Starting phenix.real_space_refine on Sun Mar 24 01:47:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogg_20057/03_2024/6ogg_20057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogg_20057/03_2024/6ogg_20057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogg_20057/03_2024/6ogg_20057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogg_20057/03_2024/6ogg_20057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogg_20057/03_2024/6ogg_20057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogg_20057/03_2024/6ogg_20057.pdb" } resolution = 4.2 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= 0.006 sd= 0.455 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 4650 5.49 5 S 152 5.16 5 C 74487 2.51 5 N 27520 2.21 5 O 40924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 34": "OE1" <-> "OE2" Residue "b ASP 65": "OD1" <-> "OD2" Residue "b PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 18": "OD1" <-> "OD2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 86": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ASP 91": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 122": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 18": "OE1" <-> "OE2" 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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 123": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g ASP 7": "OD1" <-> "OD2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 76": "OE1" <-> "OE2" Residue "g ASP 86": "OD1" <-> "OD2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 149": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ASP 91": "OD1" <-> "OD2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 75": "OE1" <-> "OE2" Residue "m TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 111": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 117": "OD1" <-> "OD2" 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 GLU 60": "OE1" <-> "OE2" Residue "o GLU 80": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ASP 89": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ASP 15": "OD1" <-> "OD2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p GLU 26": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p GLU 101": "OE1" <-> "OE2" 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 "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 46": "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 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u GLU 87": "OE1" <-> "OE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "v PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "x GLU 40": "OE1" <-> "OE2" Residue "x PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "x TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 13": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 38": "OE1" <-> "OE2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I ASP 98": "OD1" <-> "OD2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P ASP 71": "OD1" <-> "OD2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 82": "OE1" <-> "OE2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y ASP 58": "OD1" <-> "OD2" Residue "Z ASP 12": "OD1" <-> "OD2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 166": "OD1" <-> "OD2" Residue "a PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 187": "OE1" <-> "OE2" Residue "a GLU 190": "OE1" <-> "OE2" Residue "8 ASP 13": "OD1" <-> "OD2" Residue "8 ASP 19": "OD1" <-> "OD2" Residue "8 GLU 32": "OE1" <-> "OE2" Residue "8 GLU 35": "OE1" <-> "OE2" Residue "8 GLU 36": "OE1" <-> "OE2" Residue "8 GLU 40": "OE1" <-> "OE2" Residue "8 GLU 42": "OE1" <-> "OE2" Residue "8 GLU 59": "OE1" <-> "OE2" Residue "8 GLU 64": "OE1" <-> "OE2" Residue "8 ASP 68": "OD1" <-> "OD2" Residue "8 GLU 85": "OE1" <-> "OE2" Residue "8 GLU 89": "OE1" <-> "OE2" Residue "8 ASP 92": "OD1" <-> "OD2" Residue "8 GLU 94": "OE1" <-> "OE2" Residue "8 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 140": "OE1" <-> "OE2" Residue "8 GLU 172": "OE1" <-> "OE2" Residue "8 TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 213": "NH1" <-> "NH2" Residue "8 GLU 225": "OE1" <-> "OE2" Residue "8 ASP 227": "OD1" <-> "OD2" Residue "8 ASP 229": "OD1" <-> "OD2" Residue "8 GLU 233": "OE1" <-> "OE2" Residue "8 ASP 242": "OD1" <-> "OD2" Residue "8 GLU 297": "OE1" <-> "OE2" Residue "8 GLU 299": "OE1" <-> "OE2" Residue "8 GLU 341": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147733 Number of models: 1 Model: "" Number of chains: 55 Chain: "b" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} 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: "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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 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: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 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: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} 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: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1756 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "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: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "L" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "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: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 91, 'rna2p_pyr': 50, 'rna3p_pur': 783, 'rna3p_pyr': 615} Link IDs: {'rna2p': 141, 'rna3p': 1397} 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': 226, 'rna2p_pyr': 103, 'rna3p_pur': 1448, 'rna3p_pyr': 1126} Link IDs: {'rna2p': 329, 'rna3p': 2573} 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: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 63} Chain: "4" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 437 