0.8044 (ptm-80) REVERT: M 85 TYR cc_start: 0.8371 (m-80) cc_final: 0.7978 (m-80) REVERT: M 88 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8132 (tptp) REVERT: M 93 LYS cc_start: 0.8356 (ttmm) cc_final: 0.8115 (ttmm) REVERT: M 126 CYS cc_start: 0.9331 (p) cc_final: 0.9095 (p) REVERT: N 38 PHE cc_start: 0.8837 (p90) cc_final: 0.8571 (p90) REVERT: N 56 MET cc_start: 0.8906 (tmm) cc_final: 0.7333 (mmm) REVERT: P 55 ARG cc_start: 0.8786 (mpp-170) cc_final: 0.8428 (mtp180) REVERT: P 63 GLN cc_start: 0.8162 (mm110) cc_final: 0.7943 (mm110) REVERT: P 113 THR cc_start: 0.8694 (p) cc_final: 0.8409 (p) REVERT: P 127 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7507 (ttm110) REVERT: Q 33 CYS cc_start: 0.8341 (t) cc_final: 0.8041 (t) REVERT: Q 37 TYR cc_start: 0.8145 (p90) cc_final: 0.7915 (p90) REVERT: Q 65 TYR cc_start: 0.7027 (t80) cc_final: 0.6441 (t80) REVERT: Q 74 GLN cc_start: 0.8540 (pp30) cc_final: 0.8330 (pp30) REVERT: Q 107 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7977 (mmtm) REVERT: Q 115 LYS cc_start: 0.8679 (mttt) cc_final: 0.8477 (mttt) REVERT: R 2 ARG cc_start: 0.8414 (ttm170) cc_final: 0.7827 (tpt90) REVERT: R 22 TYR cc_start: 0.7545 (t80) cc_final: 0.7305 (t80) REVERT: R 74 MET cc_start: 0.8770 (ttp) cc_final: 0.8240 (tmm) REVERT: R 80 MET cc_start: 0.7609 (mmp) cc_final: 0.7296 (mmm) REVERT: S 68 ARG cc_start: 0.5685 (ttt180) cc_final: 0.5332 (ttt180) REVERT: T 42 PHE cc_start: 0.8632 (m-80) cc_final: 0.7970 (m-80) REVERT: T 61 GLN cc_start: 0.8675 (tp40) cc_final: 0.8097 (tp40) REVERT: T 64 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8054 (tptm) REVERT: T 77 TYR cc_start: 0.8770 (t80) cc_final: 0.8445 (t80) REVERT: U 51 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7326 (ttp80) REVERT: U 52 LEU cc_start: 0.8423 (mp) cc_final: 0.7561 (tt) REVERT: V 17 GLU cc_start: 0.8793 (mp0) cc_final: 0.8562 (mp0) REVERT: V 20 ILE cc_start: 0.9001 (tt) cc_final: 0.8796 (tp) REVERT: V 26 ARG cc_start: 0.8799 (mtm110) cc_final: 0.7785 (ptt-90) REVERT: V 64 ARG cc_start: 0.7486 (ttm170) cc_final: 0.7257 (ttp80) REVERT: X 43 MET cc_start: 0.8394 (mmp) cc_final: 0.7885 (mmp) REVERT: X 65 MET cc_start: 0.7860 (mtt) cc_final: 0.6999 (mmm) REVERT: X 68 HIS cc_start: 0.8305 (m90) cc_final: 0.8080 (m-70) REVERT: Y 14 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8459 (tm-30) REVERT: Y 23 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.8043 (mmt180) REVERT: Y 47 GLN cc_start: 0.9320 (tp-100) cc_final: 0.9056 (tp-100) REVERT: Z 17 ARG cc_start: 0.5597 (tpt170) cc_final: 0.5343 (ttm-80) REVERT: a 8 MET cc_start: 0.5173 (ttm) cc_final: 0.4624 (tmm) outliers start: 239 outliers final: 158 residues processed: 1766 average time/residue: 1.3561 time to fit residues: 4083.2566 Evaluate side-chains 1670 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1501 time to evaluate : 6.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 91 ASP Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 41 GLU Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 LYS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 90 ASN Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 65 THR Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 529 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 793 optimal weight: 10.0000 chunk 649 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 955 optimal weight: 10.0000 chunk 1031 optimal weight: 10.0000 chunk 850 optimal weight: 30.0000 chunk 947 optimal weight: 30.0000 chunk 325 optimal weight: 6.9990 chunk 766 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- 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 162 GLN b 259 ASN c 173 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 ASN f 63 GLN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN g 28 ASN g 66 ASN g 133 GLN j 40 HIS ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 80 ASN s 57 ASN u 39 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS B 18 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 167 HIS H 18 ASN H 122 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 73 ASN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN Q 5 GLN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN Y 2 ASN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.137 161387 Z= 0.509 Angle : 0.858 11.926 241347 Z= 0.433 Chirality : 0.046 0.304 30852 Planarity : 0.007 0.106 13007 Dihedral : 23.649 179.926 80583 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.94 % Favored : 87.90 % Rotamer: Outliers : 8.27 % Allowed : 20.33 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.10), residues: 5919 helix: -1.54 (0.11), residues: 1858 sheet: -2.04 (0.16), residues: 914 loop : -2.74 (0.10), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 212 HIS 0.038 0.002 HIS G 38 PHE 0.034 0.003 PHE D 18 TYR 0.026 0.003 TYR o 64 ARG 0.019 0.001 ARG W 60 *********************** 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 1973 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1567 time to evaluate : 6.690 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 78 GLU cc_start: 0.8200 (tt0) cc_final: 0.7361 (mt-10) REVERT: b 100 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7742 (mmm-85) REVERT: b 123 ILE cc_start: 0.9124 (mm) cc_final: 0.8775 (mt) REVERT: b 159 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8544 (p) REVERT: b 238 ASN cc_start: 0.8709 (p0) cc_final: 0.8383 (p0) REVERT: b 241 LYS cc_start: 0.8444 (mttp) cc_final: 0.8040 (mttp) REVERT: b 269 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6939 (tmm-80) REVERT: c 80 TRP cc_start: 0.8662 (m-90) cc_final: 0.8421 (m-90) REVERT: c 128 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7857 (mtp180) REVERT: d 144 GLU cc_start: 0.7863 (tt0) cc_final: 0.7570 (tt0) REVERT: d 195 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7899 (tm-30) REVERT: e 64 PRO cc_start: 0.8669 (Cg_endo) cc_final: 0.8303 (Cg_exo) REVERT: e 89 THR cc_start: 0.7494 (p) cc_final: 0.7272 (p) REVERT: e 124 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8102 (mmm160) REVERT: e 142 TYR cc_start: 0.7075 (t80) cc_final: 0.6792 (t80) REVERT: e 161 SER cc_start: 0.8679 (t) cc_final: 0.8465 (t) REVERT: f 68 ARG cc_start: 0.8616 (tmt-80) cc_final: 0.8216 (ttp80) REVERT: f 87 GLN cc_start: 0.8239 (tt0) cc_final: 0.7862 (pt0) REVERT: f 162 ARG cc_start: 0.8708 (ptp-170) cc_final: 0.8278 (ptp-170) REVERT: g 127 GLU cc_start: 0.7586 (pp20) cc_final: 0.7306 (pp20) REVERT: g 129 GLU cc_start: 0.5160 (tt0) cc_final: 0.4636 (tm-30) REVERT: h 38 MET cc_start: 0.5642 (mpp) cc_final: 0.5344 (mpp) REVERT: i 116 MET cc_start: 0.1069 (mmt) cc_final: -0.0197 (mtp) REVERT: j 37 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8141 (tpt-90) REVERT: j 95 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7100 (ttp80) REVERT: j 106 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8421 (ttpp) REVERT: j 118 MET cc_start: 0.8402 (ptp) cc_final: 0.7964 (ptp) REVERT: j 136 GLN cc_start: 0.8467 (mt0) cc_final: 0.7973 (mm-40) REVERT: k 38 ILE cc_start: 0.9284 (mm) cc_final: 0.8907 (mm) REVERT: k 73 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8233 (p0) REVERT: l 3 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9122 (tt) REVERT: l 4 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (p0) REVERT: l 135 ILE cc_start: 0.9413 (mt) cc_final: 0.9162 (tt) REVERT: l 142 ILE cc_start: 0.8692 (mt) cc_final: 0.8466 (mm) REVERT: l 143 GLU cc_start: 0.8237 (pm20) cc_final: 0.7965 (pm20) REVERT: m 13 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8422 (m170) REVERT: m 105 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6985 (mtp) REVERT: n 49 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7931 (mt-10) REVERT: n 72 ASP cc_start: 0.8596 (t0) cc_final: 0.8276 (t0) REVERT: n 74 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8341 (tm-30) REVERT: n 78 LYS cc_start: 0.9177 (tppp) cc_final: 0.8872 (tppp) REVERT: n 110 MET cc_start: 0.8392 (mmp) cc_final: 0.7998 (mmp) REVERT: p 105 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8259 (mmtt) REVERT: q 31 TYR cc_start: 0.8903 (t80) cc_final: 0.8645 (t80) REVERT: q 46 TYR cc_start: 0.8921 (t80) cc_final: 0.8687 (t80) REVERT: q 51 GLN cc_start: 0.8321 (tt0) cc_final: 0.8064 (tt0) REVERT: q 75 TYR cc_start: 0.8840 (t80) cc_final: 0.7692 (t80) REVERT: r 6 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8307 (tm-30) REVERT: r 13 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8466 (ttt-90) REVERT: r 35 PHE cc_start: 0.8542 (m-10) cc_final: 0.7934 (m-10) REVERT: s 1 MET cc_start: 0.6930 (ttm) cc_final: 0.6448 (ttm) REVERT: s 8 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8051 (mtp-110) REVERT: s 25 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8282 (ttm-80) REVERT: s 31 GLN cc_start: 0.8566 (mp10) cc_final: 0.8283 (mm-40) REVERT: s 62 ASP cc_start: 0.7654 (p0) cc_final: 0.6332 (p0) REVERT: s 74 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.7898 (tt) REVERT: s 84 ARG cc_start: 0.7947 (mmt-90) cc_final: 0.7377 (mmt90) REVERT: s 109 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7930 (p0) REVERT: t 12 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7867 (mmm-85) REVERT: t 32 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9000 (pp) REVERT: t 33 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8171 (mtmm) REVERT: t 48 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8026 (mm-40) REVERT: t 56 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7676 (mm-30) REVERT: t 80 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.7891 (p-90) REVERT: u 17 ASP cc_start: 0.7285 (t0) cc_final: 0.6933 (t0) REVERT: u 72 PHE cc_start: 0.7464 (t80) cc_final: 0.7158 (t80) REVERT: u 80 ASP cc_start: 0.7705 (t70) cc_final: 0.7435 (t0) REVERT: v 5 ASN cc_start: 0.8704 (m-40) cc_final: 0.7976 (p0) REVERT: v 26 PHE cc_start: 0.8739 (p90) cc_final: 0.8412 (p90) REVERT: v 42 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7942 (pp) REVERT: v 53 LYS cc_start: 0.9109 (mttt) cc_final: 0.8817 (mmtp) REVERT: v 70 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7559 (tp) REVERT: v 75 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8069 (tp40) REVERT: v 87 GLN cc_start: 0.8288 (mp10) cc_final: 0.7871 (mp10) REVERT: w 11 ASP cc_start: 0.8367 (t0) cc_final: 0.7756 (t0) REVERT: w 64 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8522 (ttpt) REVERT: x 55 MET cc_start: 0.8360 (mtp) cc_final: 0.8128 (mtt) REVERT: y 4 LYS cc_start: 0.9137 (pptt) cc_final: 0.8899 (pptt) REVERT: y 54 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8761 (mtpt) REVERT: z 36 GLU cc_start: 0.8255 (tt0) cc_final: 0.7722 (pp20) REVERT: D 19 ARG cc_start: 0.9197 (mtp85) cc_final: 0.8557 (mmm-85) REVERT: D 35 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8113 (mtt90) REVERT: G 6 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8070 (mmp-170) REVERT: G 26 MET cc_start: 0.8674 (tpt) cc_final: 0.8423 (tpt) REVERT: G 29 PHE cc_start: 0.8973 (m-80) cc_final: 0.8604 (m-80) REVERT: G 44 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9329 (pptt) REVERT: G 113 LEU cc_start: 0.9105 (tp) cc_final: 0.8815 (tp) REVERT: G 135 MET cc_start: 0.8914 (ppp) cc_final: 0.8510 (ppp) REVERT: G 147 LEU cc_start: 0.8649 (tt) cc_final: 0.8346 (tt) REVERT: G 166 ASP cc_start: 0.8564 (p0) cc_final: 0.8288 (p0) REVERT: G 169 HIS cc_start: 0.9317 (p-80) cc_final: 0.8979 (p-80) REVERT: G 176 ASN cc_start: 0.8882 (m110) cc_final: 0.8529 (m110) REVERT: H 15 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7768 (pttp) REVERT: H 150 VAL cc_start: 0.7627 (p) cc_final: 0.7299 (m) REVERT: I 2 ARG cc_start: 0.8469 (ttm170) cc_final: 0.8262 (mtm180) REVERT: I 13 ARG cc_start: 0.6594 (tpt170) cc_final: 0.5748 (tpt170) REVERT: I 54 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8998 (mt) REVERT: I 81 LEU cc_start: 0.8955 (mt) cc_final: 0.8703 (mt) REVERT: I 165 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7923 (tm-30) REVERT: I 169 TRP cc_start: 0.8268 (p90) cc_final: 0.7520 (p90) REVERT: I 183 ARG cc_start: 0.7551 (ppt170) cc_final: 0.6883 (ppt170) REVERT: J 30 PHE cc_start: 0.8552 (m-80) cc_final: 0.7862 (m-10) REVERT: J 35 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7658 (tp) REVERT: J 75 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8663 (pp) REVERT: J 100 GLU cc_start: 0.8443 (tp30) cc_final: 0.8069 (tp30) REVERT: J 120 HIS cc_start: 0.4901 (OUTLIER) cc_final: 0.4238 (p-80) REVERT: J 164 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3541 (pt) REVERT: K 25 TYR cc_start: 0.7469 (m-10) cc_final: 0.7210 (m-10) REVERT: K 40 GLU cc_start: 0.6587 (mt-10) cc_final: 0.5990 (mt-10) REVERT: K 45 ARG cc_start: 0.7273 (ptp-170) cc_final: 0.7065 (ptp-170) REVERT: K 78 PHE cc_start: 0.8742 (m-10) cc_final: 0.8218 (m-80) REVERT: K 81 ASN cc_start: 0.8806 (t0) cc_final: 0.8414 (t0) REVERT: K 90 MET cc_start: 0.8335 (mmm) cc_final: 0.7638 (mmt) REVERT: L 21 LEU cc_start: 0.9679 (pt) cc_final: 0.9458 (pp) REVERT: L 61 PHE cc_start: 0.8881 (t80) cc_final: 0.8556 (t80) REVERT: L 121 ASN cc_start: 0.8880 (m-40) cc_final: 0.8646 (m-40) REVERT: L 125 ASP cc_start: 0.9395 (m-30) cc_final: 0.8769 (t0) REVERT: M 12 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7930 (mtt180) REVERT: M 61 THR cc_start: 0.8274 (p) cc_final: 0.8032 (p) REVERT: M 79 ARG cc_start: 0.8684 (ptt180) cc_final: 0.8173 (ptm-80) REVERT: M 85 TYR cc_start: 0.8101 (m-80) cc_final: 0.7846 (m-80) REVERT: M 93 LYS cc_start: 0.8317 (ttmm) cc_final: 0.7996 (ttmm) REVERT: M 105 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8866 (t) REVERT: N 38 PHE cc_start: 0.8854 (p90) cc_final: 0.8608 (p90) REVERT: P 36 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: P 55 ARG cc_start: 0.8808 (mpp-170) cc_final: 0.8534 (mtp180) REVERT: P 63 GLN cc_start: 0.8349 (mm110) cc_final: 0.8103 (mm110) REVERT: P 79 LYS cc_start: 0.9312 (mmtp) cc_final: 0.9110 (mmmm) REVERT: P 113 THR cc_start: 0.8869 (p) cc_final: 0.8590 (p) REVERT: P 127 ARG cc_start: 0.7737 (ttp-110) cc_final: 0.7358 (ttp-110) REVERT: Q 33 CYS cc_start: 0.8734 (t) cc_final: 0.8085 (t) REVERT: Q 74 GLN cc_start: 0.8604 (pp30) cc_final: 0.8383 (pp30) REVERT: Q 107 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8059 (mmtm) REVERT: Q 109 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8043 (mmm-85) REVERT: Q 115 LYS cc_start: 0.8730 (mttt) cc_final: 0.8518 (mtmt) REVERT: R 74 MET cc_start: 0.8860 (ttp) cc_final: 0.8411 (tmm) REVERT: S 62 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.4218 (ptt-90) REVERT: T 57 ARG cc_start: 0.7813 (ttt-90) cc_final: 0.7277 (ttp-170) REVERT: U 1 MET cc_start: 0.7570 (ttm) cc_final: 0.7285 (ttm) REVERT: U 51 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7092 (ttp80) REVERT: U 52 LEU cc_start: 0.8280 (mp) cc_final: 0.7550 (tt) REVERT: V 68 LYS cc_start: 0.8742 (tttt) cc_final: 0.8525 (ttpt) REVERT: W 37 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8039 (mptt) REVERT: W 53 GLN cc_start: 0.8197 (mt0) cc_final: 0.7975 (mt0) REVERT: W 56 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.7688 (mpt-90) REVERT: W 63 TYR cc_start: 0.8979 (t80) cc_final: 0.8316 (t80) REVERT: X 38 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7828 (t) REVERT: X 43 MET cc_start: 0.8341 (mmp) cc_final: 0.7701 (mmp) REVERT: X 57 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.7968 (m) REVERT: X 65 MET cc_start: 0.8103 (mtt) cc_final: 0.7355 (mmm) REVERT: X 68 HIS cc_start: 0.8267 (m90) cc_final: 0.8037 (m-70) REVERT: Y 23 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7979 (mmt180) REVERT: Y 47 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8769 (tp-100) REVERT: Y 59 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7648 (mtp-110) REVERT: a 8 MET cc_start: 0.5197 (ttm) cc_final: 0.4594 (tmm) outliers start: 406 outliers final: 274 residues processed: 1753 average time/residue: 1.3396 time to fit residues: 4004.4488 Evaluate side-chains 1768 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1470 time to evaluate : 6.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 91 ASP Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 LYS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 105 MET Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 8 ILE Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 59 LEU Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 12 SER Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 943 optimal weight: 30.0000 chunk 718 optimal weight: 20.0000 chunk 495 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 455 optimal weight: 2.9990 chunk 641 optimal weight: 30.0000 chunk 958 optimal weight: 5.9990 chunk 1014 optimal weight: 7.9990 chunk 500 optimal weight: 5.9990 chunk 908 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 162 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN m 17 ASN p 11 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 ASN u 68 ASN v 49 ASN v 78 GLN ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 13 ASN D 26 ASN G 38 HIS G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 GLN U 79 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN Y 69 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 161387 Z= 0.332 Angle : 0.681 11.112 241347 Z= 0.347 Chirality : 0.039 0.319 30852 Planarity : 0.005 0.062 13007 Dihedral : 23.494 179.441 80579 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.93 % Favored : 89.93 % Rotamer: Outliers : 7.50 % Allowed : 23.92 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.10), residues: 5919 helix: -1.10 (0.11), residues: 1873 sheet: -1.87 (0.16), residues: 956 loop : -2.61 (0.10), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 212 HIS 0.008 0.002 HIS T 49 PHE 0.035 0.002 PHE D 18 TYR 0.032 0.002 TYR g 25 ARG 0.012 0.001 ARG t 73 *********************** 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 1925 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1557 time to evaluate : 6.729 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 123 ILE cc_start: 0.8962 (mm) cc_final: 0.8650 (mt) REVERT: b 159 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8562 (p) REVERT: b 238 ASN cc_start: 0.8640 (p0) cc_final: 0.8324 (p0) REVERT: c 4 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (mp) REVERT: c 7 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8547 (ttmt) REVERT: c 36 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: c 43 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: c 80 TRP cc_start: 0.8587 (m-90) cc_final: 0.8377 (m-90) REVERT: c 128 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7814 (mtp180) REVERT: d 115 GLN cc_start: 0.8660 (mt0) cc_final: 0.8023 (mt0) REVERT: d 144 GLU cc_start: 0.7756 (tt0) cc_final: 0.7401 (mp0) REVERT: d 198 GLU cc_start: 0.8121 (tp30) cc_final: 0.7630 (tp30) REVERT: e 6 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.6663 (t80) REVERT: e 64 PRO cc_start: 0.8686 (Cg_endo) cc_final: 0.8307 (Cg_exo) REVERT: e 109 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8543 (tmt-80) REVERT: e 124 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.7973 (mmm160) REVERT: e 135 ILE cc_start: 0.8927 (pt) cc_final: 0.8494 (mt) REVERT: e 161 SER cc_start: 0.8698 (t) cc_final: 0.8444 (t) REVERT: e 169 LEU cc_start: 0.8069 (mm) cc_final: 0.7617 (pp) REVERT: f 63 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8708 (mm-40) REVERT: f 82 PHE cc_start: 0.8269 (m-80) cc_final: 0.8034 (m-10) REVERT: f 162 ARG cc_start: 0.8531 (ptp-170) cc_final: 0.8262 (ptp-170) REVERT: g 129 GLU cc_start: 0.5086 (tt0) cc_final: 0.4736 (tm-30) REVERT: i 116 MET cc_start: 0.1857 (mmt) cc_final: 0.1503 (mpp) REVERT: j 44 TYR cc_start: 0.8759 (t80) cc_final: 0.8063 (t80) REVERT: j 99 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8294 (ttm110) REVERT: j 106 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8449 (tttt) REVERT: j 118 MET cc_start: 0.8367 (ptp) cc_final: 0.8155 (ptp) REVERT: j 136 GLN cc_start: 0.8491 (mt0) cc_final: 0.7933 (mm-40) REVERT: k 23 LYS cc_start: 0.7676 (tppt) cc_final: 0.7181 (tppp) REVERT: k 38 ILE cc_start: 0.9308 (mm) cc_final: 0.8952 (mm) REVERT: k 45 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7468 (tm-30) REVERT: k 73 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8114 (p0) REVERT: k 113 MET cc_start: 0.7935 (tpt) cc_final: 0.7663 (tpt) REVERT: l 3 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9076 (tt) REVERT: l 4 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8453 (p0) REVERT: l 135 ILE cc_start: 0.9407 (mt) cc_final: 0.9164 (tt) REVERT: l 143 GLU cc_start: 0.8211 (pm20) cc_final: 0.7941 (pm20) REVERT: m 47 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7313 (tm-30) REVERT: m 105 MET cc_start: 0.7367 (ttm) cc_final: 0.7034 (mtm) REVERT: n 72 ASP cc_start: 0.8491 (t0) cc_final: 0.8277 (t0) REVERT: n 78 LYS cc_start: 0.9186 (tppp) cc_final: 0.8819 (tppp) REVERT: n 110 MET cc_start: 0.8328 (mmp) cc_final: 0.8093 (mmp) REVERT: o 85 LYS cc_start: 0.9300 (mtpp) cc_final: 0.9029 (mtpp) REVERT: p 10 GLU cc_start: 0.8227 (pm20) cc_final: 0.7929 (pm20) REVERT: p 87 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7534 (ttp-170) REVERT: p 105 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8249 (mmtt) REVERT: p 111 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6577 (mm-30) REVERT: q 51 GLN cc_start: 0.8236 (tt0) cc_final: 0.7926 (tt0) REVERT: q 75 TYR cc_start: 0.8800 (t80) cc_final: 0.7606 (t80) REVERT: r 6 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8284 (tm-30) REVERT: r 13 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8508 (ttt-90) REVERT: r 60 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8459 (ttmm) REVERT: s 8 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7958 (mtp-110) REVERT: s 31 GLN cc_start: 0.8622 (mp10) cc_final: 0.8335 (mm-40) REVERT: s 52 GLU cc_start: 0.8538 (tp30) cc_final: 0.8275 (tp30) REVERT: s 84 ARG cc_start: 0.7822 (mmt-90) cc_final: 0.7472 (mmt90) REVERT: s 88 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.7804 (mmm160) REVERT: s 109 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7919 (p0) REVERT: t 32 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8903 (pp) REVERT: t 48 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7984 (mm110) REVERT: t 56 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7690 (mm-30) REVERT: t 80 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.7666 (p-90) REVERT: u 17 ASP cc_start: 0.7168 (t0) cc_final: 0.6870 (t0) REVERT: u 72 PHE cc_start: 0.7385 (t80) cc_final: 0.7090 (t80) REVERT: v 5 ASN cc_start: 0.8659 (m-40) cc_final: 0.7813 (p0) REVERT: v 42 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7888 (pp) REVERT: v 53 LYS cc_start: 0.9204 (mttt) cc_final: 0.8885 (mmtp) REVERT: v 55 GLU cc_start: 0.8862 (mp0) cc_final: 0.8100 (pm20) REVERT: v 58 SER cc_start: 0.6994 (p) cc_final: 0.6279 (t) REVERT: v 75 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8180 (tp40) REVERT: v 87 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: w 11 ASP cc_start: 0.8308 (t0) cc_final: 0.7701 (t0) REVERT: w 64 LYS cc_start: 0.8954 (ttpt) cc_final: 0.8626 (ttpp) REVERT: x 9 LYS cc_start: 0.9270 (mttm) cc_final: 0.8989 (mtpp) REVERT: x 61 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8685 (mttp) REVERT: y 1 MET cc_start: 0.8325 (mmm) cc_final: 0.7986 (mmm) REVERT: y 27 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8373 (t0) REVERT: y 31 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8198 (mm-40) REVERT: y 41 HIS cc_start: 0.8884 (p-80) cc_final: 0.8221 (p-80) REVERT: y 54 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8725 (mtpt) REVERT: z 37 ARG cc_start: 0.8576 (mmp80) cc_final: 0.8120 (mmp-170) REVERT: z 54 VAL cc_start: 0.9290 (t) cc_final: 0.9071 (p) REVERT: z 55 LYS cc_start: 0.9164 (tppt) cc_final: 0.8809 (tmtt) REVERT: z 57 GLU cc_start: 0.7914 (tp30) cc_final: 0.7477 (tp30) REVERT: D 19 ARG cc_start: 0.9226 (mtp85) cc_final: 0.8623 (mmm-85) REVERT: D 35 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8207 (mtt90) REVERT: G 6 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8075 (mmp-170) REVERT: G 26 MET cc_start: 0.8827 (tpt) cc_final: 0.8496 (tpt) REVERT: G 29 PHE cc_start: 0.8890 (m-80) cc_final: 0.8555 (m-80) REVERT: G 68 PHE cc_start: 0.8040 (m-10) cc_final: 0.7833 (m-80) REVERT: G 135 MET cc_start: 0.8920 (ppp) cc_final: 0.8531 (ppp) REVERT: G 147 LEU cc_start: 0.8649 (tt) cc_final: 0.8254 (tt) REVERT: G 166 ASP cc_start: 0.8386 (p0) cc_final: 0.8035 (p0) REVERT: G 176 ASN cc_start: 0.8948 (m110) cc_final: 0.8671 (m110) REVERT: H 15 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7938 (pttp) REVERT: H 150 VAL cc_start: 0.7606 (p) cc_final: 0.7277 (m) REVERT: I 13 ARG cc_start: 0.6452 (tpt170) cc_final: 0.5568 (tpt170) REVERT: I 54 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9002 (mp) REVERT: I 81 LEU cc_start: 0.8912 (mt) cc_final: 0.8655 (mt) REVERT: I 165 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7904 (tm-30) REVERT: I 169 TRP cc_start: 0.8205 (p90) cc_final: 0.7412 (p90) REVERT: I 183 ARG cc_start: 0.7762 (ppt170) cc_final: 0.6957 (ppt170) REVERT: I 198 LEU cc_start: 0.8658 (mm) cc_final: 0.8272 (tp) REVERT: J 30 PHE cc_start: 0.8586 (m-80) cc_final: 0.7893 (m-10) REVERT: J 75 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (pp) REVERT: J 100 GLU cc_start: 0.8392 (tp30) cc_final: 0.7872 (tp30) REVERT: J 120 HIS cc_start: 0.4805 (OUTLIER) cc_final: 0.3542 (p-80) REVERT: J 164 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.3261 (pt) REVERT: K 1 MET cc_start: 0.7821 (ttm) cc_final: 0.7464 (mmm) REVERT: K 35 LYS cc_start: 0.8445 (mmtm) cc_final: 0.7978 (mmtm) REVERT: K 59 TYR cc_start: 0.7042 (m-80) cc_final: 0.6796 (m-10) REVERT: K 81 ASN cc_start: 0.8530 (t0) cc_final: 0.8085 (t0) REVERT: K 85 ILE cc_start: 0.7608 (mt) cc_final: 0.7303 (pt) REVERT: K 90 MET cc_start: 0.8168 (mmm) cc_final: 0.7518 (mmt) REVERT: L 29 LEU cc_start: 0.8347 (mm) cc_final: 0.8016 (mm) REVERT: M 62 LEU cc_start: 0.9370 (tp) cc_final: 0.8908 (tt) REVERT: M 79 ARG cc_start: 0.8666 (ptt180) cc_final: 0.8313 (ptm-80) REVERT: M 85 TYR cc_start: 0.8193 (m-80) cc_final: 0.7818 (m-80) REVERT: M 87 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7973 (mtp-110) REVERT: M 93 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8097 (ttmm) REVERT: M 95 MET cc_start: 0.8083 (mmp) cc_final: 0.7824 (mmp) REVERT: N 38 PHE cc_start: 0.8881 (p90) cc_final: 0.8657 (p90) REVERT: N 86 LEU cc_start: 0.9376 (mt) cc_final: 0.9146 (pp) REVERT: P 52 ARG cc_start: 0.8451 (mmm160) cc_final: 0.8194 (mmm160) REVERT: P 55 ARG cc_start: 0.8877 (mpp-170) cc_final: 0.8482 (mtp85) REVERT: P 63 GLN cc_start: 0.8348 (mm110) cc_final: 0.8102 (mm110) REVERT: P 127 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.7172 (ttp-110) REVERT: Q 33 CYS cc_start: 0.8773 (t) cc_final: 0.8275 (t) REVERT: Q 82 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7949 (ptm-80) REVERT: Q 85 ARG cc_start: 0.6671 (ptm160) cc_final: 0.6039 (ptm160) REVERT: Q 107 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8163 (mmtm) REVERT: R 58 GLU cc_start: 0.7678 (tp30) cc_final: 0.6856 (tm-30) REVERT: R 74 MET cc_start: 0.8924 (ttp) cc_final: 0.8599 (tmm) REVERT: S 68 ARG cc_start: 0.5615 (ttt180) cc_final: 0.5389 (ttt180) REVERT: T 77 TYR cc_start: 0.8897 (t80) cc_final: 0.8579 (t80) REVERT: U 28 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7496 (ttp80) REVERT: U 51 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7377 (ttp-170) REVERT: U 52 LEU cc_start: 0.8338 (mp) cc_final: 0.7461 (tt) REVERT: V 17 GLU cc_start: 0.8557 (mp0) cc_final: 0.8299 (mp0) REVERT: V 26 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7428 (mtm-85) REVERT: W 37 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8018 (mptt) REVERT: W 56 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7763 (mpt-90) REVERT: W 63 TYR cc_start: 0.8905 (t80) cc_final: 0.8396 (t80) REVERT: X 43 MET cc_start: 0.8285 (mmp) cc_final: 0.7610 (mmm) REVERT: X 65 MET cc_start: 0.7904 (mtt) cc_final: 0.7018 (mmm) REVERT: Y 13 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8576 (m) REVERT: Y 14 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8084 (tm-30) REVERT: Y 59 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7717 (mtp-110) REVERT: a 8 MET cc_start: 0.5303 (ttm) cc_final: 0.4643 (tmm) outliers start: 368 outliers final: 250 residues processed: 1723 average time/residue: 1.3618 time to fit residues: 4018.8665 Evaluate side-chains 1771 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1499 time to evaluate : 8.