Starting phenix.real_space_refine on Tue Mar 26 16:28:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdd_21632/03_2024/6wdd_21632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdd_21632/03_2024/6wdd_21632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdd_21632/03_2024/6wdd_21632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdd_21632/03_2024/6wdd_21632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdd_21632/03_2024/6wdd_21632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdd_21632/03_2024/6wdd_21632_updated.pdb" } resolution = 3.2 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= 0.119 sd= 1.117 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 4803 5.49 5 S 154 5.16 5 C 75486 2.51 5 N 27960 2.21 5 O 41819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 65": "OD1" <-> "OD2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 193": "OE1" <-> "OE2" Residue "b PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 39": "OD1" <-> "OD2" 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 ARG 169": "NH1" <-> "NH2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 2": "OE1" <-> "OE2" 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 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d GLU 197": "OE1" <-> "OE2" Residue "e GLU 31": "OE1" <-> "OE2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 97": "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 ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e ASP 162": "OD1" <-> "OD2" Residue "e ASP 173": "OD1" <-> "OD2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 38": "OD1" <-> "OD2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g GLU 114": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 115": "OD1" <-> "OD2" Residue "i GLU 140": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 43": "OE1" <-> "OE2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "j ASP 141": "OD1" <-> "OD2" Residue "k ASP 12": "OD1" <-> "OD2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k GLU 106": "OE1" <-> "OE2" Residue "k GLU 110": "OE1" <-> "OE2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l 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 ASP 70": "OD1" <-> "OD2" Residue "m GLU 90": "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 ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 33": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ASP 95": "OD1" <-> "OD2" Residue "s ASP 22": "OD1" <-> "OD2" Residue "s TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 77": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ASP 94": "OD1" <-> "OD2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 5": "OE1" <-> "OE2" Residue "t GLU 25": "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 GLU 61": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u GLU 87": "OE1" <-> "OE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 42": "OE1" <-> "OE2" Residue "x GLU 69": "OE1" <-> "OE2" Residue "y GLU 24": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ASP 39": "OD1" <-> "OD2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" 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 ASP 7": "OD1" <-> "OD2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ASP 53": "OD1" <-> "OD2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "Y GLU 14": "OE1" <-> "OE2" Residue "Y GLU 52": "OE1" <-> "OE2" Residue "Y ASP 58": "OD1" <-> "OD2" Residue "Z ASP 12": "OD1" <-> "OD2" 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150222 Number of models: 1 Model: "" Number of chains: 60 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "h" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 90, 'rna2p_pyr': 49, 'rna3p_pur': 784, 'rna3p_pyr': 616} Link IDs: {'rna2p': 139, 'rna3p': 1399} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 211, 'rna2p_pyr': 94, 'rna3p_pur': 1463, 'rna3p_pyr': 1135} Link IDs: {'rna2p': 305, 'rna3p': 2597} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "4" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "7" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 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: 56.71, per 1000 atoms: 0.38 Number of scatterers: 150222 At special positions: 0 Unit cell: (279.93, 266.6, 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 4803 15.00 O 41819 8.00 N 27960 7.00 C 75486 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: 62.83 Conformation dependent library (CDL) restraints added in 6.9 seconds 11838 Ramachandran restraints generated. 5919 Oldfield, 0 Emsley, 5919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 184 helices and 64 sheets defined 38.7% alpha, 16.3% beta 1516 base pairs and 2807 stacking pairs defined. Time for finding SS restraints: 74.92 Creating SS restraints... Processing helix chain 'b' and resid 10 through 16 removed outlier: 7.390A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL b 16 " --> pdb=" O ARG b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 10 through 16' Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.964A 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: 3.935A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.708A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.181A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 6.000A 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: 4.172A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 5.398A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 removed outlier: 3.742A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 103 removed outlier: 4.456A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 103' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.841A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.537A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.644A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP d 140 " --> pdb=" O GLN d 136 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 4.253A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.553A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 200 removed outlier: 3.521A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.843A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR e 6 " --> pdb=" O LYS e 2 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN e 20 " --> pdb=" O MET e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 4.034A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) removed outlier: 4.192A 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 61 removed outlier: 5.072A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.297A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 141 through 146 removed outlier: 6.889A pdb=" N VAL e 145 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 5.557A 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: 4.044A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 7 removed outlier: 4.183A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.616A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.592A pdb=" N ARG f 148 " --> pdb=" O ALA f 144 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG f 152 " --> pdb=" O ARG f 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 29 removed outlier: 3.655A pdb=" N PHE g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.561A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 73 removed outlier: 5.777A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA g 59 " --> pdb=" O GLU g 55 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 4.043A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.511A pdb=" N GLN h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY h 21 " --> pdb=" O GLU h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.604A pdb=" N LYS h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET h 38 " --> pdb=" O THR h 34 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 70 removed outlier: 3.923A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 3.868A 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 70' Processing helix chain 'h' and resid 71 through 78 removed outlier: 4.892A pdb=" N ALA h 75 " --> pdb=" O CYS h 71 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE h 76 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 71 through 78' Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.572A pdb=" N GLU h 98 " --> pdb=" O ARG h 94 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS h 105 " --> pdb=" O LYS h 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 114 removed outlier: 7.115A pdb=" N PHE h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU h 114 " --> pdb=" O ALA h 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 109 through 114' Processing helix chain 'i' and resid 23 through 31 removed outlier: 4.875A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY i 31 " --> pdb=" O LEU i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 49 removed outlier: 3.511A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.526A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.680A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.825A pdb=" N ARG i 126 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU i 129 " --> pdb=" O THR i 125 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.688A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.458A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.560A 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: 4.427A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'k' and resid 104 through 109 removed outlier: 3.518A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER k 109 " --> pdb=" O GLU k 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 42 removed outlier: 3.838A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.646A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.254A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 83 removed outlier: 3.961A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) Processing helix chain 'l' and resid 93 through 99 removed outlier: 5.965A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.620A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.563A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 3.929A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (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: 3.732A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.634A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.515A pdb=" N ARG n 69 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 3.563A pdb=" N VAL n 76 " --> pdb=" O ASP n 72 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 88 removed outlier: 3.963A pdb=" N ALA n 88 " --> pdb=" O GLY n 84 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 20 removed outlier: 3.840A pdb=" N ALA o 6 " --> pdb=" O ASP o 2 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 5.100A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.524A 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 Processing helix chain 'p' and resid 1 through 13 removed outlier: 3.640A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS p 13 " --> pdb=" O GLN p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.744A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.167A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 3.746A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 35 through 60 removed outlier: 4.120A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 72 removed outlier: 3.502A 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 Processing helix chain 's' and resid 13 through 25 removed outlier: 3.602A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.764A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.580A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA s 56 " --> pdb=" O GLU s 52 " (cutoff:3.500A) Processing helix chain 't' and resid 1 through 11 removed outlier: 3.670A pdb=" N GLU t 5 " --> pdb=" O MET t 1 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.737A pdb=" N MET t 24 " --> pdb=" O ALA t 20 " (cutoff:3.500A) removed outlier: 3.513A 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: 4.037A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.128A 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: 3.553A pdb=" N LEU v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 4.492A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 58 removed outlier: 3.855A pdb=" N TYR v 57 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 3.596A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 Processing helix chain 'y' and resid 1 through 7 removed outlier: 4.622A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 3.564A pdb=" N LEU y 14 " --> pdb=" O SER y 10 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU y 24 " --> pdb=" O ASN y 20 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 4.670A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA y 61 " --> pdb=" O LEU y 57 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'B' and resid 8 through 18 removed outlier: 5.099A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.572A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.712A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.937A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 4.941A 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: 4.609A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'F' and resid 30 through 35 removed outlier: 3.710A pdb=" N LYS F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLN F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 35' Processing helix chain 'G' and resid 4 through 12 Processing helix chain 'G' and resid 42 through 63 removed outlier: 3.525A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.617A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.554A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.534A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 4.193A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 147 removed outlier: 3.546A pdb=" N GLU G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.534A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.745A pdb=" N VAL G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 4.991A 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: 3.639A pdb=" N TYR G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 4.141A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 47 removed outlier: 5.279A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.765A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.564A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.603A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.558A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 3.890A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.508A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.508A pdb=" N TYR I 74 " --> pdb=" O GLN I 70 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.195A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 4.437A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 164 removed outlier: 5.796A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 3.682A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 191' Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.924A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 4.108A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.176A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 117 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 3.544A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.848A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.612A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 33 Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.541A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP K 82 " --> pdb=" O PHE K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.588A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 3.536A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.615A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.698A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.820A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 3.662A pdb=" N LYS L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.654A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 45 through 55 Proline residue: N 50 - end of helix removed outlier: 4.330A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.518A pdb=" N THR N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 101 removed outlier: 4.822A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 30 removed outlier: 4.255A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.615A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.836A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 4.649A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 75 removed outlier: 3.694A pdb=" N ALA P 66 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 5.203A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 5.073A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.707A pdb=" N THR R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.564A pdb=" N SER R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 63 removed outlier: 5.031A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.530A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.642A pdb=" N ARG R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 20 removed outlier: 3.510A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 28 removed outlier: 5.225A pdb=" N LYS S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.585A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 79 through 90 removed outlier: 4.178A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.770A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 4.434A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.830A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.580A pdb=" N ARG T 83 " --> pdb=" O GLN T 79 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY T 85 " --> pdb=" O ILE T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.629A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN U 63 " --> pdb=" O HIS U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.583A pdb=" N LEU U 74 " --> pdb=" O ARG U 70 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 16 removed outlier: 6.317A pdb=" N GLU W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 3.513A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.824A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 removed outlier: 3.669A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.690A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.247A 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 6 through 41 removed outlier: 4.693A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 removed outlier: 3.507A pdb=" N GLN Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.692A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA Y 62 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 6.046A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.468A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 32 removed outlier: 3.640A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 62 Proline residue: Z 40 - end of helix removed outlier: 3.574A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL Z 52 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU Z 62 " --> pdb=" O LYS Z 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 3.670A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 34 removed outlier: 3.616A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 3.739A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (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 74 through 78 removed outlier: 4.008A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 79 through 82 removed outlier: 4.034A pdb=" N ILE b 90 " --> pdb=" O GLU b 81 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN b 89 " --> pdb=" O ALA b 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.329A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'c' and resid 11 through 16 removed outlier: 3.626A pdb=" N THR c 16 " --> pdb=" O VAL c 20 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 79 through 84 removed outlier: 5.671A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 179 through 182 removed outlier: 3.557A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 24 through 