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 14, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "8" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2860 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Time building chain proxies: 52.83, per 1000 atoms: 0.36 Number of scatterers: 147733 At special positions: 0 Unit cell: (234.784, 260.13, 265.466, 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 152 16.00 P 4650 15.00 O 40924 8.00 N 27520 7.00 C 74487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.54 Conformation dependent library (CDL) restraints added in 8.0 seconds 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11242 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 78 sheets defined 32.4% alpha, 15.4% beta 1109 base pairs and 2638 stacking pairs defined. Time for finding SS restraints: 47.52 Creating SS restraints... Processing helix chain 'b' and resid 9 through 13 removed outlier: 3.527A pdb=" N ARG b 13 " --> pdb=" O PRO b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 196 through 202 removed outlier: 3.729A pdb=" N HIS b 199 " --> pdb=" O ASN b 196 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 212 removed outlier: 4.028A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG b 211 " --> pdb=" O ALA b 207 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP b 212 " --> pdb=" O GLY b 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 206 through 212' Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.955A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 103 removed outlier: 4.127A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 126 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 removed outlier: 4.264A pdb=" N VAL d 33 " --> pdb=" O HIS d 29 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA d 34 " --> pdb=" O GLN d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.648A pdb=" N ALA d 104 " --> pdb=" O MET d 100 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU d 105 " --> pdb=" O TYR d 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS d 106 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 141 removed outlier: 3.878A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 162 removed outlier: 3.740A pdb=" N ALA d 161 " --> pdb=" O LEU d 157 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.820A pdb=" N LEU d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE d 181 " --> pdb=" O PRO d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 3.897A pdb=" N VAL d 196 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU d 197 " --> pdb=" O VAL d 193 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET d 199 " --> pdb=" O GLN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 16 removed outlier: 4.108A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET e 16 " --> pdb=" O VAL e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 52 removed outlier: 3.753A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 59 removed outlier: 3.837A pdb=" N ALA e 58 " --> pdb=" O ALA e 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 106 removed outlier: 4.096A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA e 106 " --> pdb=" O LEU e 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.761A pdb=" N SER f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 139 through 149 removed outlier: 3.728A pdb=" N ALA f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA f 149 " --> pdb=" O ALA f 145 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 30 removed outlier: 4.269A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.766A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE g 46 " --> pdb=" O LYS g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 69 removed outlier: 3.891A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 88 No H-bonds generated for 'chain 'g' and resid 86 through 88' Processing helix chain 'g' and resid 96 through 107 removed outlier: 4.249A pdb=" N ALA g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 4.176A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG j 35 " --> pdb=" O GLU j 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 removed outlier: 3.621A pdb=" N VAL j 62 " --> pdb=" O ALA j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 71 Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.673A pdb=" N ALA j 94 " --> pdb=" O GLU j 90 " (cutoff:3.500A) Processing helix chain 'j' and resid 98 through 107 Processing helix chain 'j' and resid 112 through 121 removed outlier: 3.551A pdb=" N ARG j 116 " --> pdb=" O GLY j 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 118 removed outlier: 3.531A pdb=" N LEU k 118 " --> pdb=" O LYS k 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 6 removed outlier: 3.526A pdb=" N THR l 5 " --> pdb=" O ARG l 2 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU l 6 " --> pdb=" O LEU l 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 2 through 6' Processing helix chain 'l' and resid 37 through 41 removed outlier: 3.945A pdb=" N ARG l 41 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 74 removed outlier: 3.756A pdb=" N ALA l 71 " --> pdb=" O SER l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 138 removed outlier: 3.670A pdb=" N ILE l 135 " --> pdb=" O ALA l 131 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU l 136 " --> pdb=" O ARG l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 57 Processing helix chain 'm' and resid 109 through 124 removed outlier: 3.509A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.648A pdb=" N ALA n 19 " --> pdb=" O SER n 15 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE n 21 " --> pdb=" O ARG n 17 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 57 removed outlier: 5.464A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.936A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 