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 7 LYS Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 LYS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 12 SER Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 LYS Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain x residue 57 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 845 optimal weight: 10.0000 chunk 576 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 755 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 866 optimal weight: 10.0000 chunk 701 optimal weight: 40.0000 chunk 1 optimal weight: 5.9990 chunk 518 optimal weight: 10.0000 chunk 910 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- 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 162 GLN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 ASN f 47 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN P 14 GLN Q 5 GLN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 161387 Z= 0.334 Angle : 0.689 13.646 241347 Z= 0.349 Chirality : 0.039 0.277 30852 Planarity : 0.005 0.068 13007 Dihedral : 23.520 179.734 80578 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.81 % Favored : 89.05 % Rotamer: Outliers : 8.07 % Allowed : 24.73 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 5919 helix: -0.91 (0.11), residues: 1869 sheet: -1.75 (0.16), residues: 928 loop : -2.49 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 212 HIS 0.015 0.002 HIS O 15 PHE 0.034 0.002 PHE M 65 TYR 0.041 0.002 TYR g 25 ARG 0.017 0.001 ARG e 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 1920 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 1524 time to evaluate : 6.639 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: b 78 GLU cc_start: 0.8082 (tt0) cc_final: 0.7827 (mt-10) REVERT: b 100 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7872 (mtt90) REVERT: b 123 ILE cc_start: 0.8955 (mm) cc_final: 0.8621 (mt) REVERT: b 159 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8570 (p) REVERT: b 238 ASN cc_start: 0.8551 (p0) cc_final: 0.8287 (p0) REVERT: b 269 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6928 (tmm-80) REVERT: c 43 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: c 80 TRP cc_start: 0.8573 (m-90) cc_final: 0.8323 (m-90) REVERT: c 128 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7844 (mtp180) REVERT: d 115 GLN cc_start: 0.8536 (mt0) cc_final: 0.7940 (mt0) REVERT: d 144 GLU cc_start: 0.7797 (tt0) cc_final: 0.7405 (mp0) REVERT: d 198 GLU cc_start: 0.8145 (tp30) cc_final: 0.7647 (tp30) REVERT: e 6 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6565 (t80) REVERT: e 43 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8221 (tp) REVERT: e 64 PRO cc_start: 0.8662 (Cg_endo) cc_final: 0.8265 (Cg_exo) REVERT: e 86 CYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6589 (p) REVERT: e 109 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8530 (tmt-80) REVERT: e 120 SER cc_start: 0.7769 (p) cc_final: 0.6839 (t) REVERT: e 124 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8029 (mmm160) REVERT: e 134 GLN cc_start: 0.8433 (pm20) cc_final: 0.8162 (mp10) REVERT: e 135 ILE cc_start: 0.8951 (pt) cc_final: 0.8578 (mm) REVERT: e 156 THR cc_start: 0.7736 (t) cc_final: 0.7483 (t) REVERT: e 161 SER cc_start: 0.8671 (t) cc_final: 0.8223 (t) REVERT: f 82 PHE cc_start: 0.8173 (m-80) cc_final: 0.7811 (m-10) REVERT: f 142 GLN cc_start: 0.9001 (tp40) cc_final: 0.8497 (tp40) REVERT: f 148 ARG cc_start: 0.8515 (ttt-90) cc_final: 0.8273 (tpt-90) REVERT: f 150 TYR cc_start: 0.8233 (m-10) cc_final: 0.7654 (m-80) REVERT: g 45 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8737 (mm-30) REVERT: g 129 GLU cc_start: 0.4881 (tt0) cc_final: 0.4525 (tm-30) REVERT: g 137 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6381 (mt-10) REVERT: h 1 MET cc_start: 0.3808 (ptt) cc_final: 0.3435 (ttp) REVERT: h 3 LEU cc_start: 0.8576 (pp) cc_final: 0.7889 (tp) REVERT: h 38 MET cc_start: 0.5711 (mpp) cc_final: 0.5485 (mpp) REVERT: j 37 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7942 (tpt-90) REVERT: j 44 TYR cc_start: 0.8713 (t80) cc_final: 0.8018 (t80) REVERT: j 74 TYR cc_start: 0.8718 (m-10) cc_final: 0.8359 (m-10) REVERT: j 106 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8449 (tttt) REVERT: j 118 MET cc_start: 0.8339 (ptp) cc_final: 0.7774 (ptp) REVERT: j 131 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8614 (p0) REVERT: j 136 GLN cc_start: 0.8492 (mt0) cc_final: 0.7981 (mm-40) REVERT: k 23 LYS cc_start: 0.7650 (tppt) cc_final: 0.7136 (tppp) REVERT: k 38 ILE cc_start: 0.9287 (mm) cc_final: 0.8943 (mm) REVERT: k 73 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8115 (p0) REVERT: l 143 GLU cc_start: 0.8014 (pm20) cc_final: 0.7798 (pm20) REVERT: m 40 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7457 (mtp180) REVERT: m 47 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7258 (tm-30) REVERT: m 105 MET cc_start: 0.7400 (ttm) cc_final: 0.7006 (mtm) REVERT: n 72 ASP cc_start: 0.8487 (t0) cc_final: 0.8267 (t0) REVERT: n 78 LYS cc_start: 0.9174 (tppp) cc_final: 0.8860 (tppp) REVERT: n 110 MET cc_start: 0.8323 (mmp) cc_final: 0.8072 (mmp) REVERT: n 115 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8101 (mp) REVERT: o 13 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8001 (tpt-90) REVERT: p 10 GLU cc_start: 0.8147 (pm20) cc_final: 0.7915 (pm20) REVERT: p 87 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7565 (ttp-170) REVERT: p 105 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8224 (mmtt) REVERT: q 51 GLN cc_start: 0.8285 (tt0) cc_final: 0.7977 (tt0) REVERT: q 75 TYR cc_start: 0.8805 (t80) cc_final: 0.7754 (t80) REVERT: q 110 GLU cc_start: 0.8286 (tp30) cc_final: 0.7827 (tp30) REVERT: r 6 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8292 (tm-30) REVERT: r 97 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8249 (tptp) REVERT: s 8 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8047 (mtp-110) REVERT: s 25 ARG cc_start: 0.8900 (ttm-80) cc_final: 0.8168 (ttm-80) REVERT: s 59 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8222 (mm-30) REVERT: s 84 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7440 (mmt90) REVERT: t 32 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8905 (pp) REVERT: t 48 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7998 (mm-40) REVERT: t 80 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.7606 (p-90) REVERT: u 17 ASP cc_start: 0.7071 (t0) cc_final: 0.6739 (t0) REVERT: u 72 PHE cc_start: 0.7491 (t80) cc_final: 0.7123 (t80) REVERT: u 80 ASP cc_start: 0.7789 (t70) cc_final: 0.7544 (t70) REVERT: v 5 ASN cc_start: 0.8663 (m-40) cc_final: 0.7779 (p0) REVERT: v 7 GLU cc_start: 0.8232 (tp30) cc_final: 0.7537 (tm-30) REVERT: v 26 PHE cc_start: 0.8491 (p90) cc_final: 0.8243 (p90) REVERT: v 42 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.7840 (pp) REVERT: v 48 MET cc_start: 0.8461 (tpt) cc_final: 0.8087 (tpp) REVERT: v 53 LYS cc_start: 0.9193 (mttt) cc_final: 0.8885 (mmtp) REVERT: v 70 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7507 (tp) REVERT: v 75 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8248 (tp40) REVERT: v 87 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: w 11 ASP cc_start: 0.8243 (t0) cc_final: 0.7798 (t0) REVERT: w 64 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8529 (ttpp) REVERT: x 9 LYS cc_start: 0.9180 (mttm) cc_final: 0.8895 (mtpp) REVERT: y 31 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: y 41 HIS cc_start: 0.8942 (p-80) cc_final: 0.8222 (p-80) REVERT: y 45 GLN cc_start: 0.8586 (pp30) cc_final: 0.8221 (pp30) REVERT: y 54 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8729 (mtpt) REVERT: z 36 GLU cc_start: 0.8277 (tt0) cc_final: 0.7726 (tp30) REVERT: z 55 LYS cc_start: 0.9167 (tppt) cc_final: 0.8804 (tmtt) REVERT: z 57 GLU cc_start: 0.7905 (tp30) cc_final: 0.7488 (tp30) REVERT: D 19 ARG cc_start: 0.9188 (mtp85) cc_final: 0.8519 (mmm-85) REVERT: D 35 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8258 (mtt90) REVERT: G 26 MET cc_start: 0.8820 (tpt) cc_final: 0.8506 (tpt) REVERT: G 29 PHE cc_start: 0.8920 (m-80) cc_final: 0.8552 (m-80) REVERT: G 135 MET cc_start: 0.8933 (ppp) cc_final: 0.8559 (ppp) REVERT: G 147 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8268 (tt) REVERT: G 166 ASP cc_start: 0.8246 (p0) cc_final: 0.7917 (p0) REVERT: H 15 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7904 (pttp) REVERT: H 150 VAL cc_start: 0.7609 (p) cc_final: 0.7291 (m) REVERT: I 13 ARG cc_start: 0.6827 (tpt170) cc_final: 0.5952 (tpt170) REVERT: I 54 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9006 (mp) REVERT: I 81 LEU cc_start: 0.8917 (mt) cc_final: 0.8574 (mt) REVERT: I 97 LEU cc_start: 0.8621 (pt) cc_final: 0.8413 (pt) REVERT: I 134 TYR cc_start: 0.8616 (t80) cc_final: 0.8407 (t80) REVERT: I 165 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7907 (tm-30) REVERT: I 169 TRP cc_start: 0.8185 (p90) cc_final: 0.7305 (p90) REVERT: I 183 ARG cc_start: 0.7661 (ppt170) cc_final: 0.6977 (ppt170) REVERT: I 198 LEU cc_start: 0.8694 (mm) cc_final: 0.8316 (tp) REVERT: J 30 PHE cc_start: 0.8600 (m-80) cc_final: 0.7885 (m-10) REVERT: J 75 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8677 (pp) REVERT: J 97 PRO cc_start: 0.7204 (Cg_endo) cc_final: 0.6898 (Cg_exo) REVERT: J 120 HIS cc_start: 0.5054 (OUTLIER) cc_final: 0.4365 (p-80) REVERT: K 11 HIS cc_start: 0.8281 (t70) cc_final: 0.7705 (t-90) REVERT: K 40 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6086 (mt-10) REVERT: K 59 TYR cc_start: 0.7437 (m-80) cc_final: 0.7169 (m-80) REVERT: K 81 ASN cc_start: 0.8688 (t0) cc_final: 0.8230 (t0) REVERT: K 90 MET cc_start: 0.8295 (mmm) cc_final: 0.7582 (mmt) REVERT: L 29 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8099 (mm) REVERT: M 8 ASP cc_start: 0.8345 (t0) cc_final: 0.8137 (t0) REVERT: M 12 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7226 (mtm-85) REVERT: M 62 LEU cc_start: 0.9336 (tp) cc_final: 0.8865 (tt) REVERT: M 79 ARG cc_start: 0.8687 (ptt180) cc_final: 0.8295 (ptm-80) REVERT: M 85 TYR cc_start: 0.8261 (m-80) cc_final: 0.7755 (m-80) REVERT: M 86 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6944 (mmtm) REVERT: M 87 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7816 (mtp-110) REVERT: M 88 LYS cc_start: 0.9009 (tptp) cc_final: 0.8206 (tptp) REVERT: M 93 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8023 (ttmm) REVERT: M 95 MET cc_start: 0.8045 (mmp) cc_final: 0.7348 (tpp) REVERT: N 38 PHE cc_start: 0.8877 (p90) cc_final: 0.8675 (p90) REVERT: O 48 ARG cc_start: 0.6229 (mtm-85) cc_final: 0.5541 (mmt-90) REVERT: P 52 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8151 (mmm160) REVERT: P 55 ARG cc_start: 0.8917 (mpp-170) cc_final: 0.8470 (mtp85) REVERT: P 63 GLN cc_start: 0.8318 (mm110) cc_final: 0.8072 (mm110) REVERT: P 127 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7158 (ttp-110) REVERT: Q 33 CYS cc_start: 0.8769 (t) cc_final: 0.8271 (t) REVERT: Q 82 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7955 (ptm-80) REVERT: Q 85 ARG cc_start: 0.6667 (ptm160) cc_final: 0.6022 (ptm160) REVERT: Q 107 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8094 (mmtm) REVERT: R 68 LEU cc_start: 0.9072 (tt) cc_final: 0.8861 (pp) REVERT: R 74 MET cc_start: 0.9019 (ttp) cc_final: 0.8706 (tmm) REVERT: S 5 MET cc_start: 0.7016 (mmm) cc_final: 0.6583 (mtt) REVERT: T 39 GLN cc_start: 0.7528 (mm110) cc_final: 0.7319 (mm-40) REVERT: U 28 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7521 (ttp80) REVERT: U 51 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7311 (ttp-170) REVERT: U 52 LEU cc_start: 0.8371 (mp) cc_final: 0.7506 (tt) REVERT: V 26 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7773 (mtm180) REVERT: W 53 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8339 (mm-40) REVERT: W 56 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.7775 (mpt-90) REVERT: W 63 TYR cc_start: 0.8969 (t80) cc_final: 0.8417 (t80) REVERT: X 38 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7329 (t) REVERT: X 43 MET cc_start: 0.8317 (mmp) cc_final: 0.7643 (mmm) REVERT: X 65 MET cc_start: 0.7891 (mtt) cc_final: 0.7089 (mmm) REVERT: Y 13 SER cc_start: 0.8917 (t) cc_final: 0.8510 (m) REVERT: Y 14 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8162 (tm-30) REVERT: Y 59 ARG cc_start: 0.8043 (ttm170) cc_final: 0.7642 (mtp-110) REVERT: Z 24 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7554 (ptmt) REVERT: a 8 MET cc_start: 0.5135 (ttm) cc_final: 0.4596 (tmm) outliers start: 396 outliers final: 291 residues processed: 1717 average time/residue: 1.3279 time to fit residues: 3903.7187 Evaluate side-chains 1775 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1457 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 LYS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 80 THR Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 LYS Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 11 LYS Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 341 optimal weight: 8.9990 chunk 913 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 595 optimal weight: 30.0000 chunk 250 optimal weight: 10.0000 chunk 1015 optimal weight: 8.9990 chunk 843 optimal weight: 30.0000 chunk 470 optimal weight: 7.9990 chunk 84 optimal weight: 0.3980 chunk 336 optimal weight: 5.9990 chunk 533 optimal weight: 30.