28 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.625A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'd' and resid 1 through 4 Processing sheet with id= 11, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.518A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL d 187 " --> pdb=" O LEU d 147 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.826A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS e 86 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE e 33 " --> pdb=" O LEU e 90 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR e 154 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN e 36 " --> pdb=" O ASP e 152 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'f' and resid 15 through 18 removed outlier: 3.503A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 15, first strand: chain 'f' and resid 81 through 88 removed outlier: 3.540A pdb=" N LEU f 132 " --> pdb=" O LYS f 84 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'f' and resid 93 through 97 removed outlier: 3.647A pdb=" N ARG f 94 " --> pdb=" O SER f 105 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'g' and resid 76 through 81 removed outlier: 7.153A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU g 114 " --> pdb=" O GLN g 133 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.808A pdb=" N ALA h 25 " --> pdb=" O SER h 85 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER h 85 " --> pdb=" O ALA h 25 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'i' and resid 56 through 60 Processing sheet with id= 20, first strand: chain 'j' and resid 14 through 19 removed outlier: 3.540A pdb=" N LEU j 57 " --> pdb=" O VAL j 18 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'j' and resid 74 through 78 removed outlier: 7.010A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'k' and resid 18 through 21 removed outlier: 3.680A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'l' and resid 88 through 91 removed outlier: 3.721A pdb=" N LYS l 141 " --> pdb=" O VAL l 120 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU l 143 " --> pdb=" O VAL l 122 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'm' and resid 62 through 65 removed outlier: 3.523A pdb=" N TRP m 64 " --> pdb=" O GLU m 104 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET m 105 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS m 34 " --> pdb=" O THR m 129 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'm' and resid 71 through 74 removed outlier: 3.728A pdb=" N TYR m 91 " --> pdb=" O ILE m 73 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'n' and resid 33 through 36 removed outlier: 5.740A pdb=" N ARG n 103 " --> pdb=" O ASN n 107 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY n 101 " --> pdb=" O PRO n 109 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA n 111 " --> pdb=" O LYS n 99 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS n 99 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE n 113 " --> pdb=" O ILE n 97 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE n 97 " --> pdb=" O ILE n 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU n 115 " --> pdb=" O THR n 95 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR n 95 " --> pdb=" O LEU n 115 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.553A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'p' and resid 25 through 32 Processing sheet with id= 29, first strand: chain 'p' and resid 48 through 51 removed outlier: 3.668A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.018A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'r' and resid 65 through 72 removed outlier: 5.214A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 's' and resid 2 through 8 removed outlier: 4.454A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL s 106 " --> pdb=" O THR s 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 's' and resid 73 through 79 removed outlier: 5.392A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 't' and resid 29 through 33 removed outlier: 4.688A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 82 through 85 Processing sheet with id= 36, first strand: chain 'v' and resid 69 through 72 removed outlier: 3.524A pdb=" N ILE v 4 " --> pdb=" O THR v 62 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE v 29 " --> pdb=" O ILE v 89 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'w' and resid 63 through 67 Processing sheet with id= 38, first strand: chain 'x' and resid 11 through 18 removed outlier: 4.659A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 40, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.596A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 19 through 23 removed outlier: 7.296A pdb=" N ILE C 47 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 37 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 50 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'F' and resid 14 through 19 removed outlier: 3.540A pdb=" N ILE F 26 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'G' and resid 14 through 17 removed outlier: 5.540A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 66 through 70 Processing sheet with id= 45, first strand: chain 'H' and resid 18 through 21 removed outlier: 5.957A pdb=" N ASN H 18 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR H 20 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG H 58 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'H' and resid 164 through 169 removed outlier: 3.577A pdb=" N VAL H 152 " --> pdb=" O GLU H 165 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE H 148 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'I' and resid 140 through 143 Processing sheet with id= 48, first strand: chain 'J' and resid 11 through 15 removed outlier: 3.988A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY J 39 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.681A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 32 through 39 removed outlier: 4.602A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'K' and resid 38 through 43 removed outlier: 5.132A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU K 61 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS K 58 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR K 92 " --> pdb=" O HIS K 3 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 53, first strand: chain 'M' and resid 23 through 28 removed outlier: 3.669A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'M' and resid 73 through 76 removed outlier: 4.122A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'N' and resid 4 through 10 removed outlier: 4.674A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE N 19 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS N 26 " --> pdb=" O LEU N 60 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'O' and resid 42 through 52 removed outlier: 4.980A pdb=" N LEU O 71 " --> pdb=" O PRO O 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG O 7 " --> pdb=" O SER O 101 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'P' and resid 29 through 34 removed outlier: 4.279A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Q' and resid 28 through 32 removed outlier: 5.332A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG Q 82 " --> pdb=" O HIS Q 95 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Q' and resid 34 through 40 removed outlier: 4.764A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Q 49 " --> pdb=" O THR Q 39 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.643A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL U 19 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL U 21 " --> pdb=" O ARG U 35 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ARG U 35 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'V' and resid 6 through 10 removed outlier: 7.166A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X' and resid 29 through 33 removed outlier: 3.872A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'a' and resid 59 through 65 removed outlier: 6.503A pdb=" N VAL a 59 " --> pdb=" O ASN a 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a' and resid 169 through 174 removed outlier: 6.644A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) 1647 hydrogen bonds defined for protein. 4854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3790 hydrogen bonds 6108 hydrogen bond angles 0 basepair planarities 1516 basepair parallelities 2807 stacking parallelities Total time for adding SS restraints: 240.12 Time building geometry restraints manager: 68.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 33866 1.34 - 1.47: 66854 1.47 - 1.59: 53080 1.59 - 1.72: 9141 1.72 - 1.84: 278 Bond restraints: 163219 Sorted by residual: bond pdb=" CA VAL J 55 " pdb=" CB VAL J 55 " ideal model delta sigma weight residual 1.539 1.569 -0.030 5.40e-03 3.43e+04 3.11e+01 bond pdb=" CA PRO i 73 " pdb=" C PRO i 73 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 bond pdb=" CA VAL e 107 " pdb=" CB VAL e 107 " ideal model delta sigma weight residual 1.539 1.556 -0.017 5.40e-03 3.43e+04 1.01e+01 bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.82e+00 bond pdb=" CB PHE 7 101 " pdb=" CG PHE 7 101 " ideal model delta sigma weight residual 1.502 1.442 0.060 2.30e-02 1.89e+03 6.79e+00 ... (remaining 163214 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 29298 106.45 - 113.34: 96213 113.34 - 120.23: 60055 120.23 - 127.11: 47141 127.11 - 134.00: 11495 Bond angle restraints: 244202 Sorted by residual: angle pdb=" C LEU E 61 " pdb=" N PRO E 62 " pdb=" CA PRO E 62 " ideal model delta sigma weight residual 118.97 127.89 -8.92 1.04e+00 9.25e-01 7.35e+01 angle pdb=" N GLY M 67 " pdb=" CA GLY M 67 " pdb=" C GLY M 67 " ideal model delta sigma weight residual 113.37 102.01 11.36 1.34e+00 5.57e-01 7.18e+01 angle pdb=" N THR S 49 " pdb=" CA THR S 49 " pdb=" C THR S 49 " ideal model delta sigma weight residual 112.23 101.71 10.52 1.26e+00 6.30e-01 6.97e+01 angle pdb=" N SER Y 5 " pdb=" CA SER Y 5 " pdb=" C SER Y 5 " ideal model delta sigma weight residual 112.92 102.85 10.07 1.23e+00 6.61e-01 6.70e+01 angle pdb=" N TYR T 68 " pdb=" CA TYR T 68 " pdb=" C TYR T 68 " ideal model delta sigma weight residual 112.23 102.02 10.21 1.26e+00 6.30e-01 6.56e+01 ... (remaining 244197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 93316 35.57 - 71.14: 10014 71.14 - 106.71: 1290 106.71 - 142.28: 9 142.28 - 177.85: 18 Dihedral angle restraints: 104647 sinusoidal: 87485 harmonic: 17162 Sorted by residual: 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 80.04 66.96 1 8.00e+00 1.56e-02 9.13e+01 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 31.63 -66.63 1 8.00e+00 1.56e-02 9.05e+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 26.24 173.76 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 104644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 24014 0.092 - 0.185: 6629 0.185 - 0.277: 533 0.277 - 0.369: 58 0.369 - 0.462: 2 Chirality restraints: 31236 Sorted by residual: chirality pdb=" CA LYS Q 43 " pdb=" N LYS Q 43 " pdb=" C LYS Q 43 " pdb=" CB LYS Q 43 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 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 -2.29 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CA PRO b 28 " pdb=" N PRO b 28 " pdb=" C PRO b 28 " pdb=" CB PRO b 28 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 31233 not shown) Planarity restraints: 13084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 775 " -0.115 2.00e-02 2.50e+03 4.81e-02 6.94e+01 pdb=" N9 G 1 775 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G 1 775 " 0.046 2.00e-02 2.50e+03 pdb=" N7 G 1 775 " 0.047 2.00e-02 2.50e+03 pdb=" C5 G 1 775 " 0.027 2.00e-02 2.50e+03 pdb=" C6 G 1 775 " -0.021 2.00e-02 2.50e+03 pdb=" O6 G 1 775 " -0.074 2.00e-02 2.50e+03 pdb=" N1 G 1 775 " -0.021 2.00e-02 2.50e+03 pdb=" C2 G 1 775 " 0.012 2.00e-02 2.50e+03 pdb=" N2 G 1 775 " 0.019 2.00e-02 2.50e+03 pdb=" N3 G 1 775 " 0.036 2.00e-02 2.50e+03 pdb=" C4 G 1 775 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " -0.103 2.00e-02 2.50e+03 4.40e-02 5.80e+01 pdb=" N9 G 12061 " 0.003 2.00e-02 2.50e+03 pdb=" C8 G 12061 " 0.047 2.00e-02 2.50e+03 pdb=" N7 G 12061 " 0.048 2.00e-02 2.50e+03 pdb=" C5 G 12061 " 0.021 2.00e-02 2.50e+03 pdb=" C6 G 12061 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G 12061 " -0.071 2.00e-02 2.50e+03 pdb=" N1 G 12061 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G 12061 " 0.011 2.00e-02 2.50e+03 pdb=" N2 G 12061 " 0.025 2.00e-02 2.50e+03 pdb=" N3 G 12061 " 0.024 2.00e-02 2.50e+03 pdb=" C4 G 12061 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 446 " 0.100 2.00e-02 2.50e+03 4.22e-02 5.35e+01 pdb=" N9 G 1 446 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G 1 446 " -0.046 2.00e-02 2.50e+03 pdb=" N7 G 1 446 " -0.044 2.00e-02 2.50e+03 pdb=" C5 G 1 446 " -0.020 2.00e-02 2.50e+03 pdb=" C6 G 1 446 " 0.021 2.00e-02 2.50e+03 pdb=" O6 G 1 446 " 0.064 2.00e-02 2.50e+03 pdb=" N1 G 1 446 " 0.017 2.00e-02 2.50e+03 pdb=" C2 G 1 446 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G 1 446 " -0.023 2.00e-02 2.50e+03 pdb=" N3 G 1 446 " -0.026 2.00e-02 2.50e+03 pdb=" C4 G 1 446 " -0.028 2.00e-02 2.50e+03 ... (remaining 13081 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 18659 2.76 - 3.47: 196832 3.47 - 4.19: 477200 4.19 - 4.90: 651770 Nonbonded interactions: 1344462 Sorted by model distance: nonbonded pdb=" O3' A 7 76 " pdb=" C PHE 7 101 " model vdw 1.327 3.270 nonbonded pdb=" O GLU y 12 " pdb=" OD1 ASN y 15 " model vdw 2.219 3.040 nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.232 2.440 nonbonded pdb=" O ARG n 69 " pdb=" OG1 THR n 70 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR d 35 " pdb=" OD2 ASP d 176 " model vdw 2.276 2.440 ... (remaining 1344457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '5' and resid 1 through 76) selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 11.100 Check model and map are aligned: 1.630 Set scattering table: 1.000 Process input model: 540.260 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 562.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 0.060 163219 Z= 0.359 Angle : 0.923 14.096 244202 Z= 0.616 Chirality : 0.078 0.462 31236 Planarity : 0.007 0.065 13084 Dihedral : 22.164 177.851 93571 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 1.72 % Allowed : 10.56 % Favored : 87.72 % Rotamer: Outliers : 0.49 % Allowed : 5.85 % Favored : 93.66 % 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: -4.87 (0.08), residues: 5919 helix: -3.83 (0.07), residues: 1804 sheet: -2.72 (0.14), residues: 990 loop : -3.04 (0.09), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP S 41 HIS 0.002 0.000 HIS o 100 PHE 0.028 0.005 PHE G 161 TYR 0.048 0.007 TYR N 5 ARG 0.005 0.001 ARG D 33 *********************** 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 2110 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 2086 time to evaluate : 6.264 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: b 22 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7739 (tm-30) REVERT: b 95 TYR cc_start: 0.7905 (m-80) cc_final: 0.7522 (m-80) REVERT: b 96 LYS cc_start: 0.8220 (tptt) cc_final: 0.7877 (tmtt) REVERT: b 109 LEU cc_start: 0.8612 (tp) cc_final: 0.8216 (tp) REVERT: b 120 ASP cc_start: 0.8307 (p0) cc_final: 0.8069 (p0) REVERT: b 131 MET cc_start: 0.8575 (mtm) cc_final: 0.8350 (mtm) REVERT: b 179 GLU cc_start: 0.7404 (tt0) cc_final: 0.6786 (tt0) REVERT: b 182 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8682 (mttm) REVERT: b 260 LYS cc_start: 0.8649 (mttt) cc_final: 0.8437 (mmtm) REVERT: c 26 VAL cc_start: 0.9062 (t) cc_final: 0.8791 (t) REVERT: c 28 GLU cc_start: 0.7955 (pp20) cc_final: 0.7657 (pp20) REVERT: c 90 PHE cc_start: 0.7490 (m-80) cc_final: 0.7148 (m-80) REVERT: c 128 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7629 (mtp180) REVERT: d 1 MET cc_start: 0.8589 (tpp) cc_final: 0.7695 (tpp) REVERT: d 24 ASN cc_start: 0.8263 (t0) cc_final: 0.7964 (t0) REVERT: d 35 TYR cc_start: 0.8950 (t80) cc_final: 0.8638 (t80) REVERT: d 91 ASP cc_start: 0.7687 (t0) cc_final: 0.7369 (t0) REVERT: d 156 ASN cc_start: 0.7244 (t0) cc_final: 0.6967 (t0) REVERT: d 188 MET cc_start: 0.7822 (ttm) cc_final: 0.7590 (ttm) REVERT: d 194 LYS cc_start: 0.8963 (tptt) cc_final: 0.8620 (tppt) REVERT: e 6 TYR cc_start: 0.9001 (t80) cc_final: 0.8571 (t80) REVERT: e 25 MET cc_start: 0.7646 (mmm) cc_final: 0.7413 (mmm) REVERT: e 90 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7779 (tt) REVERT: e 94 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8373 (ptt-90) REVERT: e 95 MET cc_start: 0.8725 (ppp) cc_final: 0.8345 (ppp) REVERT: e 102 LEU cc_start: 0.8907 (mm) cc_final: 0.8561 (mm) REVERT: e 111 ARG cc_start: 0.4743 (ttp80) cc_final: 0.4206 (tpp80) REVERT: f 38 ASP cc_start: 0.8331 (p0) cc_final: 0.8055 (t0) REVERT: f 72 ASN cc_start: 0.8898 (t0) cc_final: 0.8635 (t0) REVERT: f 87 GLN cc_start: 0.8187 (tt0) cc_final: 0.7764 (pm20) REVERT: f 100 ASN cc_start: 0.6976 (p0) cc_final: 0.6629 (p0) REVERT: g 27 ARG cc_start: 0.8416 (ttp-170) cc_final: 0.7931 (ttm170) REVERT: g 28 ASN cc_start: 0.8253 (m-40) cc_final: 0.7696 (m-40) REVERT: g 46 PHE cc_start: 0.8299 (m-80) cc_final: 0.7920 (m-10) REVERT: h 52 MET cc_start: 0.1142 (tmm) cc_final: 0.0873 (tmm) REVERT: j 44 TYR cc_start: 0.8458 (t80) cc_final: 0.8022 (t80) REVERT: j 52 ASP cc_start: 0.7863 (m-30) cc_final: 0.7605 (m-30) REVERT: j 91 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7807 (mt-10) REVERT: j 118 MET cc_start: 0.7475 (ptp) cc_final: 0.7124 (ptp) REVERT: j 136 GLN cc_start: 0.8778 (mt0) cc_final: 0.8066 (mm-40) REVERT: k 1 MET cc_start: 0.6209 (ttm) cc_final: 0.5973 (ttm) REVERT: k 32 TYR cc_start: 0.8668 (m-80) cc_final: 0.8373 (m-10) REVERT: k 88 ASN cc_start: 0.7955 (m-40) cc_final: 0.7610 (m-40) REVERT: k 110 GLU cc_start: 0.7677 (tp30) cc_final: 0.7364 (tp30) REVERT: k 113 MET cc_start: 0.6821 (mmp) cc_final: 0.6608 (mmm) REVERT: l 36 LYS cc_start: 0.9079 (mttt) cc_final: 0.8710 (mttp) REVERT: l 59 ARG cc_start: 0.8535 (mtp180) cc_final: 0.8169 (mtp180) REVERT: l 69 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7916 (ttm-80) REVERT: l 89 VAL cc_start: 0.8527 (m) cc_final: 0.8321 (m) REVERT: l 121 THR cc_start: 0.8883 (m) cc_final: 0.8498 (p) REVERT: m 73 ILE cc_start: 0.9188 (mm) cc_final: 0.8448 (mm) REVERT: m 90 GLU cc_start: 0.6711 (mp0) cc_final: 0.6503 (mp0) REVERT: m 115 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7393 (mt-10) REVERT: n 6 SER cc_start: 0.8674 (m) cc_final: 0.8278 (m) REVERT: n 35 LYS cc_start: 0.8052 (tttm) cc_final: 0.7847 (tttm) REVERT: o 16 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.8104 (mmm-85) REVERT: o 36 TYR cc_start: 0.7864 (m-80) cc_final: 0.7459 (m-10) REVERT: o 38 GLN cc_start: 0.8207 (pt0) cc_final: 0.8006 (pm20) REVERT: o 58 ILE cc_start: 0.7277 (mm) cc_final: 0.6901 (mm) REVERT: o 80 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8532 (mt-10) REVERT: o 94 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8085 (ttp-170) REVERT: o 97 PHE cc_start: 0.8074 (m-80) cc_final: 0.7797 (m-10) REVERT: o 98 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8115 (tp-100) REVERT: p 26 GLU cc_start: 0.8151 (pp20) cc_final: 0.7694 (pp20) REVERT: p 87 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7589 (ttp80) REVERT: p 100 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7686 (mtt180) REVERT: q 15 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8378 (ttmm) REVERT: q 96 ASP cc_start: 0.7828 (t70) cc_final: 0.7591 (t70) REVERT: q 101 ASP cc_start: 0.8333 (t70) cc_final: 0.7944 (t0) REVERT: r 11 GLN cc_start: 0.8781 (mp10) cc_final: 0.8522 (mt0) REVERT: s 86 MET cc_start: 0.8109 (ttp) cc_final: 0.7741 (ttm) REVERT: s 99 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7222 (mtt180) REVERT: t 2 ILE cc_start: 0.4316 (OUTLIER) cc_final: 0.3341 (pt) REVERT: t 9 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7718 (mttp) REVERT: t 12 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7533 (mmm160) REVERT: t 51 PHE cc_start: 0.7963 (m-80) cc_final: 0.7634 (m-80) REVERT: t 73 ARG cc_start: 0.5613 (mpt-90) cc_final: 0.4750 (mtm110) REVERT: u 8 ASP cc_start: 0.8168 (t0) cc_final: 0.7681 (t70) REVERT: v 2 PHE cc_start: 0.7383 (m-80) cc_final: 0.7044 (m-80) REVERT: v 26 PHE cc_start: 0.9114 (p90) cc_final: 0.8819 (p90) REVERT: v 41 GLU cc_start: 0.7250 (pp20) cc_final: 0.6304 (pp20) REVERT: v 42 LEU cc_start: 0.8643 (pt) cc_final: 0.8196 (pt) REVERT: v 71 LYS cc_start: 0.8319 (pttp) cc_final: 0.7968 (pttp) REVERT: v 80 HIS cc_start: 0.8260 (t-90) cc_final: 0.7984 (t-90) REVERT: w 39 THR cc_start: 0.7286 (m) cc_final: 0.7003 (t) REVERT: w 62 LYS cc_start: 0.8788 (mttm) cc_final: 0.8393 (mtmm) REVERT: w 68 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8160 (mttt) REVERT: w 76 ILE cc_start: 0.8699 (mt) cc_final: 0.8425 (mt) REVERT: x 2 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7496 (mtt180) REVERT: x 15 ASN cc_start: 0.8995 (m-40) cc_final: 0.8738 (m110) REVERT: x 40 GLU cc_start: 0.8469 (pp20) cc_final: 0.7954 (pp20) REVERT: x 49 ARG cc_start: 0.7585 (ttt180) cc_final: 0.7331 (ttt180) REVERT: x 63 ILE cc_start: 0.8328 (tp) cc_final: 0.8000 (tp) REVERT: x 67 LEU cc_start: 0.9066 (mp) cc_final: 0.8696 (tp) REVERT: y 20 ASN cc_start: 0.9305 (m-40) cc_final: 0.8887 (t0) REVERT: y 25 GLN cc_start: 0.8562 (tp40) cc_final: 0.7989 (tm-30) REVERT: y 29 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.7843 (ttm110) REVERT: y 54 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8107 (mmmm) REVERT: z 20 LYS cc_start: 0.8854 (mttp) cc_final: 0.8482 (mtmm) REVERT: z 29 ARG cc_start: 0.8223 (mmt180) cc_final: 0.7885 (mmt-90) REVERT: z 30 ARG cc_start: 0.7902 (pmt170) cc_final: 0.7413 (mtm-85) REVERT: z 48 ASN cc_start: 0.8528 (t0) cc_final: 0.8157 (t0) REVERT: B 36 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8240 (mttt) REVERT: B 47 TYR cc_start: 0.7947 (m-80) cc_final: 0.7548 (m-80) REVERT: C 37 LYS cc_start: 0.7949 (mttm) cc_final: 0.7694 (mmtp) REVERT: D 9 VAL cc_start: 0.9201 (p) cc_final: 0.8938 (p) REVERT: D 10 LEU cc_start: 0.9076 (tp) cc_final: 0.8729 (tt) REVERT: D 25 LYS cc_start: 0.8525 (ptmm) cc_final: 0.8147 (ptmt) REVERT: F 2 LYS cc_start: 0.7840 (mttp) cc_final: 0.7633 (mttp) REVERT: F 36 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7647 (ttm170) REVERT: G 18 GLN cc_start: 0.8721 (mt0) cc_final: 0.8426 (mt0) REVERT: G 35 ASN cc_start: 0.7877 (t0) cc_final: 0.7654 (t0) REVERT: G 36 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7997 (mmtt) REVERT: G 39 ILE cc_start: 0.9031 (mp) cc_final: 0.8794 (mp) REVERT: G 48 MET cc_start: 0.8266 (mtp) cc_final: 0.7989 (mtt) REVERT: G 51 GLU cc_start: 0.8948 (pp20) cc_final: 0.8702 (pp20) REVERT: G 92 ASN cc_start: 0.9132 (p0) cc_final: 0.8615 (p0) REVERT: G 111 LYS cc_start: 0.8308 (tptp) cc_final: 0.8087 (tppt) REVERT: G 112 ARG cc_start: 0.8827 (tpp-160) cc_final: 0.8149 (tpp-160) REVERT: G 189 ASN cc_start: 0.7029 (p0) cc_final: 0.6783 (p0) REVERT: G 207 ARG cc_start: 0.8640 (ptp-110) cc_final: 0.8350 (ptp-110) REVERT: G 212 TYR cc_start: 0.8904 (m-80) cc_final: 0.7860 (m-80) REVERT: H 33 ASP cc_start: 0.8492 (t0) cc_final: 0.8283 (t0) REVERT: H 41 TYR cc_start: 0.7833 (t80) cc_final: 0.7397 (t80) REVERT: H 84 GLU cc_start: 0.8124 (tp30) cc_final: 0.7620 (tm-30) REVERT: H 85 LYS cc_start: 0.9332 (pttp) cc_final: 0.9068 (pttm) REVERT: H 124 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7911 (mt-10) REVERT: H 128 MET cc_start: 0.7358 (mmp) cc_final: 0.5893 (mtm) REVERT: H 134 LYS cc_start: 0.8697 (pttm) cc_final: 0.7896 (mmtt) REVERT: H 156 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7482 (pp) REVERT: H 205 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7308 (tm-30) REVERT: I 31 CYS cc_start: 0.6681 (OUTLIER) cc_final: 0.4733 (t) REVERT: I 43 ARG cc_start: 0.7548 (tpt170) cc_final: 0.7310 (tpt90) REVERT: I 46 ARG cc_start: 0.6419 (mtt-85) cc_final: 0.5873 (mpt180) REVERT: I 54 LEU cc_start: 0.8253 (tt) cc_final: 0.8041 (tt) REVERT: I 97 LEU cc_start: 0.8814 (tp) cc_final: 0.8593 (tt) REVERT: I 99 ASN cc_start: 0.8768 (t0) cc_final: 0.8343 (t0) REVERT: I 115 GLN cc_start: 0.8496 (tp40) cc_final: 0.8288 (tp40) REVERT: I 134 TYR cc_start: 0.7858 (t80) cc_final: 0.7554 (t80) REVERT: J 28 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.7946 (mtm110) REVERT: J 146 MET cc_start: 0.7274 (ttp) cc_final: 0.6060 (ttp) REVERT: J 151 MET cc_start: 0.8019 (tpp) cc_final: 0.7213 (ptp) REVERT: L 67 ASN cc_start: 0.7948 (m-40) cc_final: 0.7458 (m-40) REVERT: L 73 GLU cc_start: 0.6993 (pp20) cc_final: 0.6386 (pp20) REVERT: L 77 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6101 (ttm170) REVERT: L 102 TRP cc_start: 0.7730 (m-10) cc_final: 0.7419 (m-10) REVERT: L 113 LYS cc_start: 0.5817 (mmtt) cc_final: 0.4460 (mmtt) REVERT: L 130 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8489 (ptpt) REVERT: M 4 ASP cc_start: 0.7791 (t0) cc_final: 0.7220 (t0) REVERT: M 8 ASP cc_start: 0.7957 (t70) cc_final: 0.7658 (t70) REVERT: M 17 GLN cc_start: 0.8123 (mm110) cc_final: 0.7841 (mm-40) REVERT: M 82 LEU cc_start: 0.8355 (tp) cc_final: 0.7995 (tp) REVERT: M 89 ASP cc_start: 0.8972 (m-30) cc_final: 0.8682 (m-30) REVERT: N 63 TYR cc_start: 0.8239 (t80) cc_final: 0.7983 (t80) REVERT: N 79 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8019 (ttp-170) REVERT: N 112 ARG cc_start: 0.8762 (ptm-80) cc_final: 0.8429 (tmm-80) REVERT: O 16 ARG cc_start: 0.7652 (ptt180) cc_final: 0.7126 (ttt90) REVERT: O 53 ILE cc_start: 0.7264 (pt) cc_final: 0.7036 (pt) REVERT: P 27 ASN cc_start: 0.6567 (m-40) cc_final: 0.6362 (m-40) REVERT: P 55 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7962 (mtt180) REVERT: P 84 MET cc_start: 0.7971 (ttm) cc_final: 0.7610 (ttm) REVERT: P 104 PHE cc_start: 0.8006 (m-80) cc_final: 0.7804 (m-80) REVERT: Q 110 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6976 (mtmt) REVERT: R 8 ILE cc_start: 0.7807 (mt) cc_final: 0.7589 (mm) REVERT: R 71 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7911 (mt-10) REVERT: R 99 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: S 40 ARG cc_start: 0.6898 (mtp180) cc_final: 0.6401 (ttp80) REVERT: T 39 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8321 (mm110) REVERT: T 56 LEU cc_start: 0.8680 (mm) cc_final: 0.8472 (mm) REVERT: T 65 LEU cc_start: 0.8950 (mt) cc_final: 0.8712 (mt) REVERT: T 66 LEU cc_start: 0.8896 (mt) cc_final: 0.8634 (tp) REVERT: U 25 ARG cc_start: 0.6773 (mtm180) cc_final: 0.6452 (mtm180) REVERT: U 60 TRP cc_start: 0.8142 (m100) cc_final: 0.7891 (m100) REVERT: V 10 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7557 (tpt-90) REVERT: V 18 LYS cc_start: 0.8795 (tptt) cc_final: 0.8487 (tptt) REVERT: V 56 ASP cc_start: 0.9051 (p0) cc_final: 0.8807 (p0) REVERT: V 61 ARG cc_start: 0.7853 (ptt90) cc_final: 0.7390 (ttp-170) REVERT: V 72 TRP cc_start: 0.7180 (m100) cc_final: 0.6433 (m100) REVERT: W 29 LYS cc_start: 0.8483 (mttt) cc_final: 0.8173 (mtmm) REVERT: W 47 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7692 (mpt180) REVERT: W 49 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7416 (tttm) REVERT: W 53 GLN cc_start: 0.8903 (mt0) cc_final: 0.8662 (mt0) REVERT: X 30 LEU cc_start: 0.6979 (tt) cc_final: 0.6667 (tp) REVERT: X 68 HIS cc_start: 0.8030 (m90) cc_final: 0.7612 (m-70) REVERT: X 80 ARG cc_start: 0.5911 (mmt180) cc_final: 0.5488 (mmm-85) REVERT: Y 12 GLN cc_start: 0.8136 (tt0) cc_final: 0.7912 (tt0) REVERT: Y 23 ARG cc_start: 0.7171 (mmm-85) cc_final: 0.6827 (mmt-90) REVERT: Y 54 GLN cc_start: 0.7569 (tt0) cc_final: 0.7228 (tm-30) REVERT: Y 60 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8233 (mm-40) REVERT: Z 42 THR cc_start: 0.9006 (m) cc_final: 0.8687 (m) REVERT: Z 65 ARG cc_start: 0.6028 (tmt170) cc_final: 0.5549 (tmt170) outliers start: 24 outliers final: 5 residues processed: 2102 average time/residue: 1.4361 time to fit residues: 5020.9791 Evaluate side-chains 1688 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1678 time to evaluate : 6.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain R residue 99 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 10.0000 chunk 801 optimal weight: 8.9990 chunk 444 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 540 optimal weight: 20.0000 chunk 428 optimal weight: 3.9990 chunk 828 optimal weight: 10.0000 chunk 320 optimal weight: 0.9990 chunk 503 optimal weight: 9.9990 chunk 616 optimal weight: 10.0000 chunk 959 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 45 ASN b 89 ASN ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 ASN b 225 ASN b 238 ASN c 173 GLN d 24 ASN d 30 GLN d 97 ASN f 110 HIS f 138 GLN f 142 GLN g 11 ASN g 18 GLN g 43 ASN g 133 GLN g 135 HIS g 145 ASN h 6 GLN i 5 GLN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS k 5 GLN k 13 ASN l 4 ASN m 13 HIS m 22 GLN n 16 HIS n 62 ASN o 100 HIS p 2 ASN q 43 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 55 GLN r 82 HIS s 60 HIS ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN v 88 HIS y 20 ASN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN C 18 HIS E 27 ASN G 38 HIS G 176 ASN H 18 ASN H 99 GLN I 39 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN K 3 HIS K 14 GLN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 141 HIS ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN O 58 ASN P 108 ASN Q 111 GLN R 51 GLN T 36 ASN T 41 HIS ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 9 HIS ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Y 20 ASN Y 54 GLN a 188 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 163219 Z= 0.327 Angle : 0.733 15.385 244202 Z= 0.379 Chirality : 0.043 0.484 31236 Planarity : 0.006 0.071 13084 Dihedral : 22.836 178.736 81784 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.51 % Favored : 91.27 % Rotamer: Outliers : 4.62 % Allowed : 16.07 % Favored : 79.30 % 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: -3.44 (0.09), residues: 5919 helix: -1.76 (0.10), residues: 1863 sheet: -2.12 (0.15), residues: 978 loop : -2.70 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 212 HIS 0.014 0.002 HIS O 15 PHE 0.022 0.002 PHE G 90 TYR 0.022 0.002 TYR T 77 ARG 0.022 0.001 ARG v 21 *********************** 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 2002 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1775 time to evaluate : 6.222 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: b 95 TYR cc_start: 0.8225 (m-80) cc_final: 0.7641 (m-80) REVERT: b 96 LYS cc_start: 0.8482 (tptt) cc_final: 0.8205 (ttpt) REVERT: b 99 GLU cc_start: 0.7360 (tt0) cc_final: 0.7047 (tt0) REVERT: b 131 MET cc_start: 0.8779 (mtm) cc_final: 0.8355 (mtm) REVERT: b 179 GLU cc_start: 0.6894 (tt0) cc_final: 0.6364 (tt0) REVERT: c 168 GLU cc_start: 0.7318 (mp0) cc_final: 0.6897 (mp0) REVERT: c 169 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: d 24 ASN cc_start: 0.8347 (t0) cc_final: 0.7845 (t0) REVERT: d 91 ASP cc_start: 0.7868 (t0) cc_final: 0.7603 (t0) REVERT: d 145 ASP cc_start: 0.8311 (t0) cc_final: 0.7830 (t0) REVERT: d 171 ASP cc_start: 0.6894 (p0) cc_final: 0.6605 (p0) REVERT: d 183 PHE cc_start: 0.7975 (m-80) cc_final: 0.7554 (m-80) REVERT: e 3 LEU cc_start: 0.7709 (pp) cc_final: 0.7341 (pp) REVERT: e 6 TYR cc_start: 0.9119 (t80) cc_final: 0.8698 (t80) REVERT: e 37 MET cc_start: 0.6262 (ttp) cc_final: 0.5900 (ttp) REVERT: e 41 GLU cc_start: 0.7155 (mp0) cc_final: 0.6795 (mp0) REVERT: e 56 LEU cc_start: 0.8321 (mt) cc_final: 0.8098 (mt) REVERT: e 102 LEU cc_start: 0.8854 (mm) cc_final: 0.8469 (mm) REVERT: e 111 ARG cc_start: 0.4496 (ttp80) cc_final: 0.4090 (tpp80) REVERT: f 100 ASN cc_start: 0.6916 (p0) cc_final: 0.6578 (p0) REVERT: f 142 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8722 (tp40) REVERT: f 150 TYR cc_start: 0.8088 (m-80) cc_final: 0.7636 (m-80) REVERT: f 162 ARG cc_start: 0.6962 (ptp-170) cc_final: 0.6570 (ptp-170) REVERT: g 27 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.8008 (ttm170) REVERT: g 28 ASN cc_start: 0.8167 (m-40) cc_final: 0.7642 (m-40) REVERT: g 29 PHE cc_start: 0.8274 (t80) cc_final: 0.8016 (t80) REVERT: g 46 PHE cc_start: 0.8318 (m-80) cc_final: 0.7940 (m-10) REVERT: g 133 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: h 52 MET cc_start: 0.0985 (tmm) cc_final: 0.0576 (tmm) REVERT: j 44 TYR cc_start: 0.8531 (t80) cc_final: 0.8229 (t80) REVERT: j 52 ASP cc_start: 0.8013 (m-30) cc_final: 0.7554 (m-30) REVERT: j 136 GLN cc_start: 0.8757 (mt0) cc_final: 0.8013 (mm-40) REVERT: k 1 MET cc_start: 0.6309 (ttm) cc_final: 0.6077 (ttm) REVERT: k 88 ASN cc_start: 0.8242 (m-40) cc_final: 0.7992 (m-40) REVERT: l 36 LYS cc_start: 0.8893 (mttt) cc_final: 0.8432 (mttp) REVERT: l 59 ARG cc_start: 0.8398 (mtp180) cc_final: 0.8097 (mtp180) REVERT: l 69 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: l 121 THR cc_start: 0.9122 (m) cc_final: 0.8782 (p) REVERT: m 96 ILE cc_start: 0.9132 (mm) cc_final: 0.8803 (tt) REVERT: n 9 GLN cc_start: 0.8409 (mt0) cc_final: 0.8103 (mt0) REVERT: n 35 LYS cc_start: 0.8436 (tttm) cc_final: 0.7827 (tttm) REVERT: n 110 MET cc_start: 0.8203 (mmt) cc_final: 0.7511 (mmt) REVERT: o 34 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5796 (t-90) REVERT: o 58 ILE cc_start: 0.7273 (mm) cc_final: 0.7054 (mm) REVERT: o 98 GLN cc_start: 0.8479 (tp-100) cc_final: 0.7982 (tp40) REVERT: p 26 GLU cc_start: 0.8359 (pp20) cc_final: 0.7916 (pp20) REVERT: q 15 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8247 (ttmm) REVERT: r 11 GLN cc_start: 0.8682 (mp10) cc_final: 0.8455 (mt0) REVERT: r 97 LYS cc_start: 0.8927 (tttt) cc_final: 0.8631 (tttm) REVERT: s 86 MET cc_start: 0.8056 (ttp) cc_final: 0.7815 (ttt) REVERT: s 99 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7359 (mtt180) REVERT: t 4 GLU cc_start: 0.8870 (tt0) cc_final: 0.8640 (tt0) REVERT: t 9 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8022 (mttp) REVERT: t 12 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7443 (mmm160) REVERT: t 42 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7496 (mt-10) REVERT: u 36 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7944 (tm-30) REVERT: u 71 ILE cc_start: 0.9353 (pt) cc_final: 0.9026 (mp) REVERT: v 1 MET cc_start: 0.7449 (mmp) cc_final: 0.6777 (tpt) REVERT: v 41 GLU cc_start: 0.7130 (pp20) cc_final: 0.6926 (pp20) REVERT: v 42 LEU cc_start: 0.8569 (pt) cc_final: 0.8342 (pt) REVERT: v 71 LYS cc_start: 0.7949 (pttp) cc_final: 0.7655 (pttp) REVERT: w 62 LYS cc_start: 0.8644 (mttm) cc_final: 0.8249 (mtmm) REVERT: w 68 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8241 (mttt) REVERT: x 2 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7588 (mtt180) REVERT: x 16 ASN cc_start: 0.8139 (t0) cc_final: 0.7361 (t0) REVERT: x 40 GLU cc_start: 0.8506 (pp20) cc_final: 0.8052 (pp20) REVERT: x 49 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7278 (ttt180) REVERT: y 1 MET cc_start: 0.6040 (mmm) cc_final: 0.5257 (mmm) REVERT: y 5 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: y 20 ASN cc_start: 0.9263 (m110) cc_final: 0.8999 (t0) REVERT: y 25 GLN cc_start: 0.8371 (tp40) cc_final: 0.8131 (tm-30) REVERT: y 29 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8189 (ttm110) REVERT: y 44 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8887 (ttmt) REVERT: z 20 LYS cc_start: 0.8795 (mttp) cc_final: 0.8423 (mttp) REVERT: z 29 ARG cc_start: 0.8288 (mmt180) cc_final: 0.8051 (mmt-90) REVERT: z 30 ARG cc_start: 0.7769 (pmt170) cc_final: 0.7500 (mtm-85) REVERT: z 48 ASN cc_start: 0.8516 (t0) cc_final: 0.8044 (t0) REVERT: B 36 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8249 (mttt) REVERT: D 9 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8862 (p) REVERT: E 51 LYS cc_start: 0.7328 (ptmm) cc_final: 0.7049 (tmtt) REVERT: F 36 ARG cc_start: 0.7967 (ttp-170) cc_final: 0.7522 (ttm170) REVERT: G 18 GLN cc_start: 0.8610 (mt0) cc_final: 0.8290 (mt0) REVERT: G 36 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8046 (mmtt) REVERT: G 39 ILE cc_start: 0.9088 (mp) cc_final: 0.8870 (mp) REVERT: G 92 ASN cc_start: 0.9237 (p0) cc_final: 0.8817 (p0) REVERT: G 139 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: G 142 LYS cc_start: 0.7662 (mmmm) cc_final: 0.7146 (mmtm) REVERT: G 212 TYR cc_start: 0.8750 (m-80) cc_final: 0.8037 (m-80) REVERT: H 41 TYR cc_start: 0.7575 (t80) cc_final: 0.7366 (t80) REVERT: H 124 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8099 (mt-10) REVERT: H 128 MET cc_start: 0.7268 (mmp) cc_final: 0.5838 (mtm) REVERT: H 169 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: H 206 ILE cc_start: 0.6501 (tt) cc_final: 0.6253 (tt) REVERT: I 43 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7346 (tpt90) REVERT: I 46 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.6103 (mpt180) REVERT: I 53 GLN cc_start: 0.7627 (mt0) cc_final: 0.6944 (mt0) REVERT: I 102 TYR cc_start: 0.8093 (t80) cc_final: 0.7870 (t80) REVERT: I 134 TYR cc_start: 0.7972 (t80) cc_final: 0.7714 (t80) REVERT: J 81 GLN cc_start: 0.7761 (mp10) cc_final: 0.7121 (mp10) REVERT: J 151 MET cc_start: 0.8154 (tpp) cc_final: 0.7881 (mmp) REVERT: K 1 MET cc_start: 0.8151 (ptp) cc_final: 0.7490 (ptp) REVERT: K 5 GLU cc_start: 0.8351 (tt0) cc_final: 0.7939 (tt0) REVERT: K 75 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7746 (mt-10) REVERT: L 102 TRP cc_start: 0.7496 (m-10) cc_final: 0.7202 (m-10) REVERT: L 105 GLU cc_start: 0.8246 (tp30) cc_final: 0.8003 (tp30) REVERT: L 113 LYS cc_start: 0.5951 (mmtt) cc_final: 0.5740 (tptt) REVERT: L 138 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6524 (tm-30) REVERT: M 4 ASP cc_start: 0.7673 (t0) cc_final: 0.6815 (t0) REVERT: M 8 ASP cc_start: 0.7898 (t70) cc_final: 0.7489 (t70) REVERT: M 89 ASP cc_start: 0.8973 (m-30) cc_final: 0.8702 (m-30) REVERT: N 79 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8130 (ttp-170) REVERT: N 108 ARG cc_start: 0.8764 (mtm180) cc_final: 0.8212 (mtm-85) REVERT: N 112 ARG cc_start: 0.8852 (ptm-80) cc_final: 0.8468 (ttp-170) REVERT: N 125 GLN cc_start: 0.6707 (tt0) cc_final: 0.6224 (tt0) REVERT: O 25 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8973 (mm) REVERT: O 45 ARG cc_start: 0.6105 (ptm160) cc_final: 0.5877 (ptm160) REVERT: O 62 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.7137 (mtp85) REVERT: P 84 MET cc_start: 0.7738 (ttm) cc_final: 0.7423 (ttm) REVERT: Q 9 LYS cc_start: 0.7916 (tppt) cc_final: 0.7578 (ttpt) REVERT: Q 110 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7357 (mtmt) REVERT: R 51 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: R 71 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8049 (mt-10) REVERT: R 77 LYS cc_start: 0.8754 (tppp) cc_final: 0.8524 (tppt) REVERT: S 40 ARG cc_start: 0.6806 (mtp180) cc_final: 0.6382 (ttp80) REVERT: S 65 GLN cc_start: 0.8249 (mt0) cc_final: 0.7734 (mt0) REVERT: T 9 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7931 (mtmm) REVERT: T 27 GLN cc_start: 0.8545 (mt0) cc_final: 0.8165 (mt0) REVERT: T 34 GLN cc_start: 0.8577 (tp40) cc_final: 0.8012 (mm110) REVERT: T 56 LEU cc_start: 0.8844 (mm) cc_final: 0.8531 (mm) REVERT: U 18 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7260 (mm-40) REVERT: U 25 ARG cc_start: 0.6967 (mtm180) cc_final: 0.6674 (mtm180) REVERT: U 35 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7471 (tmm-80) REVERT: V 10 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7331 (tpt-90) REVERT: V 17 GLU cc_start: 0.7229 (mp0) cc_final: 0.6668 (mp0) REVERT: V 18 LYS cc_start: 0.8772 (tptt) cc_final: 0.8560 (tptt) REVERT: V 20 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7134 (tp) REVERT: V 56 ASP cc_start: 0.9045 (p0) cc_final: 0.8835 (p0) REVERT: W 29 LYS cc_start: 0.8513 (mttt) cc_final: 0.8078 (mttt) REVERT: W 47 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7313 (mpt180) REVERT: W 49 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7355 (tttm) REVERT: W 53 GLN cc_start: 0.8783 (mt0) cc_final: 0.8581 (mt0) REVERT: Y 56 ILE cc_start: 0.8164 (mp) cc_final: 0.7723 (tp) REVERT: Y 60 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8049 (mm-40) REVERT: Y 68 LYS cc_start: 0.7546 (pttt) cc_final: 0.7161 (pttm) REVERT: Z 61 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8495 (pmt-80) REVERT: Z 65 ARG cc_start: 0.6558 (tmt170) cc_final: 0.6182 (tmt170) REVERT: a 48 LEU cc_start: 0.7196 (tp) cc_final: 0.6441 (mp) outliers start: 227 outliers final: 141 residues processed: 1860 average time/residue: 1.3909 time to fit residues: 4410.8148 Evaluate side-chains 1778 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1627 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 199 MET Chi-restraints excluded: chain e residue 30 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 97 GLU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 