69 Processing helix chain 'n' and resid 72 through 79 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 20 removed outlier: 3.690A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 62 removed outlier: 3.741A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 82 removed outlier: 3.908A pdb=" N ALA o 71 " --> pdb=" O ASN o 67 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS o 76 " --> pdb=" O ALA o 72 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 113 removed outlier: 4.151A pdb=" N ASP o 108 " --> pdb=" O GLN o 104 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 12 removed outlier: 3.527A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.602A pdb=" N LEU p 99 " --> pdb=" O LEU p 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 108 removed outlier: 3.672A pdb=" N ALA p 107 " --> pdb=" O GLY p 104 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 17 Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 72 removed outlier: 4.408A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA q 37 " --> pdb=" O VAL q 33 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE q 39 " --> pdb=" O PHE q 35 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP q 60 " --> pdb=" O PHE q 56 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE q 61 " --> pdb=" O ARG q 57 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA q 62 " --> pdb=" O GLN q 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA q 67 " --> pdb=" O ARG q 63 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 removed outlier: 4.105A pdb=" N ASN q 80 " --> pdb=" O SER q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 100 removed outlier: 4.021A pdb=" N ASP q 96 " --> pdb=" O LYS q 92 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 117 removed outlier: 3.577A pdb=" N VAL q 109 " --> pdb=" O PHE q 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 23 removed outlier: 3.916A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.700A pdb=" N ALA s 32 " --> pdb=" O LYS s 28 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.653A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 10 removed outlier: 3.799A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 28 removed outlier: 3.611A pdb=" N MET t 24 " --> pdb=" O ALA t 20 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 Processing helix chain 'u' and resid 65 through 67 No H-bonds generated for 'chain 'u' and resid 65 through 67' Processing helix chain 'v' and resid 13 through 23 Processing helix chain 'v' and resid 43 through 49 removed outlier: 4.443A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 58 removed outlier: 3.878A pdb=" N TYR v 57 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 52 through 61 removed outlier: 3.544A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 73 removed outlier: 3.651A pdb=" N ALA x 68 " --> pdb=" O ASP x 64 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 23 removed outlier: 3.611A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) Processing helix chain 'y' and resid 26 through 33 removed outlier: 3.642A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) Processing helix chain 'y' and resid 41 through 61 removed outlier: 4.001A pdb=" N ARG y 52 " --> pdb=" O ARG y 48 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.711A pdb=" N THR z 22 " --> pdb=" O LYS z 18 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU z 23 " --> pdb=" O HIS z 19 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 48 Processing helix chain 'z' and resid 50 through 52 No H-bonds generated for 'chain 'z' and resid 50 through 52' Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 8 through 11 removed outlier: 3.771A pdb=" N LYS E 11 " --> pdb=" O GLY E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 11' Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.635A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 30 through 34 removed outlier: 3.643A pdb=" N LYS F 34 " --> pdb=" O PRO F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 63 removed outlier: 4.168A pdb=" N ALA G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 removed outlier: 4.158A pdb=" N ALA G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 3.608A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 146 removed outlier: 3.574A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 176 removed outlier: 4.112A pdb=" N ILE G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 223 removed outlier: 3.767A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 44 removed outlier: 3.794A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 80 through 92 removed outlier: 3.739A pdb=" N ARG H 87 " --> pdb=" O VAL H 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 110 removed outlier: 4.208A pdb=" N LEU H 110 " --> pdb=" O LYS H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 111 through 124 removed outlier: 4.379A pdb=" N SER H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 4.412A pdb=" N LYS H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL H 137 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 15 removed outlier: 3.664A pdb=" N ARG I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 64 removed outlier: 3.522A pdb=" N GLN I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS I 57 " --> pdb=" O GLN I 53 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG I 62 " --> pdb=" O GLN I 58 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.700A pdb=" N TYR I 75 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 94 removed outlier: 4.390A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.706A pdb=" N LEU I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 154 through 162 removed outlier: 3.814A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 204 