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- 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 162 GLN b 225 ASN ** d 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 ASN f 110 HIS ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 2 ASN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS O 20 GLN P 14 GLN Q 5 GLN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 HIS Y 47 GLN ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 161387 Z= 0.336 Angle : 0.686 13.663 241347 Z= 0.347 Chirality : 0.039 0.274 30852 Planarity : 0.005 0.070 13007 Dihedral : 23.545 179.714 80575 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.49 % Favored : 89.37 % Rotamer: Outliers : 8.07 % Allowed : 25.81 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.10), residues: 5919 helix: -0.81 (0.11), residues: 1863 sheet: -1.70 (0.16), residues: 940 loop : -2.40 (0.10), residues: 3116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 95 HIS 0.008 0.002 HIS j 80 PHE 0.036 0.002 PHE M 65 TYR 0.039 0.002 TYR g 25 ARG 0.010 0.001 ARG d 21 *********************** 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 1888 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 1492 time to evaluate : 6.586 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: b 12 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7791 (tpt-90) REVERT: b 123 ILE cc_start: 0.8952 (mm) cc_final: 0.8621 (mt) REVERT: b 159 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8500 (p) REVERT: b 238 ASN cc_start: 0.8575 (p0) cc_final: 0.8325 (p0) REVERT: b 269 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6854 (tmm-80) REVERT: c 4 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8427 (mp) REVERT: c 15 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: c 43 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8605 (m-30) REVERT: c 80 TRP cc_start: 0.8570 (m-90) cc_final: 0.8350 (m-90) REVERT: c 128 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7927 (mtp180) REVERT: d 144 GLU cc_start: 0.7812 (tt0) cc_final: 0.7397 (mp0) REVERT: d 198 GLU cc_start: 0.8195 (tp30) cc_final: 0.7701 (tp30) REVERT: e 6 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.6564 (t80) REVERT: e 43 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8310 (tp) REVERT: e 64 PRO cc_start: 0.8694 (Cg_endo) cc_final: 0.8304 (Cg_exo) REVERT: e 86 CYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6498 (p) REVERT: e 109 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8383 (tmt-80) REVERT: e 120 SER cc_start: 0.7895 (p) cc_final: 0.6956 (t) REVERT: e 124 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8065 (mmm160) REVERT: e 134 GLN cc_start: 0.8518 (pm20) cc_final: 0.8207 (mp10) REVERT: e 135 ILE cc_start: 0.8862 (pt) cc_final: 0.8540 (mm) REVERT: e 156 THR cc_start: 0.7619 (t) cc_final: 0.7350 (t) REVERT: e 161 SER cc_start: 0.8661 (t) cc_final: 0.8239 (t) REVERT: e 169 LEU cc_start: 0.8037 (mm) cc_final: 0.7526 (pp) REVERT: f 150 TYR cc_start: 0.8268 (m-10) cc_final: 0.7722 (m-80) REVERT: g 6 LEU cc_start: 0.8107 (mm) cc_final: 0.7787 (mm) REVERT: g 129 GLU cc_start: 0.4908 (tt0) cc_final: 0.4541 (tm-30) REVERT: h 38 MET cc_start: 0.5628 (mpp) cc_final: 0.5293 (mpp) REVERT: j 37 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7905 (tpt-90) REVERT: j 44 TYR cc_start: 0.8719 (t80) cc_final: 0.8038 (t80) REVERT: j 74 TYR cc_start: 0.8737 (m-10) cc_final: 0.8397 (m-10) REVERT: j 106 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8443 (tttt) REVERT: j 118 MET cc_start: 0.8379 (ptp) cc_final: 0.7840 (ptp) REVERT: j 131 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8499 (p0) REVERT: j 136 GLN cc_start: 0.8477 (mt0) cc_final: 0.7895 (mm-40) REVERT: k 23 LYS cc_start: 0.7680 (tppt) cc_final: 0.7319 (tptp) REVERT: k 38 ILE cc_start: 0.9301 (mm) cc_final: 0.8961 (mm) REVERT: k 73 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8103 (p0) REVERT: k 113 MET cc_start: 0.8072 (tpt) cc_final: 0.7794 (tpt) REVERT: l 3 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9161 (tt) REVERT: l 91 ASP cc_start: 0.8386 (p0) cc_final: 0.8087 (p0) REVERT: l 112 LEU cc_start: 0.8427 (mt) cc_final: 0.8184 (mt) REVERT: l 143 GLU cc_start: 0.8022 (pm20) cc_final: 0.7818 (pm20) REVERT: m 40 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7546 (mtp180) REVERT: m 47 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7295 (tm-30) REVERT: m 105 MET cc_start: 0.7421 (ttm) cc_final: 0.6983 (mtm) REVERT: n 72 ASP cc_start: 0.8492 (t0) cc_final: 0.8152 (t0) REVERT: n 78 LYS cc_start: 0.9176 (tppp) cc_final: 0.8854 (tppp) REVERT: n 110 MET cc_start: 0.8290 (mmp) cc_final: 0.7992 (mmp) REVERT: n 115 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8076 (mp) REVERT: o 13 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8111 (tpt-90) REVERT: o 19 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8328 (tm-30) REVERT: o 85 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8936 (mtpp) REVERT: p 10 GLU cc_start: 0.8220 (pm20) cc_final: 0.7974 (pm20) REVERT: q 51 GLN cc_start: 0.8272 (tt0) cc_final: 0.7964 (tt0) REVERT: r 6 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8214 (tm-30) REVERT: r 13 ARG cc_start: 0.8764 (ttt-90) cc_final: 0.8503 (ptm-80) REVERT: r 60 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8479 (ttmt) REVERT: r 97 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8257 (tptp) REVERT: s 1 MET cc_start: 0.6716 (ttm) cc_final: 0.6308 (ttm) REVERT: s 8 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8043 (mtp-110) REVERT: s 25 ARG cc_start: 0.8921 (ttm-80) cc_final: 0.8213 (ttm-80) REVERT: s 52 GLU cc_start: 0.8666 (tp30) cc_final: 0.8367 (tp30) REVERT: s 59 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8214 (mm-30) REVERT: s 84 ARG cc_start: 0.7773 (mmt-90) cc_final: 0.7407 (mmt90) REVERT: s 88 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.7830 (mmm160) REVERT: t 32 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8906 (pp) REVERT: t 80 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.7701 (p-90) REVERT: u 17 ASP cc_start: 0.7085 (t0) cc_final: 0.6752 (t0) REVERT: u 21 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7419 (mtp85) REVERT: u 72 PHE cc_start: 0.7454 (t80) cc_final: 0.6927 (t80) REVERT: v 7 GLU cc_start: 0.8096 (tp30) cc_final: 0.7162 (tm-30) REVERT: v 25 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7182 (tmtt) REVERT: v 42 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.7913 (pp) REVERT: v 43 ASP cc_start: 0.8702 (t0) cc_final: 0.8411 (t0) REVERT: v 50 MET cc_start: 0.8859 (tpp) cc_final: 0.8636 (ttt) REVERT: v 53 LYS cc_start: 0.9172 (mttt) cc_final: 0.8734 (mmtp) REVERT: v 55 GLU cc_start: 0.8810 (pm20) cc_final: 0.8517 (pm20) REVERT: v 68 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7854 (mptt) REVERT: v 87 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: w 11 ASP cc_start: 0.8255 (t0) cc_final: 0.7898 (t0) REVERT: w 64 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8539 (ttpp) REVERT: x 9 LYS cc_start: 0.9174 (mttm) cc_final: 0.8911 (mtpp) REVERT: x 61 LYS cc_start: 0.8875 (mttp) cc_final: 0.8661 (mttp) REVERT: y 31 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: y 41 HIS cc_start: 0.8908 (p-80) cc_final: 0.8217 (p-80) REVERT: y 45 GLN cc_start: 0.8591 (pp30) cc_final: 0.8294 (pp30) REVERT: y 54 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8724 (mtpt) REVERT: z 36 GLU cc_start: 0.8284 (tt0) cc_final: 0.8005 (tp30) REVERT: z 54 VAL cc_start: 0.9274 (t) cc_final: 0.8992 (p) REVERT: z 57 GLU cc_start: 0.7909 (tp30) cc_final: 0.7466 (tp30) REVERT: D 19 ARG cc_start: 0.9202 (mtp85) cc_final: 0.8550 (mmm-85) REVERT: D 35 ARG cc_start: 0.8474 (mtt90) cc_final: 0.8245 (mtt90) REVERT: G 5 MET cc_start: 0.3943 (tpt) cc_final: 0.3496 (tpt) REVERT: G 6 ARG cc_start: 0.8790 (ttp80) cc_final: 0.8058 (mmp-170) REVERT: G 26 MET cc_start: 0.8814 (tpt) cc_final: 0.8516 (tpt) REVERT: G 29 PHE cc_start: 0.8922 (m-80) cc_final: 0.8524 (m-80) REVERT: G 113 LEU cc_start: 0.8903 (tp) cc_final: 0.8593 (mt) REVERT: G 135 MET cc_start: 0.8798 (ppp) cc_final: 0.8408 (ppp) REVERT: G 147 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8327 (tt) REVERT: G 166 ASP cc_start: 0.8235 (p0) cc_final: 0.7980 (p0) REVERT: G 176 ASN cc_start: 0.8745 (m110) cc_final: 0.8399 (m110) REVERT: G 195 VAL cc_start: 0.8280 (t) cc_final: 0.7861 (p) REVERT: H 15 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7924 (pttp) REVERT: H 122 GLN cc_start: 0.7572 (mt0) cc_final: 0.7209 (mm110) REVERT: H 150 VAL cc_start: 0.7598 (p) cc_final: 0.7284 (m) REVERT: I 13 ARG cc_start: 0.6998 (tpt170) cc_final: 0.6164 (tpt170) REVERT: I 54 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8964 (mp) REVERT: I 81 LEU cc_start: 0.8897 (mt) cc_final: 0.8571 (mt) REVERT: I 97 LEU cc_start: 0.8610 (pt) cc_final: 0.8383 (pt) REVERT: I 134 TYR cc_start: 0.8581 (t80) cc_final: 0.8351 (t80) REVERT: I 165 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7866 (tm-30) REVERT: I 169 TRP cc_start: 0.8238 (p90) cc_final: 0.7417 (p90) REVERT: I 183 ARG cc_start: 0.7699 (ppt170) cc_final: 0.6862 (ppt170) REVERT: I 198 LEU cc_start: 0.8687 (mm) cc_final: 0.8298 (tp) REVERT: J 30 PHE cc_start: 0.8623 (m-80) cc_final: 0.7911 (m-10) REVERT: J 120 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.4710 (p-80) REVERT: J 164 LEU cc_start: 0.3014 (OUTLIER) cc_final: 0.2738 (pt) REVERT: K 11 HIS cc_start: 0.8175 (t70) cc_final: 0.7863 (t-90) REVERT: K 47 LEU cc_start: 0.6706 (mt) cc_final: 0.6414 (mp) REVERT: K 59 TYR cc_start: 0.7352 (m-80) cc_final: 0.7044 (m-80) REVERT: K 81 ASN cc_start: 0.8643 (t0) cc_final: 0.8198 (t0) REVERT: K 90 MET cc_start: 0.8449 (mmm) cc_final: 0.7672 (mmt) REVERT: L 27 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6262 (t0) REVERT: L 29 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (mm) REVERT: M 12 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7272 (mtm-85) REVERT: M 26 MET cc_start: 0.7304 (ttp) cc_final: 0.6883 (ttt) REVERT: M 44 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7380 (t80) REVERT: M 62 LEU cc_start: 0.9470 (tp) cc_final: 0.9093 (tt) REVERT: M 79 ARG cc_start: 0.8668 (ptt180) cc_final: 0.8288 (ptm-80) REVERT: M 86 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6981 (mmtm) REVERT: M 88 LYS cc_start: 0.8973 (tptp) cc_final: 0.8221 (tptp) REVERT: M 93 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8070 (ttmm) REVERT: M 95 MET cc_start: 0.8073 (mmp) cc_final: 0.7505 (tpp) REVERT: N 56 MET cc_start: 0.8619 (ppp) cc_final: 0.6935 (mmm) REVERT: O 48 ARG cc_start: 0.6268 (mtm-85) cc_final: 0.5575 (mmt-90) REVERT: P 52 ARG cc_start: 0.8402 (mmm160) cc_final: 0.8147 (mmm160) REVERT: P 55 ARG cc_start: 0.8941 (mpp-170) cc_final: 0.8643 (mtp180) REVERT: P 63 GLN cc_start: 0.8274 (mm110) cc_final: 0.7900 (mm-40) REVERT: P 127 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.7132 (ttp-110) REVERT: Q 33 CYS cc_start: 0.8762 (t) cc_final: 0.8187 (t) REVERT: Q 82 ARG cc_start: 0.8225 (ptm160) cc_final: 0.7946 (ptm-80) REVERT: Q 85 ARG cc_start: 0.6622 (ptm160) cc_final: 0.5973 (ptm160) REVERT: Q 107 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8107 (mmtm) REVERT: S 5 MET cc_start: 0.7105 (mmm) cc_final: 0.6787 (mtt) REVERT: T 58 MET cc_start: 0.8570 (ptp) cc_final: 0.8113 (mtp) REVERT: U 51 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7326 (ttp-170) REVERT: U 52 LEU cc_start: 0.8385 (mp) cc_final: 0.7527 (tt) REVERT: V 64 ARG cc_start: 0.7093 (ttm170) cc_final: 0.6879 (ttp80) REVERT: W 53 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8491 (mm-40) REVERT: W 63 TYR cc_start: 0.8970 (t80) cc_final: 0.8459 (t80) REVERT: X 38 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7282 (t) REVERT: X 43 MET cc_start: 0.8437 (mmp) cc_final: 0.7912 (mmm) REVERT: X 65 MET cc_start: 0.7971 (mtt) cc_final: 0.7200 (mmm) REVERT: X 68 HIS cc_start: 0.7792 (m-70) cc_final: 0.7424 (m-70) REVERT: Y 13 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8511 (m) REVERT: Y 14 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8110 (tm-30) REVERT: Y 17 ARG cc_start: 0.8563 (ppt170) cc_final: 0.8120 (tmm160) REVERT: Y 59 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7651 (mtp-110) REVERT: Z 24 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7502 (ptmt) REVERT: a 8 MET cc_start: 0.5233 (ttm) cc_final: 0.4688 (tmm) outliers start: 396 outliers final: 304 residues processed: 1684 average time/residue: 1.2981 time to fit residues: 3750.5584 Evaluate side-chains 1779 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1442 time to evaluate : 6.