83 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 142 GLN Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 98 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain o residue 33 ARG Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 91 PHE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 65 THR Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 43 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 798 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 961 optimal weight: 10.0000 chunk 1038 optimal weight: 10.0000 chunk 856 optimal weight: 10.0000 chunk 953 optimal weight: 10.0000 chunk 327 optimal weight: 4.9990 chunk 771 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 133 ASN c 42 ASN d 41 GLN d 115 GLN e 36 ASN f 44 HIS g 2 GLN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS o 38 GLN p 51 ASN q 55 GLN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 HIS x 15 ASN ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 GLN B 18 HIS E 27 ASN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN H 139 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN ** L 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS M 75 GLN R 13 HIS S 48 GLN T 39 GLN U 9 HIS ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 163219 Z= 0.363 Angle : 0.709 13.804 244202 Z= 0.364 Chirality : 0.041 0.279 31236 Planarity : 0.006 0.088 13084 Dihedral : 23.029 177.395 81776 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.05 % Favored : 89.76 % Rotamer: Outliers : 6.09 % Allowed : 19.54 % Favored : 74.37 % 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: -0.97 (0.11), residues: 1858 sheet: -1.89 (0.16), residues: 962 loop : -2.53 (0.10), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.036 0.002 HIS G 38 PHE 0.022 0.002 PHE G 90 TYR 0.043 0.003 TYR T 77 ARG 0.015 0.001 ARG v 21 *********************** 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 1999 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1700 time to evaluate : 6.307 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: b 96 LYS cc_start: 0.8504 (tptt) cc_final: 0.8188 (tmtt) REVERT: b 131 MET cc_start: 0.8655 (mtm) cc_final: 0.8305 (mtm) REVERT: b 212 TRP cc_start: 0.8158 (p90) cc_final: 0.7795 (p90) REVERT: d 24 ASN cc_start: 0.8455 (t0) cc_final: 0.7921 (t0) REVERT: d 91 ASP cc_start: 0.8034 (t0) cc_final: 0.7699 (t0) REVERT: d 145 ASP cc_start: 0.7890 (t0) cc_final: 0.7430 (t0) REVERT: d 183 PHE cc_start: 0.8059 (m-80) cc_final: 0.7737 (m-80) REVERT: e 41 GLU cc_start: 0.7187 (mp0) cc_final: 0.6926 (mp0) REVERT: e 102 LEU cc_start: 0.8951 (mm) cc_final: 0.8499 (mm) REVERT: e 169 LEU cc_start: 0.8650 (tp) cc_final: 0.8385 (tp) REVERT: f 2 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7320 (ttm110) REVERT: f 85 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7599 (mptt) REVERT: f 100 ASN cc_start: 0.6956 (p0) cc_final: 0.6690 (p0) REVERT: f 142 GLN cc_start: 0.9170 (tp40) cc_final: 0.8890 (tp40) REVERT: g 27 ARG cc_start: 0.8472 (ttp-170) cc_final: 0.8024 (ttm170) REVERT: g 28 ASN cc_start: 0.8101 (m-40) cc_final: 0.7572 (m-40) REVERT: g 29 PHE cc_start: 0.8247 (t80) cc_final: 0.8021 (t80) REVERT: g 46 PHE cc_start: 0.8443 (m-80) cc_final: 0.8058 (m-10) REVERT: h 1 MET cc_start: 0.4123 (ptp) cc_final: 0.2726 (ttp) REVERT: h 52 MET cc_start: 0.1127 (tmm) cc_final: 0.0640 (tmm) REVERT: j 44 TYR cc_start: 0.8589 (t80) cc_final: 0.8251 (t80) REVERT: j 136 GLN cc_start: 0.8771 (mt0) cc_final: 0.8024 (mm-40) REVERT: k 1 MET cc_start: 0.6300 (ttm) cc_final: 0.6089 (ttm) REVERT: k 88 ASN cc_start: 0.8264 (m-40) cc_final: 0.8028 (m-40) REVERT: k 121 GLU cc_start: 0.8395 (tp30) cc_final: 0.8021 (mt-10) REVERT: l 69 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: l 121 THR cc_start: 0.9072 (m) cc_final: 0.8709 (p) REVERT: m 3 GLN cc_start: 0.8532 (tt0) cc_final: 0.8235 (tp-100) REVERT: m 73 ILE cc_start: 0.9112 (mm) cc_final: 0.8666 (tt) REVERT: m 110 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7295 (tm-30) REVERT: n 5 LYS cc_start: 0.9296 (mtpp) cc_final: 0.9095 (mtpp) REVERT: n 9 GLN cc_start: 0.8339 (mt0) cc_final: 0.8059 (mt0) REVERT: n 82 GLU cc_start: 0.7142 (mp0) cc_final: 0.6910 (mp0) REVERT: n 110 MET cc_start: 0.8297 (mmt) cc_final: 0.7787 (mmt) REVERT: o 98 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8090 (tp40) REVERT: p 15 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7684 (p0) REVERT: p 26 GLU cc_start: 0.8357 (pp20) cc_final: 0.7836 (pp20) REVERT: p 105 LYS cc_start: 0.9173 (tptt) cc_final: 0.8743 (tptt) REVERT: q 15 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8212 (ttmm) REVERT: q 96 ASP cc_start: 0.7564 (t70) cc_final: 0.7340 (t70) REVERT: r 11 GLN cc_start: 0.8883 (mp10) cc_final: 0.8589 (mt0) REVERT: r 71 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8961 (tttt) REVERT: r 91 GLN cc_start: 0.8100 (tp40) cc_final: 0.7700 (tp40) REVERT: r 97 LYS cc_start: 0.8835 (tttt) cc_final: 0.8579 (tttm) REVERT: s 86 MET cc_start: 0.8016 (ttp) cc_final: 0.7788 (ttt) REVERT: s 99 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.7486 (mtt180) REVERT: t 9 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7954 (mttp) REVERT: t 12 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7413 (mmm160) REVERT: t 77 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7243 (mtt-85) REVERT: u 36 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7862 (tm-30) REVERT: u 71 ILE cc_start: 0.9354 (pt) cc_final: 0.9146 (mp) REVERT: u 100 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7297 (tm-30) REVERT: v 1 MET cc_start: 0.7757 (mmp) cc_final: 0.6769 (tpt) REVERT: v 71 LYS cc_start: 0.7958 (pttp) cc_final: 0.7620 (pttp) REVERT: w 62 LYS cc_start: 0.8653 (mttm) cc_final: 0.8391 (mtpp) REVERT: w 68 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8313 (mttt) REVERT: x 2 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7795 (mtt180) REVERT: x 16 ASN cc_start: 0.8220 (t0) cc_final: 0.7350 (t0) REVERT: x 40 GLU cc_start: 0.8592 (pp20) cc_final: 0.8123 (pp20) REVERT: y 20 ASN cc_start: 0.9312 (m110) cc_final: 0.8992 (t0) REVERT: y 25 GLN cc_start: 0.8288 (tp40) cc_final: 0.8078 (tm-30) REVERT: y 44 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8840 (ttmt) REVERT: z 5 LYS cc_start: 0.7502 (mmmt) cc_final: 0.7145 (tttm) REVERT: z 29 ARG cc_start: 0.8389 (mmt180) cc_final: 0.8087 (mmt-90) REVERT: z 30 ARG cc_start: 0.7864 (pmt170) cc_final: 0.7379 (mtm-85) REVERT: z 48 ASN cc_start: 0.8506 (t0) cc_final: 0.8051 (t0) REVERT: B 36 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8357 (mttt) REVERT: D 14 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7780 (mtt-85) REVERT: D 25 LYS cc_start: 0.8388 (ptmt) cc_final: 0.8186 (ptmt) REVERT: E 51 LYS cc_start: 0.7377 (ptmm) cc_final: 0.7003 (tmtt) REVERT: F 36 ARG cc_start: 0.8129 (ttp-170) cc_final: 0.7632 (ttm170) REVERT: G 18 GLN cc_start: 0.8511 (mt0) cc_final: 0.8300 (mt0) REVERT: G 35 ASN cc_start: 0.7757 (t0) cc_final: 0.7426 (t0) REVERT: G 36 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7677 (mmtt) REVERT: G 92 ASN cc_start: 0.9317 (p0) cc_final: 0.8979 (p0) REVERT: G 136 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7841 (mtm-85) REVERT: G 142 LYS cc_start: 0.7460 (mmmm) cc_final: 0.7245 (mmtm) REVERT: G 212 TYR cc_start: 0.8775 (m-10) cc_final: 0.8060 (m-80) REVERT: H 33 ASP cc_start: 0.8488 (t0) cc_final: 0.8111 (p0) REVERT: H 41 TYR cc_start: 0.7412 (t80) cc_final: 0.7204 (t80) REVERT: H 128 MET cc_start: 0.7225 (mmp) cc_final: 0.5814 (mtm) REVERT: H 169 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: H 206 ILE cc_start: 0.6579 (tt) cc_final: 0.6181 (tt) REVERT: I 2 ARG cc_start: 0.6484 (mtp-110) cc_final: 0.5793 (ptm-80) REVERT: I 43 ARG cc_start: 0.7599 (tpt170) cc_final: 0.7337 (tpt90) REVERT: I 46 ARG cc_start: 0.6337 (mtt-85) cc_final: 0.5845 (mpt180) REVERT: I 53 GLN cc_start: 0.7577 (mt0) cc_final: 0.7131 (mt0) REVERT: I 166 LYS cc_start: 0.7696 (mmtp) cc_final: 0.7089 (mmmt) REVERT: J 11 GLN cc_start: 0.8015 (tt0) cc_final: 0.7689 (tt0) REVERT: J 151 MET cc_start: 0.8171 (tpp) cc_final: 0.7291 (ptp) REVERT: K 1 MET cc_start: 0.8308 (ptp) cc_final: 0.7442 (ptp) REVERT: K 56 LYS cc_start: 0.7279 (mmmt) cc_final: 0.6888 (mmmt) REVERT: K 75 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7811 (mt-10) REVERT: L 77 ARG cc_start: 0.7290 (ttp-170) cc_final: 0.6975 (ttp80) REVERT: L 102 TRP cc_start: 0.7690 (m-10) cc_final: 0.7306 (m-10) REVERT: L 138 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6856 (tm-30) REVERT: L 139 ASP cc_start: 0.7759 (m-30) cc_final: 0.7180 (m-30) REVERT: M 4 ASP cc_start: 0.7921 (t0) cc_final: 0.7207 (t0) REVERT: M 79 ARG cc_start: 0.9297 (mtm110) cc_final: 0.8935 (mtm110) REVERT: M 89 ASP cc_start: 0.8979 (m-30) cc_final: 0.8696 (m-30) REVERT: N 45 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7666 (ptp) REVERT: N 79 ARG cc_start: 0.8565 (ttp80) cc_final: 0.8053 (ttp80) REVERT: N 108 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8051 (mtm-85) REVERT: N 125 GLN cc_start: 0.6806 (tt0) cc_final: 0.6327 (tt0) REVERT: O 25 ILE cc_start: 0.9328 (pt) cc_final: 0.9023 (mm) REVERT: O 45 ARG cc_start: 0.6504 (ptm160) cc_final: 0.6267 (ptm160) REVERT: O 53 ILE cc_start: 0.7608 (pt) cc_final: 0.7145 (pt) REVERT: P 67 GLU cc_start: 0.8588 (mp0) cc_final: 0.8262 (mp0) REVERT: P 84 MET cc_start: 0.7801 (ttm) cc_final: 0.7366 (ttm) REVERT: P 96 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7232 (mp) REVERT: Q 110 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7324 (mtmt) REVERT: R 11 HIS cc_start: 0.5963 (p-80) cc_final: 0.5706 (p-80) REVERT: R 51 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: R 71 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7964 (mt-10) REVERT: R 77 LYS cc_start: 0.8760 (tppp) cc_final: 0.8279 (mmtm) REVERT: S 40 ARG cc_start: 0.6891 (mtp180) cc_final: 0.6360 (ttp80) REVERT: S 64 ARG cc_start: 0.8358 (ttm110) cc_final: 0.7949 (mtp180) REVERT: S 65 GLN cc_start: 0.8168 (mt0) cc_final: 0.7682 (mt0) REVERT: T 34 GLN cc_start: 0.8547 (tp40) cc_final: 0.8331 (mm-40) REVERT: T 48 ASP cc_start: 0.7780 (t0) cc_final: 0.7340 (t70) REVERT: T 56 LEU cc_start: 0.8788 (mm) cc_final: 0.8499 (mm) REVERT: T 67 ASP cc_start: 0.8546 (m-30) cc_final: 0.8233 (m-30) REVERT: U 18 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7320 (mm-40) REVERT: V 10 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7372 (tpt-90) REVERT: V 61 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.8009 (ttp-170) REVERT: V 72 TRP cc_start: 0.7684 (m100) cc_final: 0.7359 (m100) REVERT: W 29 LYS cc_start: 0.8703 (mttt) cc_final: 0.8312 (mtmm) REVERT: W 47 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7573 (mmt90) REVERT: W 49 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7311 (tttm) REVERT: W 53 GLN cc_start: 0.8764 (mt0) cc_final: 0.8558 (mt0) REVERT: Y 47 GLN cc_start: 0.8615 (tp-100) cc_final: 0.8406 (tp-100) REVERT: Y 54 GLN cc_start: 0.7383 (tm-30) cc_final: 0.7126 (tm-30) REVERT: Y 60 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8112 (mm-40) REVERT: Y 68 LYS cc_start: 0.7433 (pttt) cc_final: 0.7149 (pttm) REVERT: Z 65 ARG cc_start: 0.6958 (tmt170) cc_final: 0.6506 (tmt170) REVERT: a 25 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: a 48 LEU cc_start: 0.7307 (tp) cc_final: 0.6814 (mp) outliers start: 299 outliers final: 214 residues processed: 1821 average time/residue: 1.4494 time to fit residues: 4549.6495 Evaluate side-chains 1834 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1612 time to evaluate : 6.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain o residue 33 ARG Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 121 ASN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain V residue 15 LYS Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 25 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 50.0000 chunk 722 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 106 optimal weight: 0.0020 chunk 458 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 965 optimal weight: 10.0000 chunk 1021 optimal weight: 10.0000 chunk 504 optimal weight: 10.0000 chunk 914 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 238 ASN c 185 ASN d 41 GLN f 44 HIS ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS o 104 GLN p 51 ASN q 55 GLN q 71 ASN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 HIS x 15 ASN ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN E 27 ASN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS M 75 GLN R 51 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 163219 Z= 0.365 Angle : 0.702 10.837 244202 Z= 0.360 Chirality : 0.040 0.279 31236 Planarity : 0.005 0.077 13084 Dihedral : 23.107 179.690 81774 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 6.50 % Allowed : 21.39 % Favored : 72.11 % 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: -2.62 (0.10), residues: 5919 helix: -0.64 (0.11), residues: 1854 sheet: -1.85 (0.16), residues: 976 loop : -2.45 (0.10), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP m 64 HIS 0.015 0.002 HIS v 88 PHE 0.020 0.002 PHE H 202 TYR 0.025 0.002 TYR T 77 ARG 0.009 0.001 ARG e 94 *********************** 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 1989 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1670 time to evaluate : 5.561 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: b 12 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8287 (ttt90) REVERT: b 22 GLU cc_start: 0.8527 (mp0) cc_final: 0.7539 (tm-30) REVERT: b 25 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8385 (mmtp) REVERT: b 131 MET cc_start: 0.8683 (mtm) cc_final: 0.8359 (mtm) REVERT: b 212 TRP cc_start: 0.8213 (p90) cc_final: 0.7904 (p90) REVERT: c 94 GLN cc_start: 0.8214 (mt0) cc_final: 0.7861 (mt0) REVERT: c 168 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: d 24 ASN cc_start: 0.8498 (t0) cc_final: 0.8004 (t0) REVERT: d 91 ASP cc_start: 0.8083 (t0) cc_final: 0.7693 (t0) REVERT: d 145 ASP cc_start: 0.8028 (t0) cc_final: 0.7587 (t0) REVERT: d 183 PHE cc_start: 0.8020 (m-80) cc_final: 0.7793 (m-80) REVERT: e 21 TYR cc_start: 0.7020 (m-10) cc_final: 0.6804 (m-10) REVERT: e 41 GLU cc_start: 0.7264 (mp0) cc_final: 0.7024 (mp0) REVERT: e 169 LEU cc_start: 0.8642 (tp) cc_final: 0.8401 (tp) REVERT: f 41 GLU cc_start: 0.8790 (tp30) cc_final: 0.8302 (tp30) REVERT: f 100 ASN cc_start: 0.6898 (p0) cc_final: 0.6624 (p0) REVERT: f 123 GLU cc_start: 0.8052 (tp30) cc_final: 0.7728 (tm-30) REVERT: g 27 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.7885 (ttm170) REVERT: g 28 ASN cc_start: 0.8181 (m-40) cc_final: 0.7647 (m-40) REVERT: g 29 PHE cc_start: 0.8262 (t80) cc_final: 0.7922 (t80) REVERT: g 46 PHE cc_start: 0.8383 (m-80) cc_final: 0.8085 (m-10) REVERT: h 1 MET cc_start: 0.4142 (ptp) cc_final: 0.2573 (ttp) REVERT: h 52 MET cc_start: 0.0709 (tmm) cc_final: 0.0284 (tmm) REVERT: j 44 TYR cc_start: 0.8572 (t80) cc_final: 0.8225 (t80) REVERT: j 136 GLN cc_start: 0.8737 (mt0) cc_final: 0.8011 (mm-40) REVERT: k 106 GLU cc_start: 0.6693 (mp0) cc_final: 0.6469 (mp0) REVERT: l 121 THR cc_start: 0.9130 (m) cc_final: 0.8802 (p) REVERT: m 1 MET cc_start: 0.7232 (tpp) cc_final: 0.6884 (tmm) REVERT: m 3 GLN cc_start: 0.8534 (tt0) cc_final: 0.8172 (tp-100) REVERT: m 96 ILE cc_start: 0.9088 (mm) cc_final: 0.8767 (tt) REVERT: m 115 GLU cc_start: 0.7153 (mp0) cc_final: 0.6617 (mp0) REVERT: n 9 GLN cc_start: 0.8334 (mt0) cc_final: 0.8038 (mt0) REVERT: n 110 MET cc_start: 0.7961 (mmt) cc_final: 0.7586 (mmt) REVERT: o 80 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8979 (mt-10) REVERT: o 98 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8170 (tp40) REVERT: p 15 ASP cc_start: 0.8040 (p0) cc_final: 0.7697 (p0) REVERT: p 26 GLU cc_start: 0.8266 (pp20) cc_final: 0.7760 (pp20) REVERT: q 15 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8216 (ttmm) REVERT: q 84 LYS cc_start: 0.8623 (mttt) cc_final: 0.8379 (mtmt) REVERT: r 11 GLN cc_start: 0.8904 (mp10) cc_final: 0.8651 (mt0) REVERT: r 13 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7137 (ttt180) REVERT: r 97 LYS cc_start: 0.8832 (tttt) cc_final: 0.8561 (tttm) REVERT: s 86 MET cc_start: 0.8010 (ttp) cc_final: 0.7751 (ttt) REVERT: s 99 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7361 (mtt180) REVERT: t 4 GLU cc_start: 0.8917 (tt0) cc_final: 0.8705 (tt0) REVERT: t 9 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8016 (mttp) REVERT: t 12 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7223 (mmp-170) REVERT: t 50 LEU cc_start: 0.9218 (tp) cc_final: 0.9008 (tp) REVERT: u 36 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7788 (tm-30) REVERT: u 71 ILE cc_start: 0.9372 (pt) cc_final: 0.9118 (mp) REVERT: u 100 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7383 (tm-30) REVERT: v 1 MET cc_start: 0.7702 (mmp) cc_final: 0.6777 (tpt) REVERT: v 71 LYS cc_start: 0.7966 (pttp) cc_final: 0.7619 (pttp) REVERT: w 62 LYS cc_start: 0.8594 (mttm) cc_final: 0.8381 (mtpp) REVERT: w 68 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8282 (mttt) REVERT: w 71 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (pttp) REVERT: x 2 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7657 (mtt180) REVERT: x 16 ASN cc_start: 0.8190 (t0) cc_final: 0.7347 (t0) REVERT: x 40 GLU cc_start: 0.8625 (pp20) cc_final: 0.8209 (pp20) REVERT: y 20 ASN cc_start: 0.9268 (m110) cc_final: 0.8965 (t0) REVERT: y 39 GLN cc_start: 0.7795 (mm110) cc_final: 0.7513 (mm110) REVERT: y 44 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8838 (ttmt) REVERT: z 5 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6824 (ttmt) REVERT: z 20 LYS cc_start: 0.8859 (mttp) cc_final: 0.8570 (mttp) REVERT: z 30 ARG cc_start: 0.7745 (pmt170) cc_final: 0.7346 (mtm-85) REVERT: z 48 ASN cc_start: 0.8543 (t0) cc_final: 0.8040 (t0) REVERT: B 36 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8360 (mttt) REVERT: C 45 HIS cc_start: 0.8027 (m90) cc_final: 0.7277 (m90) REVERT: D 14 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7759 (mtt-85) REVERT: G 18 GLN cc_start: 0.8614 (mt0) cc_final: 0.8235 (mt0) REVERT: G 35 ASN cc_start: 0.7842 (t0) cc_final: 0.7471 (t0) REVERT: G 36 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7816 (mmtt) REVERT: G 56 LEU cc_start: 0.8937 (mm) cc_final: 0.8614 (mm) REVERT: G 92 ASN cc_start: 0.9294 (p0) cc_final: 0.8998 (p0) REVERT: G 114 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7707 (mmmt) REVERT: G 117 GLU cc_start: 0.9196 (tt0) cc_final: 0.8974 (tt0) REVERT: G 136 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7840 (mtm-85) REVERT: G 142 LYS cc_start: 0.7478 (mmmm) cc_final: 0.7224 (mmtm) REVERT: G 174 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7760 (mt-10) REVERT: G 212 TYR cc_start: 0.8874 (m-10) cc_final: 0.8101 (m-80) REVERT: H 33 ASP cc_start: 0.8551 (t0) cc_final: 0.8307 (p0) REVERT: H 41 TYR cc_start: 0.7477 (t80) cc_final: 0.7225 (t80) REVERT: H 128 MET cc_start: 0.7182 (mmt) cc_final: 0.5837 (mtm) REVERT: H 206 ILE cc_start: 0.6599 (tt) cc_final: 0.6192 (tt) REVERT: I 2 ARG cc_start: 0.6541 (mtp-110) cc_final: 0.6235 (mtp85) REVERT: I 43 ARG cc_start: 0.7507 (tpt170) cc_final: 0.7049 (tpt90) REVERT: I 46 ARG cc_start: 0.6403 (mtt-85) cc_final: 0.5897 (mpt180) REVERT: I 53 GLN cc_start: 0.7750 (mt0) cc_final: 0.7540 (mt0) REVERT: I 177 MET cc_start: 0.4505 (mtp) cc_final: 0.3852 (tpp) REVERT: I 195 ASN cc_start: 0.7691 (t0) cc_final: 0.7453 (t0) REVERT: J 11 GLN cc_start: 0.7999 (tt0) cc_final: 0.7748 (tt0) REVERT: J 146 MET cc_start: 0.7560 (ttp) cc_final: 0.7326 (ttp) REVERT: J 151 MET cc_start: 0.8187 (tpp) cc_final: 0.7304 (ptp) REVERT: K 1 MET cc_start: 0.8320 (ptp) cc_final: 0.7474 (ptp) REVERT: K 25 TYR cc_start: 0.8409 (m-10) cc_final: 0.8185 (m-10) REVERT: K 56 LYS cc_start: 0.7146 (mmmt) cc_final: 0.6619 (mmmt) REVERT: K 75 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7697 (mt-10) REVERT: K 79 ARG cc_start: 0.7841 (ptp90) cc_final: 0.7628 (ptp90) REVERT: L 77 ARG cc_start: 0.7291 (ttp-170) cc_final: 0.6965 (ttp80) REVERT: L 102 TRP cc_start: 0.7555 (m-10) cc_final: 0.7179 (m-10) REVERT: L 115 MET cc_start: 0.7364 (mmm) cc_final: 0.7052 (mmm) REVERT: L 138 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6887 (tm-30) REVERT: M 4 ASP cc_start: 0.7938 (t0) cc_final: 0.7229 (t0) REVERT: M 26 MET cc_start: 0.8552 (ptt) cc_final: 0.8315 (ptt) REVERT: M 79 ARG cc_start: 0.9309 (mtm110) cc_final: 0.8809 (mtm110) REVERT: M 89 ASP cc_start: 0.8950 (m-30) cc_final: 0.8682 (m-30) REVERT: N 45 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7652 (ptp) REVERT: N 56 MET cc_start: 0.7281 (tmm) cc_final: 0.6809 (ttm) REVERT: N 79 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8090 (ttp80) REVERT: N 108 ARG cc_start: 0.8712 (mtm180) cc_final: 0.7936 (mtm-85) REVERT: N 125 GLN cc_start: 0.6989 (tt0) cc_final: 0.6516 (tt0) REVERT: O 44 THR cc_start: 0.8469 (p) cc_final: 0.8054 (t) REVERT: O 53 ILE cc_start: 0.7750 (pt) cc_final: 0.7474 (pt) REVERT: O 62 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7329 (mtp85) REVERT: P 82 GLU cc_start: 0.6970 (mp0) cc_final: 0.6548 (mp0) REVERT: P 96 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7302 (mp) REVERT: Q 108 ASP cc_start: 0.7637 (t0) cc_final: 0.7181 (t0) REVERT: Q 110 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7281 (mtmt) REVERT: R 11 HIS cc_start: 0.6001 (p-80) cc_final: 0.5797 (p-80) REVERT: R 51 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: R 71 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7959 (mt-10) REVERT: R 74 MET cc_start: 0.8261 (tmm) cc_final: 0.7920 (tpt) REVERT: R 77 LYS cc_start: 0.8613 (tppp) cc_final: 0.8394 (tppp) REVERT: S 40 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6372 (ttp80) REVERT: S 64 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7839 (ptp-110) REVERT: S 65 GLN cc_start: 0.8177 (mt0) cc_final: 0.7679 (mt0) REVERT: S 88 MET cc_start: 0.7836 (mmt) cc_final: 0.7362 (mmp) REVERT: T 17 ASP cc_start: 0.8634 (p0) cc_final: 0.8158 (p0) REVERT: T 48 ASP cc_start: 0.7583 (t0) cc_final: 0.7264 (t70) REVERT: T 56 LEU cc_start: 0.8835 (mm) cc_final: 0.8571 (mm) REVERT: T 67 ASP cc_start: 0.8507 (m-30) cc_final: 0.8184 (m-30) REVERT: V 10 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7413 (tpt-90) REVERT: V 17 GLU cc_start: 0.7190 (mp0) cc_final: 0.6476 (mp0) REVERT: V 61 ARG cc_start: 0.8257 (ttp-170) cc_final: 0.7908 (ttp-170) REVERT: V 72 TRP cc_start: 0.7672 (m100) cc_final: 0.7254 (m100) REVERT: W 29 LYS cc_start: 0.8725 (mttt) cc_final: 0.8354 (mtmm) REVERT: W 49 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7387 (tttm) REVERT: X 12 LEU cc_start: 0.8492 (mm) cc_final: 0.8223 (mm) REVERT: Y 26 MET cc_start: 0.7976 (tmm) cc_final: 0.7771 (tmm) REVERT: Y 54 GLN cc_start: 0.7355 (tm-30) cc_final: 0.6948 (tm-30) REVERT: Y 60 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8197 (mm-40) REVERT: Y 68 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6927 (ptmt) REVERT: Z 65 ARG cc_start: 0.7309 (tmt170) cc_final: 0.6675 (tmt170) outliers start: 319 outliers final: 251 residues processed: 1806 average time/residue: 1.3381 time to fit residues: 4136.7798 Evaluate side-chains 1882 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1622 time to evaluate : 6.