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 69 removed outlier: 3.686A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 146 removed outlier: 3.807A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 156 Processing helix chain 'K' and resid 13 through 16 removed outlier: 3.730A pdb=" N GLU K 16 " --> pdb=" O ASP K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 13 through 16' Processing helix chain 'K' and resid 17 through 31 removed outlier: 3.850A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR K 30 " --> pdb=" O THR K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.612A pdb=" N THR K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 4.023A pdb=" N PHE L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 48 removed outlier: 3.524A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 54 Processing helix chain 'L' and resid 91 through 108 removed outlier: 4.109A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG L 108 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 128 removed outlier: 4.155A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 142 removed outlier: 3.614A pdb=" N ARG L 142 " --> pdb=" O GLU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.521A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU M 10 " --> pdb=" O ILE M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 42 removed outlier: 3.786A pdb=" N ALA M 36 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN M 37 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 119 Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.545A pdb=" N TYR N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 33 through 38' Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 85 through 89 removed outlier: 4.043A pdb=" N GLU N 88 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR N 89 " --> pdb=" O LEU N 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 89' Processing helix chain 'N' and resid 90 through 101 removed outlier: 4.372A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 31 removed outlier: 5.228A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 84 removed outlier: 3.665A pdb=" N THR O 83 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL O 84 " --> pdb=" O GLU O 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 80 through 84' Processing helix chain 'P' and resid 45 through 50 removed outlier: 3.728A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 69 Processing helix chain 'P' and resid 95 through 101 removed outlier: 4.242A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 9 Processing helix chain 'Q' and resid 114 through 118 removed outlier: 3.728A pdb=" N VAL Q 118 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 18 Processing helix chain 'R' and resid 28 through 37 removed outlier: 3.799A pdb=" N ILE R 32 " --> pdb=" O ARG R 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.551A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.572A pdb=" N ARG R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET R 80 " --> pdb=" O ILE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.702A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG R 91 " --> pdb=" O GLY R 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY R 93 " --> pdb=" O ARG R 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 9 through 14 removed outlier: 3.841A pdb=" N ALA S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 38 through 46 Processing helix chain 'S' and resid 47 through 50 removed outlier: 3.804A pdb=" N LEU S 50 " --> pdb=" O LEU S 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 47 through 50' Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 79 through 88 removed outlier: 4.110A pdb=" N VAL S 83 " --> pdb=" O SER S 79 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 removed outlier: 3.770A pdb=" N THR T 7 " --> pdb=" O SER T 3 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 43 removed outlier: 3.781A pdb=" N ASN T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.518A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG T 57 " --> pdb=" O ARG T 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU T 69 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS T 70 " --> pdb=" O LEU T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 removed outlier: 3.616A pdb=" N TYR T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 removed outlier: 3.661A pdb=" N TRP U 60 " --> pdb=" O ARG U 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 78 removed outlier: 3.800A pdb=" N ALA U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU U 74 " --> pdb=" O ARG U 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.662A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 64 removed outlier: 4.445A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG W 56 " --> pdb=" O ARG W 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 19 removed outlier: 3.683A pdb=" N VAL X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 39 removed outlier: 3.943A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS Y 15 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Y 16 " --> pdb=" O GLN Y 12 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN Y 20 " --> pdb=" O ALA Y 16 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA Y 21 " --> pdb=" O ARG Y 17 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 52 Processing helix chain 'Y' and resid 53 through 63 removed outlier: 3.750A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 86 removed outlier: 3.553A pdb=" N LYS Y 75 " --> pdb=" O ALA Y 71 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN Y 77 " --> pdb=" O ARG Y 73 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 42 Processing helix chain 'Z' and resid 43 through 57 removed outlier: 4.241A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG Z 54 " --> pdb=" O SER Z 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 15 removed outlier: 3.870A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 31 removed outlier: 3.679A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU a 29 " --> pdb=" O GLU a 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 34 No H-bonds generated for 'chain 'a' and resid 32 through 34' Processing helix chain 'a' and resid 183 through 199 removed outlier: 3.955A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU a 196 " --> pdb=" O LEU a 192 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA a 199 " --> pdb=" O ALA a 195 " (cutoff:3.500A) Processing helix chain '8' and resid 7 through 26 removed outlier: 3.580A pdb=" N THR 8 15 " --> pdb=" O ILE 8 11 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 8 17 " --> pdb=" O ASP 8 13 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER 8 18 " --> pdb=" O LEU 8 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU 8 21 " --> pdb=" O ARG 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 40 removed outlier: 3.709A pdb=" N LYS 8 31 " --> pdb=" O TYR 8 27 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 48 removed outlier: 3.841A pdb=" N TRP 8 47 " --> pdb=" O PRO 8 44 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN 8 48 " --> pdb=" O ASP 8 45 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 54 Processing helix chain '8' and resid 58 through 63 removed outlier: 4.116A pdb=" N SER 8 62 " --> pdb=" O LYS 8 58 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU 8 63 " --> pdb=" O GLU 8 59 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 58 through 63' Processing helix chain '8' and resid 63 through 79 removed outlier: 3.516A pdb=" N VAL 8 67 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY 8 76 " --> pdb=" O GLN 8 72 " (cutoff:3.500A) Processing helix chain '8' and resid 79 through 84 Processing helix chain '8' and resid 93 through 118 removed outlier: 3.783A pdb=" N ALA 8 111 " --> pdb=" O GLU 8 107 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN 8 112 " --> pdb=" O GLU 8 108 " (cutoff:3.500A) Processing helix chain '8' and resid 138 through 160 removed outlier: 4.481A pdb=" N GLN 8 142 " --> pdb=" O GLY 8 138 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP 8 143 " --> pdb=" O THR 8 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 8 158 " --> pdb=" O ARG 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 192 through 196 removed outlier: 3.599A pdb=" N THR 8 196 " --> pdb=" O ARG 8 193 " (cutoff:3.500A) Processing helix chain '8' and resid 283 through 288 Processing helix chain '8' and resid 288 through 314 removed outlier: 3.651A pdb=" N LYS 8 294 " --> pdb=" O GLN 8 290 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU 8 299 " --> pdb=" O LEU 8 295 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN 8 301 " --> pdb=" O GLU 8 297 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS 8 302 " --> pdb=" O LEU 8 298 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS 8 307 " --> pdb=" O LYS 8 303 " (cutoff:3.500A) Processing helix chain '8' and resid 344 through 349 removed outlier: 3.848A pdb=" N LEU 8 349 " --> pdb=" O THR 8 345 " (cutoff:3.500A) Processing helix chain '8' and resid 354 through 359 removed outlier: 3.878A pdb=" N ALA 8 359 " --> pdb=" O GLN 8 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 7.451A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 6.391A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 4 through 15 removed outlier: 4.705A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE c 27 " --> pdb=" O LEU c 187 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU c 187 " --> pdb=" O ILE c 27 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU c 186 " --> pdb=" O VAL c 180 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL c 180 " --> pdb=" O LEU c 186 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL c 107 " --> pdb=" O SER c 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 34 through 38 removed outlier: 5.540A pdb=" N VAL c 34 " --> pdb=" O THR c 51 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR c 51 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 117 through 118 Processing sheet with id=AA8, first strand: chain 'd' and resid 118 through 120 removed outlier: 3.847A pdb=" N LEU d 147 " --> pdb=" O LYS d 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL d 187 " --> pdb=" O LEU d 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 65 through 68 removed outlier: 6.487A pdb=" N LEU e 65 " --> pdb=" O CYS e 86 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N CYS e 86 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR e 67 " --> pdb=" O ILE e 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 126 through 131 Processing sheet with id=AB2, first strand: chain 'f' and resid 7 through 9 removed outlier: 3.620A pdb=" N GLU f 41 " --> pdb=" O GLY f 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 15 through 19 removed outlier: 3.536A pdb=" N ILE f 25 " --> pdb=" O LEU f 32 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU f 32 " --> pdb=" O ILE f 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 121 through 123 removed outlier: 4.179A pdb=" N THR f 121 " --> pdb=" O LYS f 133 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS f 133 " --> pdb=" O THR f 121 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU f 123 " --> pdb=" O VAL f 131 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL f 131 " --> pdb=" O GLU f 123 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE f 130 " --> pdb=" O LEU f 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 101 through 102 Processing sheet with id=AB6, first strand: chain 'g' and resid 3 through 5 removed outlier: 3.596A pdb=" N VAL