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 15 PHE Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 80 ASP Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 74 SER Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 12 SER Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 44 PHE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 979 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 578 optimal weight: 40.0000 chunk 741 optimal weight: 10.0000 chunk 574 optimal weight: 40.0000 chunk 855 optimal weight: 10.0000 chunk 567 optimal weight: 10.0000 chunk 1012 optimal weight: 30.0000 chunk 633 optimal weight: 30.0000 chunk 616 optimal weight: 20.0000 chunk 467 optimal weight: 5.9990 overall best weight: 9.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 167 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 5 ASN v 75 GLN v 78 GLN w 42 HIS ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** I 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN Q 5 GLN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 HIS ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 161387 Z= 0.490 Angle : 0.830 12.257 241347 Z= 0.414 Chirality : 0.045 0.293 30852 Planarity : 0.006 0.095 13007 Dihedral : 23.795 178.510 80575 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.42 % Favored : 87.43 % Rotamer: Outliers : 9.09 % Allowed : 26.05 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 5919 helix: -1.02 (0.11), residues: 1861 sheet: -1.82 (0.16), residues: 925 loop : -2.53 (0.10), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP t 80 HIS 0.009 0.002 HIS Q 76 PHE 0.034 0.003 PHE M 65 TYR 0.048 0.003 TYR g 25 ARG 0.015 0.001 ARG b 202 *********************** 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 1915 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 446 poor density : 1469 time to evaluate : 6.683 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: b 12 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7939 (tpt-90) REVERT: b 123 ILE cc_start: 0.9073 (mm) cc_final: 0.8712 (mt) REVERT: b 159 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8504 (p) REVERT: b 238 ASN cc_start: 0.8714 (p0) cc_final: 0.8456 (p0) REVERT: b 261 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7807 (ttp80) REVERT: b 269 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7039 (tmm-80) REVERT: c 4 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8494 (mp) REVERT: c 15 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: c 36 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: c 43 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: c 128 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7872 (mtp180) REVERT: d 198 GLU cc_start: 0.8187 (tp30) cc_final: 0.7825 (tp30) REVERT: e 6 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6477 (t80) REVERT: e 64 PRO cc_start: 0.8655 (Cg_endo) cc_final: 0.8273 (Cg_exo) REVERT: e 86 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6634 (p) REVERT: e 120 SER cc_start: 0.8050 (p) cc_final: 0.7232 (t) REVERT: e 124 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.7985 (mmm160) REVERT: e 129 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7336 (pmm) REVERT: e 161 SER cc_start: 0.8072 (t) cc_final: 0.7682 (t) REVERT: e 169 LEU cc_start: 0.8036 (mm) cc_final: 0.7512 (pp) REVERT: f 68 ARG cc_start: 0.8298 (tmt-80) cc_final: 0.7958 (ttp80) REVERT: g 6 LEU cc_start: 0.8005 (mm) cc_final: 0.7685 (mm) REVERT: g 129 GLU cc_start: 0.4824 (tt0) cc_final: 0.4448 (tm-30) REVERT: h 1 MET cc_start: 0.3921 (ptt) cc_final: 0.3584 (ttp) REVERT: h 3 LEU cc_start: 0.8494 (pp) cc_final: 0.7741 (tp) REVERT: h 38 MET cc_start: 0.5832 (mpp) cc_final: 0.5503 (mpp) REVERT: j 37 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8125 (tpt-90) REVERT: j 106 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8495 (tttt) REVERT: j 118 MET cc_start: 0.8377 (ptp) cc_final: 0.7920 (ptp) REVERT: j 136 GLN cc_start: 0.8526 (mt0) cc_final: 0.7865 (mm-40) REVERT: k 17 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7860 (tpp80) REVERT: k 38 ILE cc_start: 0.9283 (mm) cc_final: 0.9062 (mp) REVERT: k 73 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8222 (p0) REVERT: l 91 ASP cc_start: 0.8697 (p0) cc_final: 0.8328 (p0) REVERT: l 143 GLU cc_start: 0.7956 (pm20) cc_final: 0.7746 (pm20) REVERT: m 40 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7325 (mtp180) REVERT: m 47 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7292 (tm-30) REVERT: n 72 ASP cc_start: 0.8617 (t0) cc_final: 0.8273 (t0) REVERT: n 78 LYS cc_start: 0.9248 (tppp) cc_final: 0.8936 (tppp) REVERT: n 110 MET cc_start: 0.8305 (mmp) cc_final: 0.7960 (mmp) REVERT: o 19 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8300 (tm-30) REVERT: o 85 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8945 (mtpp) REVERT: p 10 GLU cc_start: 0.8202 (pm20) cc_final: 0.7954 (pm20) REVERT: p 26 GLU cc_start: 0.8240 (tp30) cc_final: 0.7980 (tp30) REVERT: p 111 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: q 51 GLN cc_start: 0.8370 (tt0) cc_final: 0.8090 (tt0) REVERT: r 6 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8343 (tm-30) REVERT: r 13 ARG cc_start: 0.8801 (ttt-90) cc_final: 0.8233 (ptm160) REVERT: r 60 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8400 (ttmt) REVERT: r 86 GLN cc_start: 0.8720 (mt0) cc_final: 0.8493 (mt0) REVERT: s 1 MET cc_start: 0.6739 (ttm) cc_final: 0.6510 (ttm) REVERT: s 8 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8001 (mtp-110) REVERT: s 25 ARG cc_start: 0.8906 (ttm-80) cc_final: 0.8195 (ttm-80) REVERT: s 52 GLU cc_start: 0.8656 (tp30) cc_final: 0.8329 (tp30) REVERT: s 59 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8165 (mm-30) REVERT: s 84 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7451 (mmt90) REVERT: t 3 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6944 (tpt90) REVERT: t 32 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8942 (pp) REVERT: t 56 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7610 (mm-30) REVERT: t 80 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.7709 (p-90) REVERT: u 21 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7309 (mtp85) REVERT: u 72 PHE cc_start: 0.7422 (t80) cc_final: 0.7012 (t80) REVERT: v 7 GLU cc_start: 0.8081 (tp30) cc_final: 0.7081 (tm-30) REVERT: v 25 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7462 (tppt) REVERT: v 42 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.7894 (pp) REVERT: v 53 LYS cc_start: 0.9178 (mttt) cc_final: 0.8844 (mmtp) REVERT: v 68 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7906 (mptt) REVERT: v 75 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7959 (tp-100) REVERT: v 87 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: w 11 ASP cc_start: 0.8323 (t0) cc_final: 0.7963 (t0) REVERT: w 25 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6585 (mt-10) REVERT: w 64 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8469 (ttpp) REVERT: y 1 MET cc_start: 0.8662 (mmm) cc_final: 0.8428 (tpp) REVERT: y 31 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8178 (mp10) REVERT: y 36 GLN cc_start: 0.7248 (mp10) cc_final: 0.6995 (mp10) REVERT: y 41 HIS cc_start: 0.8867 (p-80) cc_final: 0.8158 (p-80) REVERT: y 44 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8711 (mmmt) REVERT: y 54 LYS cc_start: 0.9177 (mtpp) cc_final: 0.8766 (mtpt) REVERT: z 57 GLU cc_start: 0.7863 (tp30) cc_final: 0.7437 (tp30) REVERT: D 19 ARG cc_start: 0.9230 (mtp85) cc_final: 0.8653 (mmm-85) REVERT: D 35 ARG cc_start: 0.8378 (mtt90) cc_final: 0.8122 (mtt90) REVERT: G 26 MET cc_start: 0.8616 (tpt) cc_final: 0.8356 (tpt) REVERT: G 29 PHE cc_start: 0.8941 (m-80) cc_final: 0.8507 (m-80) REVERT: G 48 MET cc_start: 0.8686 (pmm) cc_final: 0.8258 (pmm) REVERT: G 113 LEU cc_start: 0.9071 (tp) cc_final: 0.8697 (mt) REVERT: G 135 MET cc_start: 0.8829 (ppp) cc_final: 0.8435 (ppp) REVERT: G 147 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8261 (tt) REVERT: G 195 VAL cc_start: 0.8286 (t) cc_final: 0.7858 (p) REVERT: H 15 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7901 (pttp) REVERT: H 122 GLN cc_start: 0.7703 (mt0) cc_final: 0.7452 (mm110) REVERT: H 126 ARG cc_start: 0.7647 (mtm180) cc_final: 0.7442 (mtm180) REVERT: H 150 VAL cc_start: 0.7578 (p) cc_final: 0.7262 (m) REVERT: I 13 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6195 (tpt170) REVERT: I 54 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9181 (pp) REVERT: I 97 LEU cc_start: 0.8474 (pt) cc_final: 0.8177 (pt) REVERT: I 134 TYR cc_start: 0.8652 (t80) cc_final: 0.8332 (t80) REVERT: I 165 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7830 (tm-30) REVERT: I 169 TRP cc_start: 0.8361 (p90) cc_final: 0.7667 (p90) REVERT: I 183 ARG cc_start: 0.7889 (ppt170) cc_final: 0.7027 (ppt170) REVERT: J 30 PHE cc_start: 0.8475 (m-80) cc_final: 0.7822 (m-10) REVERT: J 95 MET cc_start: 0.7284 (ptp) cc_final: 0.6884 (ptp) REVERT: J 120 HIS cc_start: 0.5639 (OUTLIER) cc_final: 0.4717 (p90) REVERT: K 40 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6259 (mt-10) REVERT: K 59 TYR cc_start: 0.7039 (m-80) cc_final: 0.6699 (m-80) REVERT: K 81 ASN cc_start: 0.8791 (t0) cc_final: 0.8278 (t0) REVERT: M 12 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.6990 (mtm-85) REVERT: M 44 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7308 (t80) REVERT: M 62 LEU cc_start: 0.9496 (tp) cc_final: 0.9238 (tt) REVERT: M 79 ARG cc_start: 0.8698 (ptt180) cc_final: 0.8248 (ptm-80) REVERT: M 86 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7059 (mmtm) REVERT: M 93 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7999 (ttmm) REVERT: N 51 LEU cc_start: 0.7961 (pp) cc_final: 0.7691 (tp) REVERT: O 48 ARG cc_start: 0.6136 (mtm-85) cc_final: 0.5395 (mmt-90) REVERT: P 17 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8164 (p0) REVERT: P 55 ARG cc_start: 0.8999 (mpp-170) cc_final: 0.8647 (mtp180) REVERT: P 63 GLN cc_start: 0.8293 (mm110) cc_final: 0.7904 (mm-40) REVERT: Q 33 CYS cc_start: 0.8688 (t) cc_final: 0.8086 (t) REVERT: Q 82 ARG cc_start: 0.8281 (ptm160) cc_final: 0.8076 (ptm-80) REVERT: Q 85 ARG cc_start: 0.6727 (ptm160) cc_final: 0.6019 (ptm160) REVERT: Q 107 LYS cc_start: 0.8351 (mmtm) cc_final: 0.7968 (mmtm) REVERT: R 33 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7526 (mp) REVERT: R 74 MET cc_start: 0.9046 (ttt) cc_final: 0.8657 (tmm) REVERT: U 1 MET cc_start: 0.7496 (tpt) cc_final: 0.7211 (tpt) REVERT: U 52 LEU cc_start: 0.8287 (mp) cc_final: 0.7652 (tt) REVERT: V 79 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8410 (tm-30) REVERT: W 49 LYS cc_start: 0.7662 (ptmt) cc_final: 0.7152 (ptmt) REVERT: W 53 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8120 (mm-40) REVERT: W 56 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.7743 (mpt-90) REVERT: W 60 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7719 (ttm170) REVERT: W 63 TYR cc_start: 0.9060 (t80) cc_final: 0.8514 (t80) REVERT: X 38 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7127 (t) REVERT: X 43 MET cc_start: 0.8437 (mmp) cc_final: 0.7919 (mmm) REVERT: X 65 MET cc_start: 0.8047 (mtt) cc_final: 0.7251 (mmm) REVERT: X 68 HIS cc_start: 0.7879 (m-70) cc_final: 0.7608 (m-70) REVERT: X 70 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8337 (mt) REVERT: Y 13 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8396 (m) REVERT: Y 14 GLU cc_start: 0.8759 (tm-30) cc_final: 0.7871 (tm-30) REVERT: Y 17 ARG cc_start: 0.8566 (ppt170) cc_final: 0.8088 (tmm160) REVERT: Y 59 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7656 (mtp-110) REVERT: Z 24 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7496 (ptmt) REVERT: a 54 LYS cc_start: 0.4128 (mmtt) cc_final: 0.3500 (mmmt) REVERT: a 218 MET cc_start: 0.3673 (ttt) cc_final: 0.3433 (tmm) outliers start: 446 outliers final: 341 residues processed: 1693 average time/residue: 1.4502 time to fit residues: 4267.2017 Evaluate side-chains 1795 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 1421 time to evaluate : 6.