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain b residue 258 SER Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 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 131 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 83 THR Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 135 HIS Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL 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 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain o residue 33 ARG Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 47 ARG Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain w residue 32 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 51 GLN Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 30.0000 chunk 579 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 760 optimal weight: 30.0000 chunk 421 optimal weight: 9.9990 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 521 optimal weight: 7.9990 chunk 917 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS o 29 HIS o 104 GLN p 14 GLN p 51 ASN q 55 GLN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN v 88 HIS x 15 ASN ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 141 HIS M 75 GLN N 31 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 163219 Z= 0.385 Angle : 0.719 13.714 244202 Z= 0.367 Chirality : 0.041 0.280 31236 Planarity : 0.006 0.108 13084 Dihedral : 23.216 178.740 81774 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.34 % Favored : 89.47 % Rotamer: Outliers : 7.72 % Allowed : 22.29 % Favored : 69.99 % 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: -2.51 (0.10), residues: 5919 helix: -0.54 (0.12), residues: 1856 sheet: -1.71 (0.16), residues: 981 loop : -2.41 (0.10), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 100 HIS 0.015 0.002 HIS v 88 PHE 0.025 0.002 PHE u 72 TYR 0.022 0.002 TYR f 156 ARG 0.007 0.001 ARG w 35 *********************** 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 2029 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 1650 time to evaluate : 6.266 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: b 12 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8341 (ttt90) REVERT: b 25 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8361 (mmtp) REVERT: b 58 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7663 (tttp) REVERT: b 131 MET cc_start: 0.8737 (mtm) cc_final: 0.8455 (mtm) REVERT: b 144 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8272 (mm-30) REVERT: b 149 LYS cc_start: 0.8913 (tptm) cc_final: 0.8266 (tptm) REVERT: b 224 MET cc_start: 0.8782 (mtt) cc_final: 0.8435 (mtt) REVERT: c 128 ARG cc_start: 0.7778 (mtp180) cc_final: 0.7293 (mtp180) REVERT: c 168 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: d 24 ASN cc_start: 0.8535 (t0) cc_final: 0.8066 (t0) REVERT: d 91 ASP cc_start: 0.8219 (t0) cc_final: 0.7729 (t0) REVERT: d 145 ASP cc_start: 0.7979 (t0) cc_final: 0.7760 (t0) REVERT: d 157 LEU cc_start: 0.8610 (mm) cc_final: 0.8067 (tt) REVERT: d 183 PHE cc_start: 0.7939 (m-80) cc_final: 0.7707 (m-80) REVERT: e 139 GLU cc_start: 0.8759 (mp0) cc_final: 0.8343 (mp0) REVERT: e 169 LEU cc_start: 0.8631 (tp) cc_final: 0.8378 (tp) REVERT: f 142 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8664 (tp40) REVERT: g 27 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.7895 (ttm170) REVERT: g 28 ASN cc_start: 0.8212 (m-40) cc_final: 0.7816 (m-40) REVERT: g 46 PHE cc_start: 0.8524 (m-10) cc_final: 0.8256 (m-10) REVERT: h 1 MET cc_start: 0.4120 (ptp) cc_final: 0.2478 (ttp) REVERT: h 52 MET cc_start: 0.0763 (tmm) cc_final: 0.0376 (tmm) REVERT: j 37 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7503 (ttt-90) REVERT: j 44 TYR cc_start: 0.8605 (t80) cc_final: 0.8229 (t80) REVERT: j 136 GLN cc_start: 0.8763 (mt0) cc_final: 0.8044 (mm-40) REVERT: k 88 ASN cc_start: 0.8389 (m-40) cc_final: 0.8118 (m110) REVERT: k 93 GLN cc_start: 0.7133 (mp10) cc_final: 0.6695 (mp10) REVERT: l 121 THR cc_start: 0.9119 (m) cc_final: 0.8788 (p) REVERT: m 1 MET cc_start: 0.7245 (tpp) cc_final: 0.6933 (tmm) REVERT: m 3 GLN cc_start: 0.8607 (tt0) cc_final: 0.8241 (tp-100) REVERT: m 47 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8083 (tp30) REVERT: m 73 ILE cc_start: 0.9144 (mm) cc_final: 0.8549 (tt) REVERT: n 9 GLN cc_start: 0.8341 (mt0) cc_final: 0.8024 (mt0) REVERT: n 82 GLU cc_start: 0.7141 (mp0) cc_final: 0.6836 (mp0) REVERT: n 110 MET cc_start: 0.7979 (mmt) cc_final: 0.7690 (mmt) REVERT: o 33 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6867 (tmm-80) REVERT: o 98 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8226 (tp40) REVERT: p 15 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7735 (p0) REVERT: p 26 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7712 (pp20) REVERT: q 15 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8171 (ttmm) REVERT: q 84 LYS cc_start: 0.8603 (mttt) cc_final: 0.8349 (mtmt) REVERT: q 91 ARG cc_start: 0.8229 (mtt90) cc_final: 0.8016 (mtt90) REVERT: r 11 GLN cc_start: 0.8870 (mp10) cc_final: 0.8587 (mt0) REVERT: r 13 ARG cc_start: 0.7642 (ttt180) cc_final: 0.7211 (ttt180) REVERT: r 48 LYS cc_start: 0.9060 (ptmm) cc_final: 0.8699 (ptmm) REVERT: r 97 LYS cc_start: 0.8812 (tttt) cc_final: 0.8445 (ttmt) REVERT: s 86 MET cc_start: 0.7990 (ttp) cc_final: 0.7719 (ttt) REVERT: s 92 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7197 (mtp85) REVERT: s 99 ARG cc_start: 0.8268 (mtt-85) cc_final: 0.7394 (mtt180) REVERT: t 9 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8066 (mttp) REVERT: t 12 ARG cc_start: 0.7659 (mmm160) cc_final: 0.7170 (mmp-170) REVERT: t 44 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8189 (tttp) REVERT: t 50 LEU cc_start: 0.9259 (tp) cc_final: 0.9054 (tp) REVERT: u 11 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8612 (mt) REVERT: u 36 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7775 (tm-30) REVERT: u 100 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7440 (tm-30) REVERT: v 1 MET cc_start: 0.7619 (mmp) cc_final: 0.6720 (tpt) REVERT: v 57 TYR cc_start: 0.7698 (m-80) cc_final: 0.7415 (m-80) REVERT: v 71 LYS cc_start: 0.7986 (pttp) cc_final: 0.7645 (pttp) REVERT: w 39 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.6958 (t) REVERT: w 62 LYS cc_start: 0.8589 (mttm) cc_final: 0.8333 (mtpp) REVERT: w 68 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8290 (mttt) REVERT: x 2 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7659 (mtt180) REVERT: x 16 ASN cc_start: 0.8219 (t0) cc_final: 0.7285 (t0) REVERT: x 40 GLU cc_start: 0.8702 (pp20) cc_final: 0.8251 (pp20) REVERT: x 49 ARG cc_start: 0.7769 (ttt180) cc_final: 0.7451 (ttt180) REVERT: y 6 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6180 (tp) REVERT: y 12 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7746 (mm-30) REVERT: y 20 ASN cc_start: 0.9234 (m110) cc_final: 0.8884 (t0) REVERT: y 44 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8796 (ttmt) REVERT: y 45 GLN cc_start: 0.7769 (tp40) cc_final: 0.7398 (tp40) REVERT: z 5 LYS cc_start: 0.7380 (mmmt) cc_final: 0.6694 (ttmt) REVERT: z 20 LYS cc_start: 0.8895 (mttp) cc_final: 0.8581 (mttp) REVERT: z 48 ASN cc_start: 0.8606 (t0) cc_final: 0.8113 (t0) REVERT: B 36 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8353 (mttt) REVERT: C 18 HIS cc_start: 0.7936 (t70) cc_final: 0.7684 (t70) REVERT: C 45 HIS cc_start: 0.8069 (m90) cc_final: 0.7270 (m90) REVERT: D 14 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: G 18 GLN cc_start: 0.8581 (mt0) cc_final: 0.8212 (mt0) REVERT: G 35 ASN cc_start: 0.7853 (t0) cc_final: 0.7593 (t0) REVERT: G 36 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7852 (mmtt) REVERT: G 92 ASN cc_start: 0.9230 (p0) cc_final: 0.8967 (p0) REVERT: G 99 MET cc_start: 0.8012 (mmm) cc_final: 0.7620 (mmm) REVERT: G 142 LYS cc_start: 0.7518 (mmmm) cc_final: 0.7241 (mmtm) REVERT: H 41 TYR cc_start: 0.7514 (t80) cc_final: 0.7249 (t80) REVERT: H 128 MET cc_start: 0.7056 (mmt) cc_final: 0.5847 (mtm) REVERT: H 169 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: H 206 ILE cc_start: 0.6609 (tt) cc_final: 0.6250 (tt) REVERT: I 43 ARG cc_start: 0.7603 (tpt170) cc_final: 0.7140 (tpt90) REVERT: I 46 ARG cc_start: 0.6482 (mtt-85) cc_final: 0.5969 (mpt180) REVERT: I 53 GLN cc_start: 0.7681 (mt0) cc_final: 0.7471 (mt0) REVERT: I 166 LYS cc_start: 0.7353 (mmmt) cc_final: 0.6646 (mmmt) REVERT: J 11 GLN cc_start: 0.8013 (tt0) cc_final: 0.7641 (tt0) REVERT: J 53 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7461 (mtp-110) REVERT: J 146 MET cc_start: 0.7548 (ttp) cc_final: 0.7243 (ttp) REVERT: J 151 MET cc_start: 0.8215 (tpp) cc_final: 0.7338 (ptp) REVERT: K 1 MET cc_start: 0.8407 (ptp) cc_final: 0.7980 (ptp) REVERT: K 56 LYS cc_start: 0.7031 (mmmt) cc_final: 0.6567 (mmmt) REVERT: K 75 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7792 (mt-10) REVERT: L 77 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.7146 (ttp80) REVERT: L 102 TRP cc_start: 0.7581 (m-10) cc_final: 0.7132 (m-10) REVERT: L 113 LYS cc_start: 0.6141 (mmtt) cc_final: 0.4868 (mmtt) REVERT: L 138 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6853 (tm-30) REVERT: M 4 ASP cc_start: 0.7955 (t0) cc_final: 0.7242 (t0) REVERT: M 79 ARG cc_start: 0.9326 (mtm110) cc_final: 0.8818 (mtm110) REVERT: M 89 ASP cc_start: 0.9057 (m-30) cc_final: 0.8743 (m-30) REVERT: M 110 MET cc_start: 0.7449 (ptp) cc_final: 0.7137 (ptt) REVERT: N 45 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7538 (ptp) REVERT: N 79 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8080 (ttp80) REVERT: N 108 ARG cc_start: 0.8639 (mtm180) cc_final: 0.7853 (mtm-85) REVERT: N 125 GLN cc_start: 0.7026 (tt0) cc_final: 0.6517 (tt0) REVERT: O 9 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7535 (mtp85) REVERT: O 16 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7363 (ttt90) REVERT: O 44 THR cc_start: 0.8354 (p) cc_final: 0.7749 (t) REVERT: O 45 ARG cc_start: 0.6600 (ptm160) cc_final: 0.6221 (ptt180) REVERT: O 53 ILE cc_start: 0.7699 (pt) cc_final: 0.7462 (pt) REVERT: O 62 ARG cc_start: 0.7580 (mtt-85) cc_final: 0.7344 (mtp85) REVERT: P 96 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7187 (mp) REVERT: Q 108 ASP cc_start: 0.7611 (t0) cc_final: 0.7136 (t0) REVERT: Q 110 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7281 (mtmt) REVERT: R 71 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7953 (mt-10) REVERT: R 77 LYS cc_start: 0.8583 (tppp) cc_final: 0.8320 (tppp) REVERT: S 40 ARG cc_start: 0.6866 (mtp180) cc_final: 0.6376 (ttp80) REVERT: S 48 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: S 64 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8267 (mtp180) REVERT: S 65 GLN cc_start: 0.8197 (mt0) cc_final: 0.7717 (mt0) REVERT: T 17 ASP cc_start: 0.8480 (p0) cc_final: 0.7958 (p0) REVERT: T 48 ASP cc_start: 0.7627 (t0) cc_final: 0.7326 (t70) REVERT: T 56 LEU cc_start: 0.8824 (mm) cc_final: 0.8554 (mm) REVERT: U 25 ARG cc_start: 0.6823 (mtm180) cc_final: 0.6514 (mtm180) REVERT: V 5 ARG cc_start: 0.6306 (ptp-170) cc_final: 0.6098 (ptp-110) REVERT: V 10 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7427 (tpt-90) REVERT: V 17 GLU cc_start: 0.7230 (mp0) cc_final: 0.6466 (mp0) REVERT: V 27 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7840 (t80) REVERT: V 72 TRP cc_start: 0.7698 (m100) cc_final: 0.7269 (m100) REVERT: W 29 LYS cc_start: 0.8628 (mttt) cc_final: 0.8270 (mttt) REVERT: W 49 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7534 (tttm) REVERT: X 79 TYR cc_start: 0.7905 (t80) cc_final: 0.7385 (t80) REVERT: Y 26 MET cc_start: 0.7942 (tmm) cc_final: 0.7736 (tmm) REVERT: Y 43 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8785 (mmtt) REVERT: Y 54 GLN cc_start: 0.7439 (tm-30) cc_final: 0.6965 (tm-30) REVERT: Y 60 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8180 (mm-40) REVERT: Y 68 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6945 (ptmt) REVERT: Y 73 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7423 (ttp-110) REVERT: Z 19 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7629 (mmtm) REVERT: Z 34 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7092 (mmt90) REVERT: Z 65 ARG cc_start: 0.7505 (tmt170) cc_final: 0.7147 (tmt170) outliers start: 379 outliers final: 281 residues processed: 1816 average time/residue: 1.3928 time to fit residues: 4359.4467 Evaluate side-chains 1905 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1599 time to evaluate : 6.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 48 LEU Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 97 GLU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 142 GLN Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 63 LYS Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 101 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 47 GLU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain o residue 33 ARG Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 47 ARG Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 92 ARG Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain s residue 105 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL 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 48 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain y residue 6 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 75 GLN Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 8.9990 chunk 920 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 599 optimal weight: 30.0000 chunk 252 optimal weight: 2.9990 chunk 1022 optimal weight: 10.0000 chunk 848 optimal weight: 10.0000 chunk 473 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 338 optimal weight: 30.0000 chunk 536 optimal weight: 8.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN f 44 HIS ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 114 HIS ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 80 HIS o 104 GLN q 55 GLN v 88 HIS x 15 ASN ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 141 HIS R 51 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 163219 Z= 0.307 Angle : 0.666 15.121 244202 Z= 0.342 Chirality : 0.039 0.359 31236 Planarity : 0.005 0.082 13084 Dihedral : 23.232 179.216 81773 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.46 % Favored : 90.35 % Rotamer: Outliers : 7.31 % Allowed : 24.12 % Favored : 68.57 % 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: -2.32 (0.10), residues: 5919 helix: -0.38 (0.12), residues: 1865 sheet: -1.61 (0.16), residues: 974 loop : -2.30 (0.10), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 212 HIS 0.031 0.002 HIS j 80 PHE 0.024 0.002 PHE Y 50 TYR 0.030 0.002 TYR f 156 ARG 0.016 0.001 ARG u 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 2008 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1649 time to evaluate : 6.310 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: b 12 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8306 (ttt90) REVERT: b 25 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8346 (mmtp) REVERT: b 58 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7637 (tttp) REVERT: b 131 MET cc_start: 0.8720 (mtm) cc_final: 0.8476 (mtm) REVERT: b 144 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8171 (mm-30) REVERT: b 212 TRP cc_start: 0.8094 (p90) cc_final: 0.7605 (p-90) REVERT: b 224 MET cc_start: 0.8890 (mtt) cc_final: 0.8599 (mtt) REVERT: c 128 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7273 (mtp180) REVERT: c 168 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: d 24 ASN cc_start: 0.8474 (t0) cc_final: 0.7992 (t0) REVERT: d 91 ASP cc_start: 0.8169 (t0) cc_final: 0.7682 (t0) REVERT: d 111 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7103 (pt0) REVERT: d 145 ASP cc_start: 0.7986 (t0) cc_final: 0.7735 (t0) REVERT: d 157 LEU cc_start: 0.8629 (mm) cc_final: 0.8079 (tt) REVERT: d 183 PHE cc_start: 0.7940 (m-80) cc_final: 0.7712 (m-80) REVERT: e 65 LEU cc_start: 0.5207 (mt) cc_final: 0.4931 (mt) REVERT: e 79 ARG cc_start: 0.6055 (mmt180) cc_final: 0.5749 (tpp-160) REVERT: e 136 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7555 (mp) REVERT: e 139 GLU cc_start: 0.8743 (mp0) cc_final: 0.8342 (mp0) REVERT: e 169 LEU cc_start: 0.8642 (tp) cc_final: 0.8311 (tp) REVERT: f 162 ARG cc_start: 0.6956 (ptp-170) cc_final: 0.6755 (ptp-170) REVERT: g 27 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8059 (ttm170) REVERT: g 28 ASN cc_start: 0.8127 (m-40) cc_final: 0.7612 (m-40) REVERT: g 46 PHE cc_start: 0.8501 (m-10) cc_final: 0.8245 (m-10) REVERT: h 1 MET cc_start: 0.4188 (ptp) cc_final: 0.2072 (ttp) REVERT: h 52 MET cc_start: 0.0786 (tmm) cc_final: 0.0398 (tmm) REVERT: j 37 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7592 (ttt-90) REVERT: j 44 TYR cc_start: 0.8573 (t80) cc_final: 0.8294 (t80) REVERT: j 80 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6556 (m90) REVERT: j 136 GLN cc_start: 0.8729 (mt0) cc_final: 0.8027 (mm-40) REVERT: l 121 THR cc_start: 0.9130 (m) cc_final: 0.8752 (p) REVERT: m 1 MET cc_start: 0.7228 (tpp) cc_final: 0.6920 (tmm) REVERT: m 3 GLN cc_start: 0.8579 (tt0) cc_final: 0.8232 (tp-100) REVERT: m 47 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (tp30) REVERT: n 9 GLN cc_start: 0.8295 (mt0) cc_final: 0.7963 (mt0) REVERT: n 82 GLU cc_start: 0.7177 (mp0) cc_final: 0.6874 (mp0) REVERT: n 110 MET cc_start: 0.8012 (mmt) cc_final: 0.7691 (mmt) REVERT: o 98 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8240 (tp40) REVERT: p 15 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7732 (p0) REVERT: p 26 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: q 15 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8039 (tptt) REVERT: q 84 LYS cc_start: 0.8554 (mttt) cc_final: 0.8282 (mtmt) REVERT: r 11 GLN cc_start: 0.8750 (mp10) cc_final: 0.8544 (mt0) REVERT: r 13 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7275 (ttt180) REVERT: r 48 LYS cc_start: 0.8993 (ptmm) cc_final: 0.8613 (ptmm) REVERT: r 97 LYS cc_start: 0.8805 (tttt) cc_final: 0.8444 (ttmt) REVERT: s 86 MET cc_start: 0.7946 (ttp) cc_final: 0.7671 (ttt) REVERT: s 99 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7416 (mtt180) REVERT: t 6 ARG cc_start: 0.8868 (tpt-90) cc_final: 0.8553 (tpt170) REVERT: t 9 LYS cc_start: 0.8452 (mtpt) cc_final: 0.7987 (mttp) REVERT: t 12 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7146 (mmp-170) REVERT: t 44 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8145 (tttp) REVERT: t 50 LEU cc_start: 0.9212 (tp) cc_final: 0.8991 (tp) REVERT: u 5 ARG cc_start: 0.8509 (mmt90) cc_final: 0.8239 (mmt90) REVERT: u 8 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8221 (t70) REVERT: u 11 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8700 (mt) REVERT: u 36 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7773 (tm-30) REVERT: u 100 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7681 (tm-30) REVERT: v 1 MET cc_start: 0.7516 (mmp) cc_final: 0.6750 (tpt) REVERT: v 57 TYR cc_start: 0.7688 (m-80) cc_final: 0.7415 (m-80) REVERT: v 71 LYS cc_start: 0.7991 (pttp) cc_final: 0.7623 (pttp) REVERT: w 25 GLU cc_start: 0.7797 (tp30) cc_final: 0.7257 (tp30) REVERT: w 39 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.7012 (t) REVERT: w 62 LYS cc_start: 0.8565 (mttm) cc_final: 0.8323 (mtpp) REVERT: w 68 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8285 (mttt) REVERT: w 71 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7751 (pttp) REVERT: x 2 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7606 (mtt180) REVERT: x 16 ASN cc_start: 0.8192 (t0) cc_final: 0.7267 (t0) REVERT: x 40 GLU cc_start: 0.8645 (pp20) cc_final: 0.8192 (pp20) REVERT: x 67 LEU cc_start: 0.9250 (tp) cc_final: 0.8960 (mm) REVERT: y 6 LEU cc_start: 0.5909 (tp) cc_final: 0.5554 (tp) REVERT: y 20 ASN cc_start: 0.9230 (m110) cc_final: 0.8922 (t0) REVERT: y 44 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8811 (ttmt) REVERT: y 45 GLN cc_start: 0.7823 (tp40) cc_final: 0.7367 (tp40) REVERT: z 5 LYS cc_start: 0.7422 (mmmt) cc_final: 0.6935 (mtpp) REVERT: z 20 LYS cc_start: 0.8879 (mttp) cc_final: 0.8567 (mttp) REVERT: z 48 ASN cc_start: 0.8568 (t0) cc_final: 0.8275 (t0) REVERT: B 36 LYS cc_start: 0.8639 (mmtp) cc_final: 0.8341 (mttt) REVERT: D 14 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7744 (mtt-85) REVERT: G 18 GLN cc_start: 0.8604 (mt0) cc_final: 0.8222 (mt0) REVERT: G 35 ASN cc_start: 0.7905 (t0) cc_final: 0.7658 (t0) REVERT: G 92 ASN cc_start: 0.9248 (p0) cc_final: 0.8983 (p0) REVERT: G 99 MET cc_start: 0.7992 (mmm) cc_final: 0.7668 (mmm) REVERT: G 136 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7795 (mtm-85) REVERT: G 142 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7420 (mmtm) REVERT: G 174 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7596 (mt-10) REVERT: G 176 ASN cc_start: 0.8385 (m-40) cc_final: 0.7925 (m-40) REVERT: H 41 TYR cc_start: 0.7485 (t80) cc_final: 0.7230 (t80) REVERT: H 128 MET cc_start: 0.7005 (mmt) cc_final: 0.5763 (mtm) REVERT: H 169 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: H 206 ILE cc_start: 0.6601 (tt) cc_final: 0.6148 (tt) REVERT: I 43 ARG cc_start: 0.7618 (tpt170) cc_final: 0.7140 (tpt90) REVERT: I 46 ARG cc_start: 0.6418 (mtt-85) cc_final: 0.5934 (mpt180) REVERT: I 53 GLN cc_start: 0.7649 (mt0) cc_final: 0.7407 (mt0) REVERT: I 80 ARG cc_start: 0.7608 (ptm-80) cc_final: 0.7285 (ptm160) REVERT: I 104 MET cc_start: 0.6948 (mmm) cc_final: 0.6265 (ttt) REVERT: I 195 ASN cc_start: 0.7642 (t0) cc_final: 0.7384 (t0) REVERT: J 11 GLN cc_start: 0.7983 (tt0) cc_final: 0.7776 (tt0) REVERT: J 146 MET cc_start: 0.7491 (ttp) cc_final: 0.7139 (ttp) REVERT: J 151 MET cc_start: 0.8117 (tpp) cc_final: 0.7241 (ptp) REVERT: K 44 ARG cc_start: 0.8762 (mtp180) cc_final: 0.8543 (mtp180) REVERT: K 62 MET cc_start: 0.8379 (mmt) cc_final: 0.7883 (mmt) REVERT: K 75 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7648 (mt-10) REVERT: K 90 MET cc_start: 0.7422 (mpp) cc_final: 0.7128 (mmt) REVERT: L 20 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8164 (mm-30) REVERT: L 77 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.7114 (ttp80) REVERT: L 102 TRP cc_start: 0.7533 (m-10) cc_final: 0.7100 (m-10) REVERT: L 112 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6253 (p0) REVERT: L 113 LYS cc_start: 0.6095 (mmtt) cc_final: 0.5116 (mmtt) REVERT: L 115 MET cc_start: 0.7294 (mmm) cc_final: 0.6938 (mmm) REVERT: L 138 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6896 (tm-30) REVERT: M 4 ASP cc_start: 0.8014 (t0) cc_final: 0.7306 (t0) REVERT: M 26 MET cc_start: 0.8485 (ptt) cc_final: 0.8248 (ptt) REVERT: M 79 ARG cc_start: 0.9325 (mtm110) cc_final: 0.8766 (mtm110) REVERT: M 89 ASP cc_start: 0.9058 (m-30) cc_final: 0.8759 (m-30) REVERT: N 45 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7498 (ptp) REVERT: N 79 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8089 (ttp80) REVERT: N 108 ARG cc_start: 0.8676 (mtm180) cc_final: 0.7896 (mtm-85) REVERT: N 125 GLN cc_start: 0.6968 (tt0) cc_final: 0.6444 (tt0) REVERT: O 16 ARG cc_start: 0.7741 (ptt180) cc_final: 0.7335 (ttt90) REVERT: O 44 THR cc_start: 0.8073 (p) cc_final: 0.7613 (t) REVERT: O 53 ILE cc_start: 0.7662 (pt) cc_final: 0.7431 (pt) REVERT: O 62 ARG cc_start: 0.7520 (mtt-85) cc_final: 0.7282 (mtp85) REVERT: P 96 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7150 (mp) REVERT: Q 108 ASP cc_start: 0.7420 (t0) cc_final: 0.7063 (t0) REVERT: Q 110 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7310 (mtmt) REVERT: R 71 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7913 (mt-10) REVERT: R 77 LYS cc_start: 0.8557 (tppp) cc_final: 0.8305 (tppp) REVERT: S 40 ARG cc_start: 0.6857 (mtp180) cc_final: 0.6387 (ttp80) REVERT: S 48 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6492 (mp10) REVERT: S 64 ARG cc_start: 0.8523 (ttm110) cc_final: 0.8003 (ptm160) REVERT: S 65 GLN cc_start: 0.8191 (mt0) cc_final: 0.7669 (mt0) REVERT: S 88 MET cc_start: 0.7879 (mmt) cc_final: 0.7592 (mmp) REVERT: T 17 ASP cc_start: 0.8462 (p0) cc_final: 0.7958 (p0) REVERT: T 56 LEU cc_start: 0.8830 (mm) cc_final: 0.8568 (mm) REVERT: T 67 ASP cc_start: 0.8332 (m-30) cc_final: 0.8044 (m-30) REVERT: U 25 ARG cc_start: 0.6791 (mtm180) cc_final: 0.6390 (mtm180) REVERT: V 5 ARG cc_start: 0.6277 (ptp-170) cc_final: 0.6074 (ptp-110) REVERT: V 17 GLU cc_start: 0.7203 (mp0) cc_final: 0.6401 (mp0) REVERT: V 27 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7868 (t80) REVERT: V 41 THR cc_start: 0.5642 (m) cc_final: 0.5229 (m) REVERT: V 72 TRP cc_start: 0.7699 (m100) cc_final: 0.7266 (m100) REVERT: W 29 LYS cc_start: 0.8733 (mttt) cc_final: 0.8355 (mttt) REVERT: W 49 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7372 (tttm) REVERT: X 12 LEU cc_start: 0.8576 (mm) cc_final: 0.7923 (mm) REVERT: X 79 TYR cc_start: 0.7977 (t80) cc_final: 0.7490 (t80) REVERT: Y 20 ASN cc_start: 0.8746 (m-40) cc_final: 0.8542 (m110) REVERT: Y 43 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8794 (mmtt) REVERT: Y 54 GLN cc_start: 0.7477 (tm-30) cc_final: 0.6938 (tm-30) REVERT: Y 60 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8168 (mm-40) REVERT: Y 68 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6903 (ptmt) REVERT: Y 73 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7487 (ttp-110) REVERT: Z 19 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7520 (mmtm) REVERT: Z 65 ARG cc_start: 0.7553 (tmt170) cc_final: 0.7203 (tmt170) outliers start: 359 outliers final: 279 residues processed: 1804 average time/residue: 1.3337 time to fit residues: 4121.7153 Evaluate side-chains 1907 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1602 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 80 HIS Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 47 GLU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 111 GLU 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 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 8 ASP 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 48 VAL Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 92 VAL Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 77 TYR Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 582 optimal weight: 10.0000 chunk 746 optimal weight: 10.0000 chunk 578 optimal weight: 0.6980 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 50.0000 chunk 1018 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 621 optimal weight: 20.0000 chunk 470 optimal weight: 9.9990 overall best weight: 7.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN f 37 ASN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN q 55 GLN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 HIS w 8 ASN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 163219 Z= 0.435 Angle : 0.759 14.578 244202 Z= 0.384 Chirality : 0.043 0.297 31236 Planarity : 0.006 0.089 13084 Dihedral : 23.313 179.281 81773 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.98 % Favored : 88.82 % Rotamer: Outliers : 7.92 % Allowed : 24.42 % Favored : 67.65 % 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: -2.45 (0.10), residues: 5919 helix: -0.47 (0.12), residues: 1865 sheet: -1.68 (0.16), residues: 992 loop : -2.39 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP b 212 HIS 0.034 0.002 HIS j 80 PHE 0.025 0.002 PHE e 19 TYR 0.026 0.002 TYR e 21 ARG 0.017 0.001 ARG u 21 *********************** 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 2026 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 1637 time to evaluate : 6.293 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: b 12 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8375 (ttt90) REVERT: b 25 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8383 (mmtp) REVERT: b 58 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7669 (tttp) REVERT: b 144 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8404 (mm-30) REVERT: b 149 LYS cc_start: 0.8724 (tptm) cc_final: 0.8149 (tptm) REVERT: b 188 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6820 (mtp85) REVERT: b 212 TRP cc_start: 0.8279 (p90) cc_final: 0.7838 (p-90) REVERT: c 128 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7393 (mtp180) REVERT: c 168 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: d 24 ASN cc_start: 0.8500 (t0) cc_final: 0.8040 (t0) REVERT: d 91 ASP cc_start: 0.8283 (t0) cc_final: 0.7799 (t0) REVERT: d 145 ASP cc_start: 0.7990 (t0) cc_final: 0.7755 (t0) REVERT: d 157 LEU cc_start: 0.8643 (mm) cc_final: 0.8089 (tt) REVERT: d 183 PHE cc_start: 0.7953 (m-80) cc_final: 0.7752 (m-80) REVERT: e 15 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7469 (tt) REVERT: e 18 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: e 31 GLU cc_start: 0.8151 (tp30) cc_final: 0.7935 (tp30) REVERT: e 79 ARG cc_start: 0.6032 (mmt180) cc_final: 0.5684 (tpp-160) REVERT: e 136 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7691 (mp) REVERT: e 139 GLU cc_start: 0.8875 (mp0) cc_final: 0.8557 (mp0) REVERT: e 169 LEU cc_start: 0.8619 (tp) cc_final: 0.8331 (tp) REVERT: f 115 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7905 (tp40) REVERT: f 123 GLU cc_start: 0.8296 (tp30) cc_final: 0.8055 (tm-30) REVERT: f 162 ARG cc_start: 0.7105 (ptp-170) cc_final: 0.6900 (ptp-170) REVERT: g 27 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.8172 (ttm170) REVERT: g 28 ASN cc_start: 0.8256 (m-40) cc_final: 0.7869 (m-40) REVERT: g 46 PHE cc_start: 0.8647 (m-10) cc_final: 0.8316 (m-10) REVERT: h 1 MET cc_start: 0.4268 (ptp) cc_final: 0.2225 (ttp) REVERT: h 52 MET cc_start: 0.0681 (tmm) cc_final: 0.0260 (tmm) REVERT: j 37 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7541 (ttt-90) REVERT: j 44 TYR cc_start: 0.8601 (t80) cc_final: 0.8355 (t80) REVERT: j 136 GLN cc_start: 0.8755 (mt0) cc_final: 0.8049 (mm-40) REVERT: k 93 GLN cc_start: 0.7073 (mp10) cc_final: 0.6795 (mp10) REVERT: l 121 THR cc_start: 0.9214 (m) cc_final: 0.8825 (p) REVERT: m 3 GLN cc_start: 0.8603 (tt0) cc_final: 0.8327 (tp-100) REVERT: m 12 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7358 (ptm) REVERT: m 47 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: m 73 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8789 (tt) REVERT: n 9 GLN cc_start: 0.8334 (mt0) cc_final: 0.7986 (mt0) REVERT: n 82 GLU cc_start: 0.7421 (mp0) cc_final: 0.7077 (mp0) REVERT: n 110 MET cc_start: 0.8029 (mmt) cc_final: 0.7785 (mmt) REVERT: o 80 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8756 (mp0) REVERT: o 98 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8256 (tp40) REVERT: p 15 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7701 (p0) REVERT: p 26 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: q 15 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8126 (tptt) REVERT: q 84 LYS cc_start: 0.8596 (mttt) cc_final: 0.8277 (mtmt) REVERT: r 11 GLN cc_start: 0.8869 (mp10) cc_final: 0.8505 (mt0) REVERT: r 13 ARG cc_start: 0.7621 (ttt180) cc_final: 0.7219 (ttt180) REVERT: r 48 LYS cc_start: 0.8907 (ptmm) cc_final: 0.8415 (ptmm) REVERT: r 97 LYS cc_start: 0.8804 (tttt) cc_final: 0.8447 (ttmt) REVERT: s 86 MET cc_start: 0.7941 (ttp) cc_final: 0.7669 (ttt) REVERT: s 99 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7399 (mtt180) REVERT: t 4 GLU cc_start: 0.8919 (tt0) cc_final: 0.8674 (tt0) REVERT: t 6 ARG cc_start: 0.8874 (tpt-90) cc_final: 0.8389 (tpt170) REVERT: t 9 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8011 (mttp) REVERT: t 12 ARG cc_start: 0.7688 (mmm160) cc_final: 0.7319 (mmp-170) REVERT: t 42 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7549 (mt-10) REVERT: t 50 LEU cc_start: 0.9206 (tp) cc_final: 0.8975 (tp) REVERT: u 5 ARG cc_start: 0.8532 (mmt90) cc_final: 0.8330 (mmt90) REVERT: u 8 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8126 (t70) REVERT: u 11 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8662 (mt) REVERT: u 36 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7774 (tm-30) REVERT: u 59 GLU cc_start: 0.7458 (tp30) cc_final: 0.7182 (tp30) REVERT: u 100 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7429 (tm-30) REVERT: v 1 MET cc_start: 0.7458 (mmp) cc_final: 0.6602 (tpt) REVERT: v 57 TYR cc_start: 0.7643 (m-80) cc_final: 0.7396 (m-80) REVERT: v 71 LYS cc_start: 0.8029 (pttp) cc_final: 0.7676 (pttp) REVERT: w 25 GLU cc_start: 0.7901 (tp30) cc_final: 0.7665 (tp30) REVERT: w 39 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.7077 (t) REVERT: w 62 LYS cc_start: 0.8582 (mttm) cc_final: 0.8334 (mtpp) REVERT: w 68 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8291 (mttt) REVERT: x 2 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7702 (mtt180) REVERT: x 16 ASN cc_start: 0.8218 (t0) cc_final: 0.7261 (t0) REVERT: x 40 GLU cc_start: 0.8742 (pp20) cc_final: 0.8291 (pp20) REVERT: y 6 LEU cc_start: 0.6144 (tp) cc_final: 0.5807 (tp) REVERT: y 20 ASN cc_start: 0.9231 (m110) cc_final: 0.8917 (t0) REVERT: y 44 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8879 (ttmt) REVERT: y 45 GLN cc_start: 0.8017 (tp40) cc_final: 0.7527 (tp40) REVERT: z 5 LYS cc_start: 0.7420 (mmmt) cc_final: 0.6933 (mtpp) REVERT: z 20 LYS cc_start: 0.8937 (mttp) cc_final: 0.8601 (mttp) REVERT: z 38 GLU cc_start: 0.8654 (pm20) cc_final: 0.8449 (pm20) REVERT: z 48 ASN cc_start: 0.8743 (t0) cc_final: 0.8271 (t0) REVERT: B 36 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8352 (mttt) REVERT: C 45 HIS cc_start: 0.8102 (m90) cc_final: 0.7259 (m90) REVERT: D 14 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7767 (mtt-85) REVERT: G 18 GLN cc_start: 0.8597 (mt0) cc_final: 0.8233 (mt0) REVERT: G 35 ASN cc_start: 0.7890 (t0) cc_final: 0.7651 (t0) REVERT: G 99 MET cc_start: 0.8043 (mmm) cc_final: 0.7633 (mmm) REVERT: G 142 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7281 (mmtm) REVERT: G 174 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7350 (mt-10) REVERT: H 31 ASN cc_start: 0.8011 (m-40) cc_final: 0.7525 (m110) REVERT: H 41 TYR cc_start: 0.7534 (t80) cc_final: 0.7268 (t80) REVERT: H 128 MET cc_start: 0.7028 (mmt) cc_final: 0.5830 (mtm) REVERT: H 169 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: H 206 ILE cc_start: 0.6404 (tt) cc_final: 0.6021 (tt) REVERT: I 2 ARG cc_start: 0.6577 (mtp-110) cc_final: 0.6245 (mtp85) REVERT: I 43 ARG cc_start: 0.7639 (tpt170) cc_final: 0.7172 (tpt90) REVERT: I 46 ARG cc_start: 0.6531 (mtt-85) cc_final: 0.6017 (mpt180) REVERT: I 53 GLN cc_start: 0.7708 (mt0) cc_final: 0.7266 (mt0) REVERT: I 104 MET cc_start: 0.6867 (mmm) cc_final: 0.6518 (ttt) REVERT: J 11 GLN cc_start: 0.8057 (tt0) cc_final: 0.7710 (tt0) REVERT: J 146 MET cc_start: 0.7467 (ttp) cc_final: 0.7123 (ttp) REVERT: J 151 MET cc_start: 0.8260 (tpp) cc_final: 0.7372 (ptp) REVERT: K 1 MET cc_start: 0.8304 (ptp) cc_final: 0.7616 (ptp) REVERT: K 44 ARG cc_start: 0.8756 (mtp180) cc_final: 0.8518 (mtp180) REVERT: K 75 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7800 (mt-10) REVERT: L 20 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8183 (mm-30) REVERT: L 102 TRP cc_start: 0.7586 (m-10) cc_final: 0.7101 (m-10) REVERT: L 113 LYS cc_start: 0.6304 (mmtt) cc_final: 0.6028 (tptt) REVERT: L 138 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6847 (tm-30) REVERT: M 4 ASP cc_start: 0.8153 (t0) cc_final: 0.7578 (t0) REVERT: M 79 ARG cc_start: 0.9323 (mtm110) cc_final: 0.8757 (mtm110) REVERT: M 89 ASP cc_start: 0.9056 (m-30) cc_final: 0.8757 (m-30) REVERT: N 45 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7368 (ptp) REVERT: N 79 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8085 (ttp80) REVERT: N 108 ARG cc_start: 0.8632 (mtm180) cc_final: 0.7827 (mtm-85) REVERT: N 125 GLN cc_start: 0.7056 (tt0) cc_final: 0.6514 (tt0) REVERT: O 16 ARG cc_start: 0.7690 (ptt180) cc_final: 0.7373 (ttt90) REVERT: P 96 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7157 (mp) REVERT: Q 108 ASP cc_start: 0.7736 (t0) cc_final: 0.7285 (t0) REVERT: Q 110 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7306 (mtmt) REVERT: R 11 HIS cc_start: 0.5993 (p-80) cc_final: 0.5559 (p-80) REVERT: R 51 GLN cc_start: 0.7976 (pm20) cc_final: 0.7530 (pm20) REVERT: R 71 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7892 (mt-10) REVERT: R 77 LYS cc_start: 0.8518 (tppp) cc_final: 0.8265 (tppp) REVERT: S 48 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: S 65 GLN cc_start: 0.8219 (mt0) cc_final: 0.7713 (mt0) REVERT: S 88 MET cc_start: 0.7971 (mmt) cc_final: 0.7727 (mmp) REVERT: T 17 ASP cc_start: 0.8310 (p0) cc_final: 0.7831 (p0) REVERT: T 56 LEU cc_start: 0.8875 (mm) cc_final: 0.8582 (mm) REVERT: U 25 ARG cc_start: 0.6839 (mtm180) cc_final: 0.6469 (mtm180) REVERT: V 17 GLU cc_start: 0.7265 (mp0) cc_final: 0.6484 (mp0) REVERT: V 27 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7693 (t80) REVERT: V 41 THR cc_start: 0.5858 (m) cc_final: 0.5460 (m) REVERT: V 72 TRP cc_start: 0.7744 (m100) cc_final: 0.7311 (m100) REVERT: W 29 LYS cc_start: 0.8618 (mttt) cc_final: 0.8234 (mttt) REVERT: W 49 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7439 (tttm) REVERT: X 12 LEU cc_start: 0.8620 (mm) cc_final: 0.8143 (mm) REVERT: X 79 TYR cc_start: 0.7899 (t80) cc_final: 0.7477 (t80) REVERT: Y 26 MET cc_start: 0.7983 (tmm) cc_final: 0.7734 (tmm) REVERT: Y 27 MET cc_start: 0.8412 (mmm) cc_final: 0.8126 (mmm) REVERT: Y 43 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8664 (mmtt) REVERT: Y 54 GLN cc_start: 0.7526 (tm-30) cc_final: 0.6862 (tm-30) REVERT: Y 60 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8206 (mm-40) REVERT: Y 68 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6976 (ptmt) REVERT: Y 73 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7496 (ttp-110) REVERT: Z 19 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7682 (mmtm) REVERT: Z 34 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7131 (mmt90) REVERT: Z 65 ARG cc_start: 0.7634 (tmt170) cc_final: 0.7246 (tmt170) outliers start: 389 outliers final: 310 residues processed: 1808 average time/residue: 1.3930 time to fit residues: 4358.5189 Evaluate side-chains 1938 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1601 time to evaluate : 6.