g 37 " --> pdb=" O ILE g 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'g' and resid 90 through 91 removed outlier: 4.723A pdb=" N LYS g 83 " --> pdb=" O PHE g 91 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL g 78 " --> pdb=" O ASN g 145 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL g 147 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE g 80 " --> pdb=" O VAL g 147 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL g 142 " --> pdb=" O VAL g 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL g 130 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 122 through 123 removed outlier: 6.477A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'j' and resid 76 through 77 Processing sheet with id=AC1, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.538A pdb=" N LEU k 8 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL k 19 " --> pdb=" O LEU k 8 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 69 through 70 removed outlier: 4.959A pdb=" N VAL k 76 " --> pdb=" O VAL p 72 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY p 68 " --> pdb=" O ASP k 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL p 60 " --> pdb=" O ARG p 71 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU p 33 " --> pdb=" O LYS p 36 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU p 26 " --> pdb=" O VAL p 85 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL p 85 " --> pdb=" O GLU p 26 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LYS p 28 " --> pdb=" O ILE p 83 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE p 83 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N TRP p 30 " --> pdb=" O ASP p 81 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP p 81 " --> pdb=" O TRP p 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 76 through 78 Processing sheet with id=AC4, first strand: chain 'l' and resid 89 through 90 removed outlier: 5.949A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'm' and resid 62 through 65 removed outlier: 6.444A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU m 104 " --> pdb=" O PHE m 31 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE m 31 " --> pdb=" O GLU m 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'm' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.663A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.757A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'o' and resid 49 through 50 Processing sheet with id=AD1, first strand: chain 'p' and resid 89 through 90 removed outlier: 4.471A pdb=" N LYS p 110 " --> pdb=" O ALA p 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 3 through 5 Processing sheet with id=AD3, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.139A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 78 removed outlier: 3.846A pdb=" N ARG r 78 " --> pdb=" O TYR r 83 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 's' and resid 7 through 10 removed outlier: 5.149A pdb=" N ARG s 8 " --> pdb=" O ILE s 103 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE s 103 " --> pdb=" O ARG s 8 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG s 92 " --> pdb=" O PRO s 87 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP s 94 " --> pdb=" O ILE s 85 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE s 85 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE s 96 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS s 83 " --> pdb=" O ILE s 96 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LYS s 98 " --> pdb=" O SER s 81 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER s 81 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 11 through 14 removed outlier: 4.048A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 't' and resid 11 through 14 removed outlier: 4.048A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 't' and resid 67 through 70 Processing sheet with id=AD9, first strand: chain 'u' and resid 34 through 36 removed outlier: 7.346A pdb=" N ILE u 34 " --> pdb=" O LYS u 25 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS u 23 " --> pdb=" O GLU u 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE2, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE3, first strand: chain 'v' and resid 3 through 8 removed outlier: 5.169A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE v 4 " --> pdb=" O THR v 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 18 through 19 removed outlier: 7.195A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'w' and resid 41 through 43 removed outlier: 6.819A pdb=" N HIS w 42 " --> pdb=" O ILE w 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG w 73 " --> pdb=" O LYS w 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'x' and resid 13 through 14 Processing sheet with id=AE7, first strand: chain 'x' and resid 32 through 39 removed outlier: 3.541A pdb=" N ARG x 44 " --> pdb=" O VAL x 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'z' and resid 34 through 38 removed outlier: 3.537A pdb=" N THR z 7 " --> pdb=" O LYS z 55 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AF1, first strand: chain 'C' and resid 6 through 11 Processing sheet with id=AF2, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AF3, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AF4, first strand: chain 'G' and resid 89 through 91 removed outlier: 4.206A pdb=" N PHE G 89 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AF6, first strand: chain 'H' and resid 63 through 68 removed outlier: 6.415A pdb=" N ILE H 63 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN H 101 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL H 65 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA H 103 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE H 67 " --> pdb=" O ALA H 