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 133 ASN Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 167 ASP Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain b residue 269 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 15 PHE Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 91 ASP Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 129 MET Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 72 ASN Chi-restraints excluded: chain f residue 87 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 17 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 72 LEU Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 7 MET Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 39 ILE Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 82 MET Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 33 ILE Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 28 LYS Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 111 GLU Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 79 ILE Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 12 SER Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 24 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 44 LYS Chi-restraints excluded: chain y residue 46 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 28 LEU Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 1 SER Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 44 PHE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 11 LYS Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 26 CYS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 626 optimal weight: 50.0000 chunk 404 optimal weight: 20.0000 chunk 604 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 643 optimal weight: 20.0000 chunk 689 optimal weight: 30.0000 chunk 500 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 795 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 167 ASN f 47 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS y 38 GLN D 13 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS I 35 GLN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS Q 5 GLN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 161387 Z= 0.228 Angle : 0.634 14.508 241347 Z= 0.320 Chirality : 0.036 0.282 30852 Planarity : 0.005 0.071 13007 Dihedral : 23.568 179.590 80575 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.46 % Favored : 90.40 % Rotamer: Outliers : 6.76 % Allowed : 28.99 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.10), residues: 5919 helix: -0.73 (0.12), residues: 1855 sheet: -1.68 (0.16), residues: 959 loop : -2.33 (0.10), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 102 HIS 0.013 0.001 HIS H 68 PHE 0.031 0.002 PHE L 25 TYR 0.037 0.002 TYR g 25 ARG 0.011 0.001 ARG H 53 *********************** 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 1862 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1530 time to evaluate : 6.635 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: b 159 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8623 (p) REVERT: b 238 ASN cc_start: 0.8500 (p0) cc_final: 0.8250 (p0) REVERT: c 80 TRP cc_start: 0.8522 (m-90) cc_final: 0.8297 (m-90) REVERT: c 128 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7850 (mtp180) REVERT: d 144 GLU cc_start: 0.7679 (tt0) cc_final: 0.7311 (mp0) REVERT: d 198 GLU cc_start: 0.8154 (tp30) cc_final: 0.7649 (tp30) REVERT: e 6 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.6452 (t80) REVERT: e 18 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7994 (mt-10) REVERT: e 56 LEU cc_start: 0.9048 (mt) cc_final: 0.8506 (mt) REVERT: e 64 PRO cc_start: 0.8645 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: e 86 CYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6008 (p) REVERT: e 120 SER cc_start: 0.7965 (p) cc_final: 0.7188 (t) REVERT: e 124 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: e 156 THR cc_start: 0.8217 (p) cc_final: 0.7966 (p) REVERT: e 174 PHE cc_start: 0.6551 (m-10) cc_final: 0.6350 (m-10) REVERT: g 6 LEU cc_start: 0.7954 (mm) cc_final: 0.7707 (mm) REVERT: g 129 GLU cc_start: 0.5382 (tt0) cc_final: 0.4994 (tm-30) REVERT: h 1 MET cc_start: 0.3781 (ptt) cc_final: 0.3395 (ttt) REVERT: h 3 LEU cc_start: 0.8361 (pp) cc_final: 0.7873 (tt) REVERT: h 6 GLN cc_start: 0.8819 (mm110) cc_final: 0.8065 (mp10) REVERT: h 86 MET cc_start: 0.6546 (pmm) cc_final: 0.6233 (pmm) REVERT: j 44 TYR cc_start: 0.8652 (t80) cc_final: 0.7722 (t80) REVERT: j 98 GLU cc_start: 0.8334 (mp0) cc_final: 0.7885 (mp0) REVERT: j 99 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8238 (ttm110) REVERT: j 106 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8423 (tttt) REVERT: j 109 LEU cc_start: 0.9171 (mt) cc_final: 0.8949 (mt) REVERT: j 118 MET cc_start: 0.8345 (ptp) cc_final: 0.7940 (ptp) REVERT: j 136 GLN cc_start: 0.8448 (mt0) cc_final: 0.7950 (mm-40) REVERT: k 23 LYS cc_start: 0.7737 (tppt) cc_final: 0.7257 (tppp) REVERT: k 73 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.7956 (p0) REVERT: k 113 MET cc_start: 0.8135 (tpt) cc_final: 0.7874 (tpt) REVERT: l 91 ASP cc_start: 0.8599 (p0) cc_final: 0.8396 (p0) REVERT: l 112 LEU cc_start: 0.8438 (mt) cc_final: 0.8193 (mt) REVERT: m 40 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: m 47 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7276 (tm-30) REVERT: m 101 VAL cc_start: 0.9314 (t) cc_final: 0.8995 (m) REVERT: n 72 ASP cc_start: 0.8353 (t0) cc_final: 0.8093 (t0) REVERT: n 78 LYS cc_start: 0.9043 (tppp) cc_final: 0.8737 (tppp) REVERT: n 110 MET cc_start: 0.8333 (mmp) cc_final: 0.8018 (mmp) REVERT: o 13 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8287 (tpt-90) REVERT: o 19 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8181 (tm-30) REVERT: p 10 GLU cc_start: 0.8199 (pm20) cc_final: 0.7951 (pm20) REVERT: q 51 GLN cc_start: 0.8188 (tt0) cc_final: 0.7857 (tt0) REVERT: r 6 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8244 (tm-30) REVERT: r 13 ARG cc_start: 0.8725 (ttt-90) cc_final: 0.8197 (ptm160) REVERT: r 40 MET cc_start: 0.7931 (ttm) cc_final: 0.7718 (ttt) REVERT: r 60 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8418 (ttmt) REVERT: r 97 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8239 (tptp) REVERT: s 1 MET cc_start: 0.6524 (ttm) cc_final: 0.6243 (ttm) REVERT: s 8 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7946 (mtp-110) REVERT: s 25 ARG cc_start: 0.8825 (ttm-80) cc_final: 0.8411 (ttm-80) REVERT: s 59 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8084 (mm-30) REVERT: s 84 ARG cc_start: 0.7857 (mmt-90) cc_final: 0.7434 (mmt90) REVERT: t 32 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8877 (pp) REVERT: t 48 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8237 (mm-40) REVERT: t 56 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7573 (mm-30) REVERT: t 80 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.7702 (p-90) REVERT: u 6 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8094 (ttm110) REVERT: u 17 ASP cc_start: 0.7005 (t0) cc_final: 0.6681 (t0) REVERT: u 72 PHE cc_start: 0.7212 (t80) cc_final: 0.6812 (t80) REVERT: v 7 GLU cc_start: 0.8082 (tp30) cc_final: 0.7209 (tm-30) REVERT: v 25 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7180 (tppt) REVERT: v 42 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7727 (pp) REVERT: v 53 LYS cc_start: 0.9155 (mttt) cc_final: 0.8798 (mmtp) REVERT: v 55 GLU cc_start: 0.8501 (pm20) cc_final: 0.8163 (pm20) REVERT: v 87 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: w 11 ASP cc_start: 0.8310 (t0) cc_final: 0.7885 (t0) REVERT: w 64 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8804 (ttpp) REVERT: x 9 LYS cc_start: 0.9255 (mttm) cc_final: 0.8981 (mtpp) REVERT: y 31 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8048 (mm-40) REVERT: y 41 HIS cc_start: 0.8929 (p-80) cc_final: 0.8318 (p-80) REVERT: y 45 GLN cc_start: 0.8518 (pp30) cc_final: 0.8159 (pp30) REVERT: y 54 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8833 (mttt) REVERT: z 36 GLU cc_start: 0.8342 (tt0) cc_final: 0.7989 (tp30) REVERT: z 57 GLU cc_start: 0.7825 (tp30) cc_final: 0.7380 (tp30) REVERT: D 3 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6892 (tpm170) REVERT: D 19 ARG cc_start: 0.9147 (mtp85) cc_final: 0.8511 (mmm-85) REVERT: E 34 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8756 (mtmm) REVERT: G 5 MET cc_start: 0.3875 (tpt) cc_final: 0.3360 (tpt) REVERT: G 6 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8125 (mmp-170) REVERT: G 17 HIS cc_start: 0.8550 (m-70) cc_final: 0.7840 (m-70) REVERT: G 29 PHE cc_start: 0.8762 (m-80) cc_final: 0.8543 (m-80) REVERT: G 48 MET cc_start: 0.8474 (pmm) cc_final: 0.8253 (pmm) REVERT: G 57 ASN cc_start: 0.8739 (t0) cc_final: 0.8440 (m-40) REVERT: G 99 MET cc_start: 0.8786 (mmt) cc_final: 0.8246 (mpp) REVERT: G 113 LEU cc_start: 0.9045 (tp) cc_final: 0.8644 (mt) REVERT: G 135 MET cc_start: 0.8804 (ppp) cc_final: 0.8420 (ppp) REVERT: G 147 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8145 (tt) REVERT: G 164 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: G 185 ILE cc_start: 0.9014 (mm) cc_final: 0.8582 (mp) REVERT: G 195 VAL cc_start: 0.8117 (t) cc_final: 0.7670 (p) REVERT: H 15 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7935 (pttp) REVERT: H 122 GLN cc_start: 0.7730 (mt0) cc_final: 0.7413 (mm110) REVERT: H 150 VAL cc_start: 0.7667 (p) cc_final: 0.7384 (m) REVERT: I 13 ARG cc_start: 0.7112 (tpt170) cc_final: 0.6289 (tpt170) REVERT: I 54 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8969 (mp) REVERT: I 97 LEU cc_start: 0.8384 (pt) cc_final: 0.8133 (pt) REVERT: I 134 TYR cc_start: 0.8517 (t80) cc_final: 0.8315 (t80) REVERT: I 165 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7856 (tm-30) REVERT: I 169 TRP cc_start: 0.8273 (p90) cc_final: 0.7533 (p90) REVERT: I 183 ARG cc_start: 0.7994 (ppt170) cc_final: 0.7274 (ppt170) REVERT: I 198 LEU cc_start: 0.8754 (mm) cc_final: 0.8317 (tp) REVERT: J 30 PHE cc_start: 0.8511 (m-80) cc_final: 0.7842 (m-10) REVERT: J 35 LEU cc_start: 0.7980 (tp) cc_final: 0.7580 (tp) REVERT: J 100 GLU cc_start: 0.8261 (tp30) cc_final: 0.7756 (tp30) REVERT: J 120 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.4519 (p90) REVERT: K 40 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6180 (mt-10) REVERT: K 47 LEU cc_start: 0.6484 (mt) cc_final: 0.6127 (mp) REVERT: K 59 TYR cc_start: 0.7154 (m-80) cc_final: 0.6930 (m-80) REVERT: K 81 ASN cc_start: 0.8688 (t0) cc_final: 0.8272 (t0) REVERT: K 90 MET cc_start: 0.8341 (mmm) cc_final: 0.7786 (mmp) REVERT: L 24 LYS cc_start: 0.9226 (pttt) cc_final: 0.8964 (pptt) REVERT: M 12 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7184 (mtm-85) REVERT: M 30 LYS cc_start: 0.9250 (mtpp) cc_final: 0.9028 (mptt) REVERT: M 44 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7182 (t80) REVERT: M 62 LEU cc_start: 0.9507 (tp) cc_final: 0.9243 (tt) REVERT: M 79 ARG cc_start: 0.8636 (ptt180) cc_final: 0.8239 (ptm-80) REVERT: M 85 TYR cc_start: 0.8288 (m-80) cc_final: 0.8035 (m-80) REVERT: M 86 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7094 (mmtm) REVERT: M 88 LYS cc_start: 0.8866 (tptp) cc_final: 0.8081 (tppt) REVERT: M 93 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8134 (ttmm) REVERT: M 95 MET cc_start: 0.8003 (tpp) cc_final: 0.7395 (tpp) REVERT: N 51 LEU cc_start: 0.7882 (pp) cc_final: 0.7671 (tp) REVERT: O 48 ARG cc_start: 0.6343 (mtm-85) cc_final: 0.5483 (mmt-90) REVERT: P 55 ARG cc_start: 0.8991 (mpp-170) cc_final: 0.8659 (mtp180) REVERT: P 63 GLN cc_start: 0.8315 (mm110) cc_final: 0.7930 (mm-40) REVERT: P 86 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8192 (ttpp) REVERT: P 127 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.7139 (ttm110) REVERT: Q 33 CYS cc_start: 0.8848 (t) cc_final: 0.8372 (t) REVERT: Q 82 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7871 (ptm-80) REVERT: Q 85 ARG cc_start: 0.6712 (ptm160) cc_final: 0.6050 (ptm160) REVERT: Q 107 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8163 (mmtm) REVERT: R 12 LYS cc_start: 0.7459 (mmtm) cc_final: 0.7220 (ttmm) REVERT: R 13 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7983 (m-70) REVERT: R 58 GLU cc_start: 0.7587 (tp30) cc_final: 0.6838 (tm-30) REVERT: R 74 MET cc_start: 0.8979 (ttt) cc_final: 0.8653 (ppp) REVERT: T 58 MET cc_start: 0.8346 (ptp) cc_final: 0.8104 (mtp) REVERT: T 64 LYS cc_start: 0.8205 (ttmm) cc_final: 0.8002 (ttmm) REVERT: U 52 LEU cc_start: 0.8401 (mp) cc_final: 0.7672 (tt) REVERT: W 49 LYS cc_start: 0.7557 (ptmt) cc_final: 0.7077 (ptmt) REVERT: W 63 TYR cc_start: 0.8818 (t80) cc_final: 0.8466 (t80) REVERT: X 38 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.6928 (t) REVERT: X 43 MET cc_start: 0.8423 (mmp) cc_final: 0.7858 (mmm) REVERT: X 55 GLN cc_start: 0.7847 (pp30) cc_final: 0.7512 (pm20) REVERT: X 65 MET cc_start: 0.7910 (mtt) cc_final: 0.7170 (mmm) REVERT: X 70 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8345 (mt) REVERT: Y 13 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8425 (m) REVERT: Y 14 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8097 (tm-30) REVERT: Y 17 ARG cc_start: 0.8524 (ppt170) cc_final: 0.8071 (tmm160) REVERT: Y 59 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7729 (mtp-110) REVERT: Z 24 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7342 (ptmt) REVERT: Z 46 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7508 (ttt180) REVERT: Z 61 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.4572 (pmt-80) REVERT: a 218 MET cc_start: 0.3550 (ttt) cc_final: 0.3182 (ppp) outliers start: 332 outliers final: 248 residues processed: 1690 average time/residue: 1.3894 time to fit residues: 4059.5700 Evaluate side-chains 1720 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1448 time to evaluate : 6.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 264 LYS Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 176 ASP Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 38 GLN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 32 PHE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 82 HIS Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 44 PHE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 920 optimal weight: 20.0000 chunk 969 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 943 optimal weight: 30.0000 chunk 567 optimal weight: 8.9990 chunk 410 optimal weight: 9.9990 chunk 740 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 852 optimal weight: 10.0000 chunk 891 optimal weight: 20.0000 chunk 939 optimal weight: 10.