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 188 ARG Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 47 GLU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 111 GLU 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 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 47 ARG Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 77 TYR Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 10.0000 chunk 406 optimal weight: 5.9990 chunk 608 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 647 optimal weight: 10.0000 chunk 694 optimal weight: 20.0000 chunk 503 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 800 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 104 GLN q 43 GLN q 55 GLN u 26 ASN ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS G 121 GLN G 176 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS O 56 HIS ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 163219 Z= 0.223 Angle : 0.626 15.243 244202 Z= 0.322 Chirality : 0.036 0.278 31236 Planarity : 0.005 0.107 13084 Dihedral : 23.282 178.213 81773 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.79 % Favored : 91.03 % Rotamer: Outliers : 6.15 % Allowed : 27.09 % Favored : 66.75 % 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: -2.17 (0.10), residues: 5919 helix: -0.23 (0.12), residues: 1860 sheet: -1.56 (0.16), residues: 1013 loop : -2.21 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 212 HIS 0.017 0.001 HIS f 44 PHE 0.023 0.002 PHE Y 50 TYR 0.023 0.002 TYR K 4 ARG 0.012 0.001 ARG w 73 *********************** 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 1949 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1647 time to evaluate : 6.486 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: b 12 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8332 (ttt90) REVERT: b 25 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8356 (mmtp) REVERT: b 58 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7638 (tttp) REVERT: b 96 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8377 (tmtt) REVERT: b 129 LEU cc_start: 0.8817 (pt) cc_final: 0.8386 (mp) REVERT: b 144 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8374 (mm-30) REVERT: b 188 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6873 (mtp85) REVERT: b 212 TRP cc_start: 0.8096 (p90) cc_final: 0.7732 (p90) REVERT: c 77 ARG cc_start: 0.7752 (ptt90) cc_final: 0.7533 (ptt90) REVERT: c 128 ARG cc_start: 0.7737 (mtp180) cc_final: 0.7353 (mtp180) REVERT: c 168 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: d 24 ASN cc_start: 0.8450 (t0) cc_final: 0.7957 (t0) REVERT: d 91 ASP cc_start: 0.8148 (t0) cc_final: 0.7679 (t0) REVERT: d 145 ASP cc_start: 0.7915 (t0) cc_final: 0.7694 (t0) REVERT: d 157 LEU cc_start: 0.8621 (mm) cc_final: 0.8054 (tt) REVERT: e 15 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7317 (tp) REVERT: e 18 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: e 79 ARG cc_start: 0.6212 (mmt180) cc_final: 0.5906 (tpp-160) REVERT: e 136 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7672 (mp) REVERT: e 139 GLU cc_start: 0.8801 (mp0) cc_final: 0.8477 (mp0) REVERT: e 169 LEU cc_start: 0.8551 (tp) cc_final: 0.8278 (tp) REVERT: f 142 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8643 (tp40) REVERT: f 151 ARG cc_start: 0.8222 (tpt170) cc_final: 0.8001 (mmt90) REVERT: f 162 ARG cc_start: 0.7007 (ptp-170) cc_final: 0.6695 (ptp-170) REVERT: g 27 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7963 (ttm170) REVERT: g 28 ASN cc_start: 0.7983 (m-40) cc_final: 0.7496 (m-40) REVERT: g 46 PHE cc_start: 0.8471 (m-10) cc_final: 0.8143 (m-10) REVERT: h 1 MET cc_start: 0.4162 (ptp) cc_final: 0.2785 (ttp) REVERT: h 52 MET cc_start: 0.1072 (tmm) cc_final: 0.0495 (tmm) REVERT: i 124 MET cc_start: 0.0971 (ppp) cc_final: 0.0737 (ppp) REVERT: j 37 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7639 (ttt-90) REVERT: j 44 TYR cc_start: 0.8556 (t80) cc_final: 0.8308 (t80) REVERT: j 109 LEU cc_start: 0.8462 (mt) cc_final: 0.8117 (mt) REVERT: j 136 GLN cc_start: 0.8752 (mt0) cc_final: 0.8010 (mm-40) REVERT: l 121 THR cc_start: 0.9207 (m) cc_final: 0.8874 (p) REVERT: m 1 MET cc_start: 0.7220 (tpp) cc_final: 0.6934 (tmm) REVERT: m 47 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: n 9 GLN cc_start: 0.8254 (mt0) cc_final: 0.7918 (mt0) REVERT: n 82 GLU cc_start: 0.7310 (mp0) cc_final: 0.6955 (mp0) REVERT: n 110 MET cc_start: 0.7987 (mmt) cc_final: 0.7729 (mmt) REVERT: o 98 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8224 (tp40) REVERT: p 15 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7693 (p0) REVERT: p 26 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7735 (pp20) REVERT: q 15 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8040 (tptt) REVERT: r 13 ARG cc_start: 0.7588 (ttt180) cc_final: 0.7204 (ttt180) REVERT: r 48 LYS cc_start: 0.8848 (ptmm) cc_final: 0.8439 (ptmm) REVERT: r 82 HIS cc_start: 0.8476 (t70) cc_final: 0.8239 (t70) REVERT: r 97 LYS cc_start: 0.8813 (tttt) cc_final: 0.8481 (ttmt) REVERT: s 1 MET cc_start: 0.7028 (tpp) cc_final: 0.5632 (tpt) REVERT: s 86 MET cc_start: 0.7938 (ttp) cc_final: 0.7661 (ttt) REVERT: s 99 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7461 (mtt180) REVERT: t 4 GLU cc_start: 0.8899 (tt0) cc_final: 0.8554 (tt0) REVERT: t 6 ARG cc_start: 0.8896 (tpt-90) cc_final: 0.8572 (tpt170) REVERT: t 12 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7267 (mmp-170) REVERT: u 8 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8072 (t70) REVERT: u 11 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8710 (mt) REVERT: u 36 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7823 (tm-30) REVERT: u 59 GLU cc_start: 0.7450 (tp30) cc_final: 0.7175 (tp30) REVERT: u 72 PHE cc_start: 0.7797 (t80) cc_final: 0.7479 (t80) REVERT: u 100 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7444 (tm-30) REVERT: v 1 MET cc_start: 0.7452 (mmp) cc_final: 0.6708 (tpt) REVERT: v 57 TYR cc_start: 0.7792 (m-80) cc_final: 0.7519 (m-80) REVERT: v 71 LYS cc_start: 0.8054 (pttp) cc_final: 0.7702 (pttp) REVERT: w 39 THR cc_start: 0.7223 (OUTLIER) cc_final: 0.6997 (t) REVERT: w 62 LYS cc_start: 0.8540 (mttm) cc_final: 0.8306 (mtpp) REVERT: w 68 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8155 (mttt) REVERT: x 2 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7681 (mtt180) REVERT: x 16 ASN cc_start: 0.8158 (t0) cc_final: 0.7230 (t0) REVERT: x 49 ARG cc_start: 0.7517 (ttt180) cc_final: 0.7302 (ttt180) REVERT: x 67 LEU cc_start: 0.9240 (tp) cc_final: 0.8921 (mm) REVERT: y 20 ASN cc_start: 0.9193 (m110) cc_final: 0.8825 (t0) REVERT: y 44 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8871 (ttmt) REVERT: y 45 GLN cc_start: 0.7998 (tp40) cc_final: 0.7548 (tp40) REVERT: y 60 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8418 (mmtm) REVERT: z 5 LYS cc_start: 0.7420 (mmmt) cc_final: 0.7019 (mtpp) REVERT: z 20 LYS cc_start: 0.8861 (mttp) cc_final: 0.8485 (mttp) REVERT: z 38 GLU cc_start: 0.8669 (pm20) cc_final: 0.8468 (pm20) REVERT: z 48 ASN cc_start: 0.8565 (t0) cc_final: 0.8288 (t0) REVERT: B 36 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8308 (mttt) REVERT: C 45 HIS cc_start: 0.7996 (m90) cc_final: 0.7204 (m90) REVERT: D 14 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7715 (mtt-85) REVERT: E 48 MET cc_start: 0.7192 (tpp) cc_final: 0.6930 (tpt) REVERT: G 18 GLN cc_start: 0.8606 (mt0) cc_final: 0.8216 (mt0) REVERT: G 35 ASN cc_start: 0.7926 (t0) cc_final: 0.7701 (t0) REVERT: G 99 MET cc_start: 0.8135 (mmm) cc_final: 0.7623 (mmm) REVERT: G 103 TRP cc_start: 0.7791 (t-100) cc_final: 0.7579 (t-100) REVERT: G 142 LYS cc_start: 0.7701 (mmmm) cc_final: 0.7427 (mmtm) REVERT: G 174 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7397 (mt-10) REVERT: G 189 ASN cc_start: 0.7003 (p0) cc_final: 0.6564 (p0) REVERT: H 41 TYR cc_start: 0.7457 (t80) cc_final: 0.7221 (t80) REVERT: H 128 MET cc_start: 0.6937 (mmt) cc_final: 0.5712 (mtm) REVERT: H 167 TYR cc_start: 0.7150 (t80) cc_final: 0.6407 (t80) REVERT: H 206 ILE cc_start: 0.6353 (tt) cc_final: 0.5918 (tt) REVERT: I 2 ARG cc_start: 0.6662 (mtp-110) cc_final: 0.6143 (mtm110) REVERT: I 43 ARG cc_start: 0.7668 (tpt170) cc_final: 0.7189 (tpt90) REVERT: I 46 ARG cc_start: 0.6384 (mtt-85) cc_final: 0.5919 (mpt180) REVERT: I 53 GLN cc_start: 0.7672 (mt0) cc_final: 0.7439 (mt0) REVERT: I 68 GLU cc_start: 0.8394 (tp30) cc_final: 0.8145 (tp30) REVERT: I 80 ARG cc_start: 0.7571 (ptm-80) cc_final: 0.7254 (ptm160) REVERT: I 104 MET cc_start: 0.6767 (mmm) cc_final: 0.6341 (ttt) REVERT: I 195 ASN cc_start: 0.7656 (t0) cc_final: 0.7451 (t0) REVERT: J 146 MET cc_start: 0.7414 (ttp) cc_final: 0.7071 (ttp) REVERT: J 151 MET cc_start: 0.8087 (tpp) cc_final: 0.7233 (ptp) REVERT: K 1 MET cc_start: 0.8263 (ptp) cc_final: 0.7622 (ptp) REVERT: K 62 MET cc_start: 0.8329 (mmt) cc_final: 0.7894 (mmt) REVERT: L 20 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8136 (mm-30) REVERT: L 77 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7221 (ttp80) REVERT: L 102 TRP cc_start: 0.7498 (m-10) cc_final: 0.7069 (m-10) REVERT: L 115 MET cc_start: 0.7200 (mmm) cc_final: 0.6840 (mmm) REVERT: L 138 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7057 (tm-30) REVERT: M 4 ASP cc_start: 0.8216 (t0) cc_final: 0.7432 (t0) REVERT: M 79 ARG cc_start: 0.9327 (mtm110) cc_final: 0.8755 (mtm110) REVERT: M 89 ASP cc_start: 0.9051 (m-30) cc_final: 0.8760 (m-30) REVERT: N 45 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7399 (ptp) REVERT: N 79 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8070 (ttp80) REVERT: N 125 GLN cc_start: 0.6980 (tt0) cc_final: 0.6498 (tt0) REVERT: O 16 ARG cc_start: 0.7619 (ptt180) cc_final: 0.7375 (ttt90) REVERT: O 53 ILE cc_start: 0.7622 (pt) cc_final: 0.7403 (pt) REVERT: O 62 ARG cc_start: 0.7575 (mtt-85) cc_final: 0.7176 (mtp85) REVERT: P 96 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7137 (mp) REVERT: Q 110 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7291 (mtmt) REVERT: R 71 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7979 (mt-10) REVERT: R 77 LYS cc_start: 0.8479 (tppp) cc_final: 0.8200 (tppt) REVERT: S 48 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: S 65 GLN cc_start: 0.8186 (mt0) cc_final: 0.7642 (mt0) REVERT: T 17 ASP cc_start: 0.8436 (p0) cc_final: 0.7950 (p0) REVERT: T 34 GLN cc_start: 0.8432 (mm110) cc_final: 0.8195 (mm110) REVERT: T 56 LEU cc_start: 0.8816 (mm) cc_final: 0.8554 (mm) REVERT: T 67 ASP cc_start: 0.8079 (m-30) cc_final: 0.7856 (m-30) REVERT: U 18 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7201 (mm-40) REVERT: U 25 ARG cc_start: 0.6808 (mtm180) cc_final: 0.6408 (mtm180) REVERT: U 35 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7507 (ttp80) REVERT: V 5 ARG cc_start: 0.6283 (ptp-170) cc_final: 0.6071 (ptp-110) REVERT: V 17 GLU cc_start: 0.7197 (mp0) cc_final: 0.6450 (mp0) REVERT: V 27 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7636 (t80) REVERT: V 41 THR cc_start: 0.5705 (m) cc_final: 0.5290 (m) REVERT: V 72 TRP cc_start: 0.7777 (m100) cc_final: 0.7408 (m100) REVERT: V 79 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7609 (tm-30) REVERT: W 22 TYR cc_start: 0.7922 (p90) cc_final: 0.7701 (p90) REVERT: W 29 LYS cc_start: 0.8575 (mttt) cc_final: 0.8175 (mttt) REVERT: W 49 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7351 (tttm) REVERT: X 12 LEU cc_start: 0.8591 (mm) cc_final: 0.7906 (mm) REVERT: X 56 HIS cc_start: 0.7984 (m90) cc_final: 0.7349 (m90) REVERT: X 64 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8230 (mm-30) REVERT: X 77 ARG cc_start: 0.5475 (mtm-85) cc_final: 0.5213 (mtm-85) REVERT: X 79 TYR cc_start: 0.7910 (t80) cc_final: 0.7445 (t80) REVERT: Y 43 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8785 (mmtt) REVERT: Y 54 GLN cc_start: 0.7481 (tm-30) cc_final: 0.6831 (tm-30) REVERT: Y 60 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8205 (mm-40) REVERT: Y 68 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6989 (ptmt) REVERT: Z 19 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7630 (mmtm) outliers start: 302 outliers final: 237 residues processed: 1778 average time/residue: 1.4825 time to fit residues: 4590.1983 Evaluate side-chains 1847 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1586 time to evaluate : 6.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 188 ARG Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 142 GLN Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 47 GLU Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 96 ILE Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 128 THR Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 40 GLN Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 10.0000 chunk 976 optimal weight: 9.9990 chunk 890 optimal weight: 10.0000 chunk 949 optimal weight: 50.0000 chunk 975 optimal weight: 10.0000 chunk 571 optimal weight: 50.0000 chunk 413 optimal weight: 10.0000 chunk 745 optimal weight: 10.0000 chunk 291 optimal weight: 0.9990 chunk 857 optimal weight: 10.0000 chunk 897 optimal weight: 10.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN o 104 GLN p 51 ASN q 55 GLN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 HIS ** y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN G 176 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS N 109 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.148 163219 Z= 0.468 Angle : 0.792 16.361 244202 Z= 0.397 Chirality : 0.044 0.328 31236 Planarity : 0.006 0.093 13084 Dihedral : 23.344 179.874 81772 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.17 % Favored : 88.65 % Rotamer: Outliers : 6.86 % Allowed : 26.58 % Favored : 66.55 % 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: -2.44 (0.10), residues: 5919 helix: -0.46 (0.12), residues: 1844 sheet: -1.66 (0.16), residues: 1030 loop : -2.39 (0.10), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 212 HIS 0.020 0.002 HIS b 24 PHE 0.030 0.002 PHE g 29 TYR 0.023 0.002 TYR r 2 ARG 0.013 0.001 ARG w 73 *********************** 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 1924 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1587 time to evaluate : 8.597 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: b 12 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8351 (ttt90) REVERT: b 25 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8149 (mmtp) REVERT: b 58 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7675 (tttp) REVERT: b 96 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8375 (tmtt) REVERT: b 144 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8291 (mm-30) REVERT: b 149 LYS cc_start: 0.8732 (tptm) cc_final: 0.8132 (tptm) REVERT: b 188 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6959 (mtp85) REVERT: b 212 TRP cc_start: 0.8186 (p90) cc_final: 0.7869 (p90) REVERT: c 128 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7436 (mtp180) REVERT: c 168 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: c 208 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8544 (mtpt) REVERT: d 24 ASN cc_start: 0.8524 (t0) cc_final: 0.8065 (t0) REVERT: d 91 ASP cc_start: 0.8311 (t0) cc_final: 0.7818 (t0) REVERT: d 145 ASP cc_start: 0.8014 (t0) cc_final: 0.7726 (t0) REVERT: d 157 LEU cc_start: 0.8656 (mm) cc_final: 0.8096 (tt) REVERT: e 15 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7710 (tp) REVERT: e 18 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: e 79 ARG cc_start: 0.6052 (mmt180) cc_final: 0.5696 (tpp-160) REVERT: e 136 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7545 (mp) REVERT: e 139 GLU cc_start: 0.8839 (mp0) cc_final: 0.8468 (mp0) REVERT: e 169 LEU cc_start: 0.8570 (tp) cc_final: 0.8297 (tp) REVERT: f 41 GLU cc_start: 0.8856 (tp30) cc_final: 0.8482 (mm-30) REVERT: f 142 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8924 (tp40) REVERT: g 27 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8107 (ttm170) REVERT: g 28 ASN cc_start: 0.8162 (m-40) cc_final: 0.7787 (m-40) REVERT: g 46 PHE cc_start: 0.8653 (m-10) cc_final: 0.8245 (m-10) REVERT: h 1 MET cc_start: 0.3935 (ptp) cc_final: 0.2593 (ttp) REVERT: h 52 MET cc_start: 0.1165 (tmm) cc_final: 0.0595 (tmm) REVERT: j 37 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7553 (ttt-90) REVERT: j 44 TYR cc_start: 0.8603 (t80) cc_final: 0.8359 (t80) REVERT: j 136 GLN cc_start: 0.8749 (mt0) cc_final: 0.8043 (mm-40) REVERT: l 121 THR cc_start: 0.9165 (m) cc_final: 0.8798 (p) REVERT: m 1 MET cc_start: 0.7279 (tpp) cc_final: 0.7002 (tmm) REVERT: m 3 GLN cc_start: 0.8601 (tt0) cc_final: 0.8267 (tp-100) REVERT: m 12 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7371 (ptm) REVERT: n 9 GLN cc_start: 0.8341 (mt0) cc_final: 0.7987 (mt0) REVERT: n 82 GLU cc_start: 0.7420 (mp0) cc_final: 0.7073 (mp0) REVERT: n 110 MET cc_start: 0.8032 (mmt) cc_final: 0.7797 (mmt) REVERT: p 15 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7780 (p0) REVERT: p 26 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7786 (pp20) REVERT: p 112 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7250 (mtm180) REVERT: q 15 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8135 (tptt) REVERT: q 84 LYS cc_start: 0.8595 (mttt) cc_final: 0.8256 (mtmt) REVERT: r 13 ARG cc_start: 0.7595 (ttt180) cc_final: 0.7292 (ttt180) REVERT: r 97 LYS cc_start: 0.8820 (tttt) cc_final: 0.8488 (ttmt) REVERT: s 1 MET cc_start: 0.6913 (tpp) cc_final: 0.5328 (tpt) REVERT: s 86 MET cc_start: 0.7939 (ttp) cc_final: 0.7674 (ttt) REVERT: s 99 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7446 (mtt180) REVERT: t 6 ARG cc_start: 0.8992 (tpt-90) cc_final: 0.8590 (tpt170) REVERT: t 9 LYS cc_start: 0.8415 (mtpt) cc_final: 0.7969 (mttp) REVERT: t 12 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7348 (mmp-170) REVERT: t 42 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7555 (mt-10) REVERT: t 50 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8957 (tp) REVERT: u 8 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8138 (t70) REVERT: u 11 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8811 (mt) REVERT: u 36 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7831 (tm-30) REVERT: u 59 GLU cc_start: 0.7454 (tp30) cc_final: 0.7073 (tp30) REVERT: u 100 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7140 (tm-30) REVERT: v 1 MET cc_start: 0.7455 (mmp) cc_final: 0.6460 (tpt) REVERT: v 57 TYR cc_start: 0.7847 (m-80) cc_final: 0.7593 (m-80) REVERT: v 71 LYS cc_start: 0.8078 (pttp) cc_final: 0.7736 (pttp) REVERT: w 39 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7081 (t) REVERT: w 62 LYS cc_start: 0.8579 (mttm) cc_final: 0.8329 (mtpp) REVERT: w 68 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8300 (mttt) REVERT: x 2 ARG cc_start: 0.8118 (mtt90) cc_final: 0.7686 (mtt180) REVERT: x 16 ASN cc_start: 0.8228 (t0) cc_final: 0.7265 (t0) REVERT: y 20 ASN cc_start: 0.9241 (m110) cc_final: 0.8947 (t0) REVERT: y 44 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8919 (ttmt) REVERT: y 45 GLN cc_start: 0.8199 (tp40) cc_final: 0.7746 (tp40) REVERT: z 5 LYS cc_start: 0.7357 (mmmt) cc_final: 0.6926 (mtpp) REVERT: z 38 GLU cc_start: 0.8710 (pm20) cc_final: 0.8466 (pm20) REVERT: z 48 ASN cc_start: 0.8760 (t0) cc_final: 0.8285 (t0) REVERT: B 36 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8328 (mttt) REVERT: C 45 HIS cc_start: 0.8171 (m90) cc_final: 0.7295 (m90) REVERT: D 14 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7780 (mtt-85) REVERT: E 48 MET cc_start: 0.7275 (tpp) cc_final: 0.6969 (tpt) REVERT: G 18 GLN cc_start: 0.8609 (mt0) cc_final: 0.8230 (mt0) REVERT: G 35 ASN cc_start: 0.7919 (t0) cc_final: 0.7702 (t0) REVERT: G 99 MET cc_start: 0.8040 (mmm) cc_final: 0.7780 (mmm) REVERT: G 142 LYS cc_start: 0.7733 (mmmm) cc_final: 0.7359 (mtpt) REVERT: H 31 ASN cc_start: 0.8037 (m-40) cc_final: 0.7589 (m110) REVERT: H 41 TYR cc_start: 0.7523 (t80) cc_final: 0.7299 (t80) REVERT: H 122 GLN cc_start: 0.8287 (mt0) cc_final: 0.7348 (mt0) REVERT: H 128 MET cc_start: 0.6981 (mmt) cc_final: 0.5697 (mtm) REVERT: H 169 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: H 206 ILE cc_start: 0.6358 (tt) cc_final: 0.5974 (tt) REVERT: I 2 ARG cc_start: 0.6571 (mtp-110) cc_final: 0.5962 (mtm110) REVERT: I 43 ARG cc_start: 0.7793 (tpt170) cc_final: 0.7313 (tpt90) REVERT: I 46 ARG cc_start: 0.6577 (mtt-85) cc_final: 0.6039 (mpt180) REVERT: I 53 GLN cc_start: 0.7830 (mt0) cc_final: 0.7368 (mt0) REVERT: I 104 MET cc_start: 0.7062 (mmm) cc_final: 0.6658 (ttt) REVERT: J 146 MET cc_start: 0.7512 (ttp) cc_final: 0.7126 (ttp) REVERT: J 151 MET cc_start: 0.8252 (tpp) cc_final: 0.7362 (ptp) REVERT: K 1 MET cc_start: 0.8450 (ptp) cc_final: 0.7860 (ptp) REVERT: L 20 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8185 (mm-30) REVERT: L 77 ARG cc_start: 0.7457 (ttp80) cc_final: 0.6590 (ttm170) REVERT: L 102 TRP cc_start: 0.7631 (m-10) cc_final: 0.7137 (m-10) REVERT: L 115 MET cc_start: 0.7503 (mmm) cc_final: 0.7072 (mmm) REVERT: L 138 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6944 (tm-30) REVERT: M 2 MET cc_start: 0.7773 (tpp) cc_final: 0.7450 (tpt) REVERT: M 4 ASP cc_start: 0.8038 (t0) cc_final: 0.7448 (t0) REVERT: M 79 ARG cc_start: 0.9324 (mtm110) cc_final: 0.8599 (mtm110) REVERT: M 89 ASP cc_start: 0.9055 (m-30) cc_final: 0.8748 (m-30) REVERT: N 45 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7397 (ptp) REVERT: N 108 ARG cc_start: 0.8625 (mtm180) cc_final: 0.7809 (mtm-85) REVERT: N 125 GLN cc_start: 0.7068 (tt0) cc_final: 0.6510 (tt0) REVERT: O 9 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7702 (mtp85) REVERT: O 16 ARG cc_start: 0.7654 (ptt180) cc_final: 0.7127 (ptm160) REVERT: P 96 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7157 (mp) REVERT: Q 108 ASP cc_start: 0.7618 (t0) cc_final: 0.7281 (t0) REVERT: Q 110 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7281 (mtmt) REVERT: R 77 LYS cc_start: 0.8448 (tppp) cc_final: 0.8165 (tppt) REVERT: S 65 GLN cc_start: 0.8219 (mt0) cc_final: 0.7958 (mt0) REVERT: S 88 MET cc_start: 0.8410 (mmp) cc_final: 0.8174 (mmt) REVERT: T 17 ASP cc_start: 0.8031 (p0) cc_final: 0.7475 (p0) REVERT: T 27 GLN cc_start: 0.8541 (mt0) cc_final: 0.8227 (mt0) REVERT: T 56 LEU cc_start: 0.8871 (mm) cc_final: 0.8589 (mm) REVERT: T 70 LYS cc_start: 0.8166 (tppt) cc_final: 0.7942 (ttmt) REVERT: U 25 ARG cc_start: 0.6835 (mtm180) cc_final: 0.6595 (mtm180) REVERT: V 17 GLU cc_start: 0.7262 (mp0) cc_final: 0.6517 (mp0) REVERT: V 27 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7692 (t80) REVERT: V 41 THR cc_start: 0.5743 (m) cc_final: 0.5307 (m) REVERT: V 72 TRP cc_start: 0.7905 (m100) cc_final: 0.7503 (m100) REVERT: W 22 TYR cc_start: 0.7933 (p90) cc_final: 0.7694 (p90) REVERT: W 29 LYS cc_start: 0.8591 (mttt) cc_final: 0.8188 (mtmm) REVERT: W 49 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7457 (tttm) REVERT: X 79 TYR cc_start: 0.7860 (t80) cc_final: 0.7484 (t80) REVERT: Y 43 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8682 (mmtt) REVERT: Y 54 GLN cc_start: 0.7535 (tm-30) cc_final: 0.6839 (tm-30) REVERT: Y 60 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8255 (mm-40) REVERT: Y 68 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6999 (ptmt) REVERT: Z 19 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7799 (mmtm) REVERT: Z 33 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7427 (mtt90) REVERT: Z 65 ARG cc_start: 0.7648 (tmt170) cc_final: 0.7370 (tmt170) outliers start: 337 outliers final: 279 residues processed: 1736 average time/residue: 1.3343 time to fit residues: 3978.7340 Evaluate side-chains 1875 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1571 time to evaluate : 6.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 188 ARG Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 142 GLN Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 111 GLU 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 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 32 GLU Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 77 TYR Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 50.0000 chunk 623 optimal weight: 30.0000 chunk 1003 optimal weight: 7.9990 chunk 612 optimal weight: 10.0000 chunk 476 optimal weight: 7.9990 chunk 697 optimal weight: 20.0000 chunk 1053 optimal weight: 10.0000 chunk 969 optimal weight: 7.9990 chunk 838 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 647 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 119 ASN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN o 98 GLN o 104 GLN q 55 GLN ** r 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS N 109 GLN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.142 163219 Z= 0.497 Angle : 0.819 15.351 244202 Z= 0.411 Chirality : 0.045 0.404 31236 Planarity : 0.006 0.085 13084 Dihedral : 23.451 179.537 81772 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.98 % Favored : 88.80 % Rotamer: Outliers : 6.97 % Allowed : 26.67 % Favored : 66.37 % 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: -2.60 (0.10), residues: 5919 helix: -0.59 (0.12), residues: 1841 sheet: -1.76 (0.16), residues: 1009 loop : -2.48 (0.10), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 212 HIS 0.041 0.002 HIS f 44 PHE 0.035 0.002 PHE g 29 TYR 0.027 0.003 TYR K 4 ARG 0.024 0.001 ARG N 108 ********************** 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 1927 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1585 time to evaluate : 6.217 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: b 12 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8371 (ttt90) REVERT: b 25 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8194 (mmtp) REVERT: b 58 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7678 (tttp) REVERT: b 96 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8400 (tmtt) REVERT: b 99 GLU cc_start: 0.7682 (tt0) cc_final: 0.7478 (tt0) REVERT: b 144 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8318 (mm-30) REVERT: b 149 LYS cc_start: 0.8934 (tptm) cc_final: 0.8278 (tptm) REVERT: b 179 GLU cc_start: 0.6628 (tt0) cc_final: 0.6317 (tt0) REVERT: b 188 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7082 (mtp85) REVERT: b 212 TRP cc_start: 0.8078 (p90) cc_final: 0.7832 (p90) REVERT: c 128 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7452 (mtp180) REVERT: c 168 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: c 208 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8503 (mtpt) REVERT: d 24 ASN cc_start: 0.8519 (t0) cc_final: 0.8066 (t0) REVERT: d 91 ASP cc_start: 0.8332 (t0) cc_final: 0.7839 (t0) REVERT: d 145 ASP cc_start: 0.8069 (t0) cc_final: 0.7804 (t0) REVERT: d 157 LEU cc_start: 0.8617 (mm) cc_final: 0.8075 (tt) REVERT: e 15 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7745 (tp) REVERT: e 18 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: e 79 ARG cc_start: 0.6065 (mmt180) cc_final: 0.5714 (tpp-160) REVERT: e 136 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7668 (mp) REVERT: e 169 LEU cc_start: 0.8546 (tp) cc_final: 0.8278 (tp) REVERT: f 41 GLU cc_start: 0.8898 (tp30) cc_final: 0.8536 (mm-30) REVERT: f 150 TYR cc_start: 0.8121 (m-80) cc_final: 0.7811 (m-80) REVERT: f 151 ARG cc_start: 0.8195 (tpt170) cc_final: 0.7927 (mmt90) REVERT: g 27 ARG cc_start: 0.8315 (ttp-170) cc_final: 0.8113 (ttm170) REVERT: g 28 ASN cc_start: 0.8218 (m-40) cc_final: 0.7812 (m-40) REVERT: g 46 PHE cc_start: 0.8576 (m-10) cc_final: 0.8217 (m-10) REVERT: h 1 MET cc_start: 0.4023 (ptp) cc_final: 0.2703 (ttm) REVERT: h 52 MET cc_start: 0.1490 (tmm) cc_final: 0.0855 (tmm) REVERT: j 37 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7583 (ttt-90) REVERT: j 44 TYR cc_start: 0.8613 (t80) cc_final: 0.8282 (t80) REVERT: j 136 GLN cc_start: 0.8741 (mt0) cc_final: 0.8010 (mm-40) REVERT: k 93 GLN cc_start: 0.6946 (mp10) cc_final: 0.6695 (mp10) REVERT: l 121 THR cc_start: 0.9174 (m) cc_final: 0.8795 (p) REVERT: m 3 GLN cc_start: 0.8616 (tt0) cc_final: 0.8326 (tp-100) REVERT: m 12 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7290 (ptm) REVERT: n 9 GLN cc_start: 0.8366 (mt0) cc_final: 0.7999 (mt0) REVERT: n 82 GLU cc_start: 0.7333 (mp0) cc_final: 0.7034 (mp0) REVERT: n 110 MET cc_start: 0.8095 (mmt) cc_final: 0.7865 (mmt) REVERT: p 26 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7636 (pp20) REVERT: p 28 LYS cc_start: 0.8415 (mttp) cc_final: 0.7863 (mttp) REVERT: p 112 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7327 (mtm180) REVERT: q 15 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8152 (tptt) REVERT: q 84 LYS cc_start: 0.8604 (mttt) cc_final: 0.8352 (mtmm) REVERT: r 13 ARG cc_start: 0.7614 (ttt180) cc_final: 0.7332 (ttt180) REVERT: r 97 LYS cc_start: 0.8956 (tttt) cc_final: 0.8638 (ttmt) REVERT: s 1 MET cc_start: 0.6875 (tpp) cc_final: 0.5138 (tpt) REVERT: s 86 MET cc_start: 0.7948 (ttp) cc_final: 0.7683 (ttt) REVERT: s 99 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.7797 (mtt-85) REVERT: t 4 GLU cc_start: 0.8847 (tt0) cc_final: 0.8557 (tt0) REVERT: t 6 ARG cc_start: 0.8979 (tpt-90) cc_final: 0.8710 (tpt170) REVERT: t 9 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8027 (mttp) REVERT: t 12 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7322 (mmp-170) REVERT: t 50 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8974 (tp) REVERT: u 8 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8074 (t70) REVERT: u 59 GLU cc_start: 0.7467 (tp30) cc_final: 0.7072 (tp30) REVERT: v 1 MET cc_start: 0.7465 (mmp) cc_final: 0.6438 (tpt) REVERT: v 57 TYR cc_start: 0.8027 (m-80) cc_final: 0.7824 (m-80) REVERT: v 71 LYS cc_start: 0.8050 (pttp) cc_final: 0.7710 (pttp) REVERT: v 80 HIS cc_start: 0.8672 (t-90) cc_final: 0.8447 (t-90) REVERT: w 62 LYS cc_start: 0.8576 (mttm) cc_final: 0.8334 (mtpp) REVERT: w 68 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8307 (mttt) REVERT: x 2 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7651 (mtt180) REVERT: x 16 ASN cc_start: 0.8229 (t0) cc_final: 0.7258 (t0) REVERT: x 49 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7544 (ttt180) REVERT: y 20 ASN cc_start: 0.9247 (m110) cc_final: 0.8956 (t0) REVERT: y 45 GLN cc_start: 0.8121 (tp40) cc_final: 0.7601 (tp40) REVERT: z 5 LYS cc_start: 0.7378 (mmmt) cc_final: 0.6876 (mttm) REVERT: z 20 LYS cc_start: 0.8969 (mttp) cc_final: 0.8632 (mttp) REVERT: z 38 GLU cc_start: 0.8728 (pm20) cc_final: 0.8490 (pm20) REVERT: z 48 ASN cc_start: 0.8821 (t0) cc_final: 0.8561 (t0) REVERT: B 36 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8343 (mttt) REVERT: C 45 HIS cc_start: 0.8071 (m90) cc_final: 0.7222 (m90) REVERT: D 14 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7815 (mtt-85) REVERT: E 48 MET cc_start: 0.7311 (tpp) cc_final: 0.7039 (tpt) REVERT: G 18 GLN cc_start: 0.8687 (mt0) cc_final: 0.8320 (mt0) REVERT: G 35 ASN cc_start: 0.7927 (t0) cc_final: 0.7711 (t0) REVERT: G 99 MET cc_start: 0.8045 (mmm) cc_final: 0.7668 (mmm) REVERT: G 142 LYS cc_start: 0.7676 (mmmm) cc_final: 0.7364 (mmtm) REVERT: H 28 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.6989 (t80) REVERT: H 41 TYR cc_start: 0.7496 (t80) cc_final: 0.7219 (t80) REVERT: H 128 MET cc_start: 0.7015 (mmt) cc_final: 0.5775 (mtm) REVERT: H 169 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: H 206 ILE cc_start: 0.6375 (tt) cc_final: 0.5957 (tt) REVERT: I 2 ARG cc_start: 0.6456 (mtp-110) cc_final: 0.6109 (mtm110) REVERT: I 43 ARG cc_start: 0.7762 (tpt170) cc_final: 0.7365 (tpt90) REVERT: I 46 ARG cc_start: 0.6543 (mtt-85) cc_final: 0.5943 (mpt180) REVERT: I 53 GLN cc_start: 0.7856 (mt0) cc_final: 0.7386 (mt0) REVERT: I 104 MET cc_start: 0.6899 (mmm) cc_final: 0.6469 (ttt) REVERT: J 146 MET cc_start: 0.7537 (ttp) cc_final: 0.7149 (ttp) REVERT: K 1 MET cc_start: 0.8501 (ptp) cc_final: 0.8035 (ptp) REVERT: K 8 PHE cc_start: 0.8282 (p90) cc_final: 0.8077 (p90) REVERT: K 62 MET cc_start: 0.8453 (mmt) cc_final: 0.8016 (mmt) REVERT: K 75 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7958 (mt-10) REVERT: L 20 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8141 (mm-30) REVERT: L 102 TRP cc_start: 0.7650 (m-10) cc_final: 0.7168 (m-10) REVERT: L 115 MET cc_start: 0.7271 (mmm) cc_final: 0.6865 (mmm) REVERT: L 138 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7130 (tm-30) REVERT: M 2 MET cc_start: 0.7714 (tpp) cc_final: 0.7501 (tpp) REVERT: M 4 ASP cc_start: 0.7913 (t0) cc_final: 0.7317 (t0) REVERT: M 79 ARG cc_start: 0.9322 (mtm110) cc_final: 0.8594 (mtm110) REVERT: M 89 ASP cc_start: 0.9057 (m-30) cc_final: 0.8754 (m-30) REVERT: N 45 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7529 (ptp) REVERT: N 79 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8008 (ttp80) REVERT: N 125 GLN cc_start: 0.7066 (tt0) cc_final: 0.6506 (tt0) REVERT: O 9 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7615 (mtm180) REVERT: O 16 ARG cc_start: 0.7749 (ptt180) cc_final: 0.7130 (ptm160) REVERT: O 25 ILE cc_start: 0.9353 (pt) cc_final: 0.9003 (mm) REVERT: P 96 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7350 (mp) REVERT: Q 108 ASP cc_start: 0.7818 (t0) cc_final: 0.7400 (t0) REVERT: Q 110 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7259 (mtmt) REVERT: R 77 LYS cc_start: 0.8503 (tppp) cc_final: 0.8232 (tppt) REVERT: S 48 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6437 (mp10) REVERT: S 65 GLN cc_start: 0.8238 (mt0) cc_final: 0.7751 (mt0) REVERT: T 17 ASP cc_start: 0.7935 (p0) cc_final: 0.7358 (p0) REVERT: T 27 GLN cc_start: 0.8553 (mt0) cc_final: 0.8227 (mt0) REVERT: T 56 LEU cc_start: 0.8844 (mm) cc_final: 0.8544 (mm) REVERT: T 80 LEU cc_start: 0.8704 (tt) cc_final: 0.8492 (tt) REVERT: V 17 GLU cc_start: 0.7249 (mp0) cc_final: 0.6592 (mp0) REVERT: V 27 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7650 (t80) REVERT: V 41 THR cc_start: 0.5611 (m) cc_final: 0.5177 (m) REVERT: V 72 TRP cc_start: 0.7905 (m100) cc_final: 0.7489 (m100) REVERT: W 29 LYS cc_start: 0.8541 (mttt) cc_final: 0.8151 (mtmm) REVERT: W 49 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7471 (tttm) REVERT: X 12 LEU cc_start: 0.8067 (mm) cc_final: 0.7854 (mm) REVERT: X 79 TYR cc_start: 0.7953 (t80) cc_final: 0.7584 (t80) REVERT: Y 43 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8697 (mmtt) REVERT: Y 54 GLN cc_start: 0.7600 (tm-30) cc_final: 0.6911 (tm-30) REVERT: Y 60 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8261 (mm-40) REVERT: Y 68 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6993 (ptmt) REVERT: Y 73 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7472 (ttp-110) REVERT: Z 19 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7950 (mmtm) REVERT: Z 34 ARG cc_start: 0.7626 (mmt90) cc_final: 0.7095 (mmt90) REVERT: Z 44 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7643 (mtt-85) outliers start: 342 outliers final: 297 residues processed: 1747 average time/residue: 1.3487 time to fit residues: 4053.7118 Evaluate side-chains 1892 residues out of total 4909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1571 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 25 LYS Chi-restraints excluded: chain b residue 37 SER Chi-restraints excluded: chain b residue 44 ASN Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 138 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 172 THR Chi-restraints excluded: chain b residue 188 ARG Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 256 THR Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 97 SER Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 126 ASN Chi-restraints excluded: chain c residue 131 ASP Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 53 THR Chi-restraints excluded: chain d residue 109 LEU Chi-restraints excluded: chain d residue 116 ASP Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 112 ASP Chi-restraints excluded: chain e residue 126 ASN Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 103 ASN Chi-restraints excluded: chain f residue 130 ILE Chi-restraints excluded: chain f residue 142 GLN Chi-restraints excluded: chain f residue 146 ASP Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain f residue 167 VAL Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 33 ASN Chi-restraints excluded: chain i residue 125 THR Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 25 LEU Chi-restraints excluded: chain j residue 37 ARG Chi-restraints excluded: chain j residue 49 ASP Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 124 VAL Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 95 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 12 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 75 GLU Chi-restraints excluded: chain m residue 80 VAL Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 111 GLU 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 132 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 32 GLU Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 58 ASP Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 34 HIS Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain o residue 95 SER Chi-restraints excluded: chain o residue 104 GLN Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 28 SER Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 82 LEU Chi-restraints excluded: chain q residue 86 SER Chi-restraints excluded: chain q residue 99 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 11 ARG Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 31 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 60 THR Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 85 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 12 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 53 GLN Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 40 ILE Chi-restraints excluded: chain v residue 53 LYS Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 88 HIS Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 60 ASP Chi-restraints excluded: chain w residue 66 GLU Chi-restraints excluded: chain x residue 22 ASN Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 34 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 31 CYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 147 ASN Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 9 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 109 GLN Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 90 LEU Chi-restraints excluded: chain O residue 91 ASP Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 35 ASP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 19 ASN Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 95 HIS Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 22 TYR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 5 MET Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain U residue 9 HIS Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 68 LYS Chi-restraints excluded: chain Y residue 73 ARG Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 50 SER Chi-restraints excluded: chain Z residue 52 VAL Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 25 GLU Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 2.9990 chunk 666 optimal weight: 8.9990 chunk 893 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 773 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 chunk 839 optimal weight: 50.0000 chunk 351 optimal weight: 6.9990 chunk 862 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 HIS ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 119 ASN ** i 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 128 ASN ** l 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 55 GLN ** v 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN L 141 HIS M 75 GLN N 109 GLN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104857 restraints weight = 320199.360| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.39 r_work: 0.3302 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 163219 Z= 0.290 Angle : 0.679 16.225 244202 Z= 0.347 Chirality : 0.039 0.645 31236 Planarity : 0.005 0.083 13084 Dihedral : 23.415 179.740 81772 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.78 % Favored : 90.07 % Rotamer: Outliers : 5.83 % Allowed : 28.05 % 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: -2.32 (0.10), residues: 5919 helix: -0.37 (0.12), residues: 1861 sheet: -1.61 (0.16), residues: 1001 loop : -2.31 (0.10), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP X 33 HIS 0.034 0.002 HIS f 44 PHE 0.032 0.002 PHE g 29 TYR 0.021 0.002 TYR r 2 ARG 0.019 0.001 ARG w 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57401.56 seconds wall clock time: 994 minutes 44.44 seconds (59684.44 seconds total)