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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** c 167 ASN f 47 ASN ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS x 15 ASN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 161387 Z= 0.503 Angle : 0.839 14.288 241347 Z= 0.417 Chirality : 0.045 0.296 30852 Planarity : 0.006 0.139 13007 Dihedral : 23.788 178.270 80574 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.28 % Favored : 87.57 % Rotamer: Outliers : 7.17 % Allowed : 29.42 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.10), residues: 5919 helix: -0.99 (0.11), residues: 1854 sheet: -1.84 (0.16), residues: 949 loop : -2.50 (0.10), residues: 3116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 102 HIS 0.036 0.002 HIS R 13 PHE 0.033 0.003 PHE M 65 TYR 0.053 0.003 TYR g 25 ARG 0.016 0.001 ARG r 21 *********************** 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 1809 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 1457 time to evaluate : 6.627 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 124 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8632 (ttpt) REVERT: b 159 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8520 (p) REVERT: b 238 ASN cc_start: 0.8713 (p0) cc_final: 0.8459 (p0) REVERT: b 261 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7637 (ttp80) REVERT: c 7 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8568 (ttmm) REVERT: c 15 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: c 48 ILE cc_start: 0.8313 (mm) cc_final: 0.8107 (mm) REVERT: c 128 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7888 (mtp180) REVERT: e 6 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6440 (t80) REVERT: e 18 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7903 (mt-10) REVERT: e 56 LEU cc_start: 0.8994 (mt) cc_final: 0.8554 (mt) REVERT: e 64 PRO cc_start: 0.8654 (Cg_endo) cc_final: 0.8309 (Cg_exo) REVERT: e 86 CYS cc_start: 0.7219 (OUTLIER) cc_final: 0.5990 (p) REVERT: e 124 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8087 (mmm-85) REVERT: e 156 THR cc_start: 0.8487 (p) cc_final: 0.8214 (p) REVERT: e 169 LEU cc_start: 0.8096 (mm) cc_final: 0.7627 (pp) REVERT: f 68 ARG cc_start: 0.8268 (tmt-80) cc_final: 0.7922 (ttp80) REVERT: g 129 GLU cc_start: 0.5261 (tt0) cc_final: 0.4837 (tm-30) REVERT: h 1 MET cc_start: 0.4103 (ptt) cc_final: 0.3865 (ttp) REVERT: i 135 MET cc_start: 0.2267 (mmp) cc_final: 0.2005 (mmp) REVERT: j 98 GLU cc_start: 0.8409 (mp0) cc_final: 0.7974 (mp0) REVERT: j 106 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8479 (tttt) REVERT: j 118 MET cc_start: 0.8393 (ptp) cc_final: 0.8098 (ptp) REVERT: j 136 GLN cc_start: 0.8494 (mt0) cc_final: 0.7866 (mm-40) REVERT: k 38 ILE cc_start: 0.9206 (mp) cc_final: 0.8950 (tp) REVERT: k 73 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8236 (p0) REVERT: l 143 GLU cc_start: 0.7919 (pm20) cc_final: 0.7537 (pm20) REVERT: m 40 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7276 (mtp180) REVERT: m 47 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7302 (tm-30) REVERT: m 95 LEU cc_start: 0.9229 (mt) cc_final: 0.9022 (mt) REVERT: n 72 ASP cc_start: 0.8574 (t0) cc_final: 0.8218 (t0) REVERT: n 78 LYS cc_start: 0.9226 (tppp) cc_final: 0.8898 (tppp) REVERT: n 110 MET cc_start: 0.8306 (mmp) cc_final: 0.7955 (mmp) REVERT: o 19 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8213 (tm-30) REVERT: p 10 GLU cc_start: 0.8389 (pm20) cc_final: 0.8141 (pm20) REVERT: q 51 GLN cc_start: 0.8361 (tt0) cc_final: 0.8078 (tt0) REVERT: r 6 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8347 (tm-30) REVERT: r 21 ARG cc_start: 0.9189 (mtp-110) cc_final: 0.8966 (mtp85) REVERT: s 1 MET cc_start: 0.6526 (ttm) cc_final: 0.6212 (ttm) REVERT: s 8 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8072 (mtp-110) REVERT: s 25 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8168 (ttm-80) REVERT: s 59 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8158 (mm-30) REVERT: s 84 ARG cc_start: 0.7819 (mmt-90) cc_final: 0.7444 (mmt90) REVERT: t 3 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6794 (tpm170) REVERT: t 32 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8940 (pp) REVERT: t 56 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7678 (mm-30) REVERT: t 80 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.7682 (p-90) REVERT: u 23 LYS cc_start: 0.8088 (tptt) cc_final: 0.7886 (tptt) REVERT: u 72 PHE cc_start: 0.7504 (t80) cc_final: 0.7120 (t80) REVERT: v 7 GLU cc_start: 0.8046 (tp30) cc_final: 0.7094 (tm-30) REVERT: v 42 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7883 (pp) REVERT: v 46 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8989 (mmmm) REVERT: v 53 LYS cc_start: 0.9187 (mttt) cc_final: 0.8822 (mmtp) REVERT: v 55 GLU cc_start: 0.8613 (pm20) cc_final: 0.8387 (pm20) REVERT: v 87 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: w 11 ASP cc_start: 0.8378 (t0) cc_final: 0.7993 (t0) REVERT: w 25 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6591 (mt-10) REVERT: w 64 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8463 (ttpp) REVERT: y 31 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: y 41 HIS cc_start: 0.8919 (p-80) cc_final: 0.8284 (p-80) REVERT: y 45 GLN cc_start: 0.8530 (pp30) cc_final: 0.7940 (pp30) REVERT: y 54 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8757 (mtpt) REVERT: z 57 GLU cc_start: 0.7837 (tp30) cc_final: 0.7383 (tp30) REVERT: D 3 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7248 (tpm170) REVERT: D 19 ARG cc_start: 0.9233 (mtp85) cc_final: 0.8638 (mmm-85) REVERT: D 41 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8162 (ttt-90) REVERT: F 19 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7478 (mtt180) REVERT: G 6 ARG cc_start: 0.8900 (ttp80) cc_final: 0.8308 (mmp-170) REVERT: G 17 HIS cc_start: 0.8588 (m-70) cc_final: 0.7861 (m-70) REVERT: G 25 LYS cc_start: 0.8557 (mmtm) cc_final: 0.7720 (tptt) REVERT: G 29 PHE cc_start: 0.8914 (m-80) cc_final: 0.8526 (m-80) REVERT: G 48 MET cc_start: 0.8510 (pmm) cc_final: 0.8269 (pmm) REVERT: G 135 MET cc_start: 0.8637 (ppp) cc_final: 0.8175 (ppp) REVERT: H 122 GLN cc_start: 0.7729 (mt0) cc_final: 0.7444 (mm110) REVERT: H 150 VAL cc_start: 0.7548 (p) cc_final: 0.7229 (m) REVERT: I 13 ARG cc_start: 0.7149 (tpt170) cc_final: 0.6301 (tpt170) REVERT: I 54 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8942 (mp) REVERT: I 81 LEU cc_start: 0.8832 (mt) cc_final: 0.8499 (mt) REVERT: I 97 LEU cc_start: 0.8407 (pt) cc_final: 0.8079 (pt) REVERT: I 134 TYR cc_start: 0.8568 (t80) cc_final: 0.8263 (t80) REVERT: I 165 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7855 (tm-30) REVERT: I 169 TRP cc_start: 0.8344 (p90) cc_final: 0.7626 (p90) REVERT: I 183 ARG cc_start: 0.7911 (ppt170) cc_final: 0.7019 (ppt170) REVERT: J 30 PHE cc_start: 0.8539 (m-80) cc_final: 0.7759 (m-10) REVERT: J 95 MET cc_start: 0.7290 (ptp) cc_final: 0.6824 (ptp) REVERT: J 120 HIS cc_start: 0.5430 (OUTLIER) cc_final: 0.4634 (p90) REVERT: K 40 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6180 (mt-10) REVERT: K 81 ASN cc_start: 0.8786 (t0) cc_final: 0.8254 (t0) REVERT: L 24 LYS cc_start: 0.9289 (pttt) cc_final: 0.8956 (pptt) REVERT: M 44 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7457 (t80) REVERT: M 62 LEU cc_start: 0.9496 (tp) cc_final: 0.9242 (tt) REVERT: M 79 ARG cc_start: 0.8653 (ptt180) cc_final: 0.8215 (ptm-80) REVERT: M 85 TYR cc_start: 0.8229 (m-80) cc_final: 0.7785 (m-80) REVERT: M 86 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7017 (mmtm) REVERT: M 93 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8091 (ttmm) REVERT: M 95 MET cc_start: 0.7928 (tpp) cc_final: 0.7308 (tpp) REVERT: O 48 ARG cc_start: 0.6351 (mtm-85) cc_final: 0.5547 (mmt-90) REVERT: P 55 ARG cc_start: 0.9003 (mpp-170) cc_final: 0.8644 (mtp180) REVERT: P 63 GLN cc_start: 0.8304 (mm110) cc_final: 0.7915 (mm-40) REVERT: P 127 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7121 (ttp-110) REVERT: Q 33 CYS cc_start: 0.8597 (t) cc_final: 0.8026 (t) REVERT: Q 85 ARG cc_start: 0.6697 (ptm160) cc_final: 0.5970 (ptm160) REVERT: Q 107 LYS cc_start: 0.8342 (mmtm) cc_final: 0.7956 (mmtm) REVERT: R 13 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.7625 (m-70) REVERT: R 33 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7494 (mp) REVERT: R 58 GLU cc_start: 0.7764 (tp30) cc_final: 0.7109 (tm-30) REVERT: R 74 MET cc_start: 0.9036 (ttt) cc_final: 0.8588 (tmm) REVERT: T 64 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7695 (tttt) REVERT: V 79 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8329 (tm-30) REVERT: W 49 LYS cc_start: 0.7603 (ptmt) cc_final: 0.7082 (ptmt) REVERT: W 63 TYR cc_start: 0.9085 (t80) cc_final: 0.8607 (t80) REVERT: X 38 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7026 (t) REVERT: X 43 MET cc_start: 0.8478 (mmp) cc_final: 0.7928 (mmm) REVERT: X 65 MET cc_start: 0.8053 (mtt) cc_final: 0.7202 (mmm) REVERT: X 68 HIS cc_start: 0.7811 (m-70) cc_final: 0.7534 (m-70) REVERT: X 70 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8334 (mt) REVERT: Y 13 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8401 (m) REVERT: Y 14 GLU cc_start: 0.8772 (tm-30) cc_final: 0.7825 (tm-30) REVERT: Y 17 ARG cc_start: 0.8560 (ppt170) cc_final: 0.8074 (tmm160) REVERT: Y 59 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7693 (mtp-110) REVERT: Z 24 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7430 (ptmt) outliers start: 352 outliers final: 295 residues processed: 1635 average time/residue: 1.3807 time to fit residues: 3890.6079 Evaluate side-chains 1750 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1430 time to evaluate : 6.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 264 LYS Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 15 PHE Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 51 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 87 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 3 ARG Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 55 VAL Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 98 ASN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 74 LYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 7 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 32 PHE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 44 PHE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 60 GLN Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 619 optimal weight: 20.0000 chunk 997 optimal weight: 5.9990 chunk 608 optimal weight: 10.0000 chunk 473 optimal weight: 0.5980 chunk 693 optimal weight: 50.0000 chunk 1046 optimal weight: 20.0000 chunk 962 optimal weight: 10.0000 chunk 832 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 643 optimal weight: 20.0000 chunk 510 optimal weight: 8.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 152 GLN c 167 ASN c 173 GLN f 47 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 38 GLN D 13 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 HIS I 35 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS P 14 GLN ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 161387 Z= 0.278 Angle : 0.681 15.339 241347 Z= 0.342 Chirality : 0.038 0.289 30852 Planarity : 0.005 0.119 13007 Dihedral : 23.646 179.721 80574 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.05 % Favored : 89.80 % Rotamer: Outliers : 6.54 % Allowed : 30.23 % Favored : 63.23 % 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: -2.65 (0.10), residues: 5919 helix: -0.84 (0.11), residues: 1859 sheet: -1.78 (0.16), residues: 965 loop : -2.37 (0.10), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 102 HIS 0.007 0.001 HIS G 169 PHE 0.036 0.002 PHE M 65 TYR 0.048 0.002 TYR g 25 ARG 0.016 0.001 ARG r 21 ********************** 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 1786 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1465 time to evaluate : 6.611 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: b 114 GLN cc_start: 0.8308 (tt0) cc_final: 0.8088 (tp40) REVERT: b 159 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8598 (p) REVERT: b 238 ASN cc_start: 0.8524 (p0) cc_final: 0.8272 (p0) REVERT: b 261 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7545 (ttp80) REVERT: c 128 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7864 (mtp180) REVERT: d 144 GLU cc_start: 0.7638 (tt0) cc_final: 0.7419 (mp0) REVERT: d 198 GLU cc_start: 0.8126 (tp30) cc_final: 0.7749 (tp30) REVERT: e 6 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.6438 (t80) REVERT: e 15 LEU cc_start: 0.8405 (mt) cc_final: 0.8115 (mt) REVERT: e 18 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8122 (mt-10) REVERT: e 56 LEU cc_start: 0.9050 (mt) cc_final: 0.8500 (mt) REVERT: e 64 PRO cc_start: 0.8638 (Cg_endo) cc_final: 0.8305 (Cg_exo) REVERT: e 86 CYS cc_start: 0.7116 (OUTLIER) cc_final: 0.5947 (p) REVERT: e 124 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8078 (mmm-85) REVERT: e 156 THR cc_start: 0.8529 (p) cc_final: 0.8262 (p) REVERT: e 169 LEU cc_start: 0.7958 (mm) cc_final: 0.7465 (pp) REVERT: h 1 MET cc_start: 0.3850 (ptt) cc_final: 0.3539 (ttt) REVERT: h 86 MET cc_start: 0.5907 (pmm) cc_final: 0.5633 (pmm) REVERT: j 44 TYR cc_start: 0.8681 (t80) cc_final: 0.7820 (t80) REVERT: j 98 GLU cc_start: 0.8371 (mp0) cc_final: 0.7897 (mp0) REVERT: j 99 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8263 (ttm110) REVERT: j 106 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8450 (tttt) REVERT: j 109 LEU cc_start: 0.9213 (mt) cc_final: 0.8943 (mt) REVERT: j 118 MET cc_start: 0.8403 (ptp) cc_final: 0.8030 (ptp) REVERT: k 38 ILE cc_start: 0.9154 (mp) cc_final: 0.8943 (tp) REVERT: k 73 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8024 (p0) REVERT: k 113 MET cc_start: 0.8146 (tpt) cc_final: 0.7897 (tpt) REVERT: l 112 LEU cc_start: 0.8452 (mt) cc_final: 0.8193 (mt) REVERT: l 143 GLU cc_start: 0.7896 (pm20) cc_final: 0.7490 (pm20) REVERT: m 40 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7490 (mtp180) REVERT: m 47 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7256 (tm-30) REVERT: n 78 LYS cc_start: 0.9062 (tppp) cc_final: 0.8756 (tppp) REVERT: n 110 MET cc_start: 0.8307 (mmp) cc_final: 0.7983 (mmp) REVERT: n 115 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8034 (mp) REVERT: o 19 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8089 (tm-30) REVERT: o 116 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8035 (tp-100) REVERT: p 10 GLU cc_start: 0.8234 (pm20) cc_final: 0.8013 (pm20) REVERT: p 108 ARG cc_start: 0.6014 (ptm160) cc_final: 0.5746 (ptp-170) REVERT: q 50 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8009 (mpt180) REVERT: q 51 GLN cc_start: 0.8229 (tt0) cc_final: 0.7904 (tt0) REVERT: r 6 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8282 (tm-30) REVERT: r 13 ARG cc_start: 0.8638 (ttt-90) cc_final: 0.8435 (ptm-80) REVERT: r 21 ARG cc_start: 0.9203 (mtp-110) cc_final: 0.8476 (mtp85) REVERT: r 40 MET cc_start: 0.7983 (ttm) cc_final: 0.7717 (ttt) REVERT: r 97 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8243 (tptp) REVERT: s 8 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8003 (mtp-110) REVERT: s 25 ARG cc_start: 0.8857 (ttm-80) cc_final: 0.8475 (ttm-80) REVERT: s 59 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8123 (mm-30) REVERT: s 84 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7429 (mmt90) REVERT: s 110 ARG cc_start: 0.7686 (ptt-90) cc_final: 0.7484 (ptt-90) REVERT: t 32 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8843 (pp) REVERT: t 48 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8333 (mm-40) REVERT: t 56 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7581 (mm-30) REVERT: t 80 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.7646 (p-90) REVERT: u 6 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8092 (ttm110) REVERT: u 17 ASP cc_start: 0.6751 (t0) cc_final: 0.6467 (t0) REVERT: u 23 LYS cc_start: 0.8173 (tptt) cc_final: 0.7919 (tptt) REVERT: u 72 PHE cc_start: 0.7339 (t80) cc_final: 0.6829 (t80) REVERT: v 7 GLU cc_start: 0.8043 (tp30) cc_final: 0.7306 (tm-30) REVERT: v 42 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7833 (pp) REVERT: v 46 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8951 (mmmm) REVERT: v 53 LYS cc_start: 0.9158 (mttt) cc_final: 0.8817 (mmtp) REVERT: v 87 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: w 11 ASP cc_start: 0.8256 (t0) cc_final: 0.7798 (t0) REVERT: w 64 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8780 (ttpp) REVERT: x 9 LYS cc_start: 0.9188 (mttm) cc_final: 0.8945 (mtpp) REVERT: y 31 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: y 41 HIS cc_start: 0.8887 (p-80) cc_final: 0.8225 (p-80) REVERT: y 54 LYS cc_start: 0.9142 (mtpp) cc_final: 0.8820 (mttt) REVERT: z 36 GLU cc_start: 0.8369 (tt0) cc_final: 0.7994 (tp30) REVERT: z 57 GLU cc_start: 0.7757 (tp30) cc_final: 0.7320 (tp30) REVERT: D 3 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6961 (tpm170) REVERT: D 19 ARG cc_start: 0.9165 (mtp85) cc_final: 0.8503 (mmm-85) REVERT: E 34 LYS cc_start: 0.9020 (ptmt) cc_final: 0.8787 (mtmm) REVERT: G 6 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8125 (mmp-170) REVERT: G 17 HIS cc_start: 0.8598 (m-70) cc_final: 0.7877 (m-70) REVERT: G 25 LYS cc_start: 0.8540 (mmtm) cc_final: 0.7663 (tptt) REVERT: G 29 PHE cc_start: 0.8879 (m-80) cc_final: 0.8570 (m-80) REVERT: G 48 MET cc_start: 0.8464 (pmm) cc_final: 0.8246 (pmm) REVERT: G 57 ASN cc_start: 0.8763 (t0) cc_final: 0.8518 (m-40) REVERT: G 135 MET cc_start: 0.8570 (ppp) cc_final: 0.8269 (ppp) REVERT: G 147 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8685 (tt) REVERT: G 164 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: H 15 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7908 (pttp) REVERT: H 122 GLN cc_start: 0.7726 (mt0) cc_final: 0.7451 (mm110) REVERT: H 150 VAL cc_start: 0.7569 (p) cc_final: 0.7271 (m) REVERT: I 2 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.7812 (ttp-170) REVERT: I 13 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6212 (tpt170) REVERT: I 54 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8982 (mp) REVERT: I 81 LEU cc_start: 0.8810 (mt) cc_final: 0.8476 (mt) REVERT: I 97 LEU cc_start: 0.8406 (pt) cc_final: 0.8106 (pt) REVERT: I 134 TYR cc_start: 0.8513 (t80) cc_final: 0.8275 (t80) REVERT: I 165 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7835 (tm-30) REVERT: I 169 TRP cc_start: 0.8236 (p90) cc_final: 0.7502 (p90) REVERT: I 183 ARG cc_start: 0.7979 (ppt170) cc_final: 0.7176 (ppt170) REVERT: J 30 PHE cc_start: 0.8511 (m-80) cc_final: 0.7857 (m-10) REVERT: J 35 LEU cc_start: 0.8089 (tp) cc_final: 0.7827 (tp) REVERT: J 95 MET cc_start: 0.7363 (ptp) cc_final: 0.6731 (ptp) REVERT: J 120 HIS cc_start: 0.4906 (OUTLIER) cc_final: 0.4117 (p90) REVERT: J 137 ARG cc_start: 0.8702 (tpp80) cc_final: 0.8111 (mpp80) REVERT: K 40 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6217 (mt-10) REVERT: K 59 TYR cc_start: 0.7059 (m-80) cc_final: 0.6788 (m-80) REVERT: K 81 ASN cc_start: 0.8704 (t0) cc_final: 0.8200 (t0) REVERT: K 90 MET cc_start: 0.8411 (mmm) cc_final: 0.7824 (mmp) REVERT: L 24 LYS cc_start: 0.9268 (pttt) cc_final: 0.8929 (pptt) REVERT: L 100 MET cc_start: 0.9315 (ptp) cc_final: 0.7947 (ttt) REVERT: M 30 LYS cc_start: 0.8379 (mptt) cc_final: 0.8168 (mptt) REVERT: M 44 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7076 (t80) REVERT: M 62 LEU cc_start: 0.9531 (tp) cc_final: 0.9254 (tt) REVERT: M 63 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7885 (mtpt) REVERT: M 79 ARG cc_start: 0.8296 (ptt180) cc_final: 0.7938 (ptm-80) REVERT: M 85 TYR cc_start: 0.8314 (m-80) cc_final: 0.8029 (m-80) REVERT: M 86 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7008 (mmtm) REVERT: M 88 LYS cc_start: 0.8948 (tptp) cc_final: 0.8211 (tptp) REVERT: M 93 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8275 (ttmm) REVERT: M 95 MET cc_start: 0.7805 (tpp) cc_final: 0.7171 (tpp) REVERT: N 45 MET cc_start: 0.8660 (pmm) cc_final: 0.8452 (pmm) REVERT: O 48 ARG cc_start: 0.6510 (mtm-85) cc_final: 0.5535 (mmt-90) REVERT: P 55 ARG cc_start: 0.8990 (mpp-170) cc_final: 0.8639 (mtp180) REVERT: P 63 GLN cc_start: 0.8284 (mm110) cc_final: 0.7923 (mm-40) REVERT: P 86 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8204 (ttpp) REVERT: P 127 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7216 (ttp-110) REVERT: Q 33 CYS cc_start: 0.8821 (t) cc_final: 0.8373 (t) REVERT: Q 85 ARG cc_start: 0.6627 (ptm160) cc_final: 0.6012 (ptm160) REVERT: Q 107 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8018 (mmtm) REVERT: R 13 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7205 (m-70) REVERT: R 33 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7446 (mp) REVERT: R 58 GLU cc_start: 0.7818 (tp30) cc_final: 0.7192 (tm-30) REVERT: R 74 MET cc_start: 0.9017 (ttt) cc_final: 0.8560 (tmm) REVERT: T 58 MET cc_start: 0.8486 (ptp) cc_final: 0.8115 (mtp) REVERT: U 52 LEU cc_start: 0.8112 (mp) cc_final: 0.7554 (tt) REVERT: W 49 LYS cc_start: 0.7597 (ptmt) cc_final: 0.7016 (ptmt) REVERT: W 63 TYR cc_start: 0.8922 (t80) cc_final: 0.8497 (t80) REVERT: X 38 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7002 (t) REVERT: X 43 MET cc_start: 0.8385 (mmp) cc_final: 0.7837 (mmm) REVERT: X 65 MET cc_start: 0.7986 (mtt) cc_final: 0.7086 (mmm) REVERT: X 68 HIS cc_start: 0.7658 (m-70) cc_final: 0.7398 (m-70) REVERT: X 70 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8341 (mt) REVERT: Y 13 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8406 (m) REVERT: Y 14 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8088 (tm-30) REVERT: Y 17 ARG cc_start: 0.8538 (ppt170) cc_final: 0.8076 (tmm160) REVERT: Z 24 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7335 (ptmt) REVERT: Z 61 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.4832 (pmt-80) REVERT: a 54 LYS cc_start: 0.4962 (mmtt) cc_final: 0.4460 (mmmt) outliers start: 321 outliers final: 264 residues processed: 1617 average time/residue: 1.3028 time to fit residues: 3610.7158 Evaluate side-chains 1724 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1433 time to evaluate : 6.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 184 GLU Chi-restraints excluded: chain b residue 186 ASP Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 264 LYS Chi-restraints excluded: chain b residue 268 ARG Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain d residue 7 ASP Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 84 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 25 MET Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 86 CYS Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 158 THR Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 LYS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 76 HIS Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 14 SER Chi-restraints excluded: chain k residue 29 HIS Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 73 ASP Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 27 LEU Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 79 LEU Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 86 GLU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 40 ARG Chi-restraints excluded: chain m residue 60 GLN Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain n residue 115 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 19 PHE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 50 ARG Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 90 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 18 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 8 ARG Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 24 ILE Chi-restraints excluded: chain s residue 40 ASN Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 9 LYS Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 80 TRP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 LYS Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain w residue 74 LYS Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 41 SER Chi-restraints excluded: chain x residue 42 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 27 ASN Chi-restraints excluded: chain y residue 31 GLN Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 13 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 161 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 44 PHE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 66 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 69 CYS Chi-restraints excluded: chain P residue 80 ASN Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 42 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 82 ARG Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain S residue 62 ARG Chi-restraints excluded: chain T residue 23 SER Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 78 LEU Chi-restraints excluded: chain Y residue 79 THR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 61 ARG Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 161 VAL Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain 7 residue 101 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 661 optimal weight: 10.0000 chunk 887 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 768 optimal weight: 30.0000 chunk 122 optimal weight: 0.3980 chunk 231 optimal weight: 0.0670 chunk 834 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 856 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 85 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN f 47 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 17 ASN ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 42 HIS ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 HIS I 35 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS Q 4 ASN R 13 HIS ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098030 restraints weight = 370426.681| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.65 r_work: 0.3359 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 161387 Z= 0.179 Angle : 0.615 15.108 241347 Z= 0.309 Chirality : 0.034 0.282 30852 Planarity : 0.005 0.068 13007 Dihedral : 23.490 178.581 80574 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.56 % Favored : 90.27 % Rotamer: Outliers : 5.17 % Allowed : 31.62 % Favored : 63.21 % 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: -2.39 (0.10), residues: 5919 helix: -0.65 (0.12), residues: 1862 sheet: -1.56 (0.16), residues: 959 loop : -2.23 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 102 HIS 0.018 0.001 HIS G 169 PHE 0.044 0.002 PHE M 65 TYR 0.040 0.002 TYR g 25 ARG 0.016 0.001 ARG r 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55426.92 seconds wall clock time: 960 minutes 36.51 seconds (57636.51 seconds total)