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'H' and resid 164 through 170 removed outlier: 3.989A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 164 through 170 Processing sheet with id=AF9, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AG1, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AG2, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AG3, first strand: chain 'J' and resid 84 through 87 removed outlier: 3.688A pdb=" N PHE J 94 " --> pdb=" O LYS J 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 123 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 43 through 46 removed outlier: 3.994A pdb=" N VAL K 60 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU K 5 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL K 89 " --> pdb=" O GLU K 5 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE K 85 " --> pdb=" O MET K 9 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 35 through 36 Processing sheet with id=AG6, first strand: chain 'M' and resid 49 through 51 Processing sheet with id=AG7, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.633A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.633A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU M 123 " --> pdb=" O SER M 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER M 104 " --> pdb=" O GLU M 123 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE M 125 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 5 through 7 removed outlier: 4.327A pdb=" N TYR N 63 " --> pdb=" O PHE N 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS N 21 " --> pdb=" O ASP N 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 9 through 12 removed outlier: 3.517A pdb=" N ALA O 12 " --> pdb=" O HIS O 70 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 50 through 52 Processing sheet with id=AH3, first strand: chain 'P' and resid 42 through 44 removed outlier: 4.459A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY P 18 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N MET P 84 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA P 20 " --> pdb=" O MET P 84 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS P 86 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE P 22 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR P 107 " --> pdb=" O LYS P 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU P 81 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE P 109 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL P 83 " --> pdb=" O ILE P 109 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 29 through 31 removed outlier: 4.038A pdb=" N LYS Q 29 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS Q 95 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.297A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'U' and resid 50 through 51 removed outlier: 4.969A pdb=" N VAL U 19 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'U' and resid 9 through 11 Processing sheet with id=AH8, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.630A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 57 through 62 removed outlier: 7.368A pdb=" N VAL V 57 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL V 77 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 31 through 32 removed outlier: 7.462A pdb=" N THR X 32 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 170 through 171 removed outlier: 3.650A pdb=" N SER a 213 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '8' and resid 179 through 183 Processing sheet with id=AI4, first strand: chain '8' and resid 213 through 218 removed outlier: 4.667A pdb=" N HIS 8 214 " --> pdb=" O ARG 8 203 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG 8 203 " --> pdb=" O HIS 8 214 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '8' and resid 243 through 244 Processing sheet with id=AI6, first strand: chain '8' and resid 263 through 264 1487 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2736 hydrogen bonds 4682 hydrogen bond angles 0 basepair planarities 1109 basepair parallelities 2638 stacking parallelities Total time for adding SS restraints: 247.14 Time building geometry restraints manager: 59.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 15041 1.32 - 1.44: 68663 1.44 - 1.57: 67083 1.57 - 1.70: 9300 1.70 - 1.82: 274 Bond restraints: 160361 Sorted by residual: bond pdb=" C VAL K 10 " pdb=" N HIS K 11 " ideal model delta sigma weight residual 1.330 1.415 -0.085 1.37e-02 5.33e+03 3.81e+01 bond pdb=" C VAL K 18 " pdb=" N PRO K 19 " ideal model delta sigma weight residual 1.336 1.411 -0.076 1.23e-02 6.61e+03 3.79e+01 bond pdb=" C ILE 8 266 " pdb=" N PRO 8 267 " ideal model delta sigma weight residual 1.334 1.377 -0.044 8.40e-03 1.42e+04 2.72e+01 bond pdb=" C ARG f 152 " pdb=" N PRO f 153 " ideal model delta sigma weight residual 1.330 1.387 -0.057 1.19e-02 7.06e+03 2.28e+01 bond pdb=" C ILE m 96 " pdb=" N GLN m 97 " ideal model delta sigma weight residual 1.327 1.192 0.135 2.86e-02 1.22e+03 2.24e+01 ... (remaining 160356 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.29: 21583 105.29 - 113.11: 99150 113.11 - 120.94: 71717 120.94 - 128.77: 42914 128.77 - 136.59: 4202 Bond angle restraints: 239566 Sorted by residual: angle pdb=" N ILE z 13 " pdb=" CA ILE z 13 " pdb=" C ILE z 13 " ideal model delta sigma weight residual 112.12 106.29 5.83 8.40e-01 1.42e+00 4.82e+01 angle pdb=" C ARG b 211 " pdb=" N TRP b 212 " pdb=" CA TRP b 212 " ideal model delta sigma weight residual 122.56 111.63 10.93 1.72e+00 3.38e-01 4.04e+01 angle pdb=" C ASN J 121 " pdb=" N VAL J 122 " pdb=" CA VAL J 122 " ideal model delta sigma weight residual 121.97 133.14 -11.17 1.80e+00 3.09e-01 3.85e+01 angle pdb=" C LYS Q 42 " pdb=" N LYS Q 43 " pdb=" CA LYS Q 43 " ideal model delta sigma weight residual 121.62 131.03 -9.41 1.57e+00 4.06e-01 3.59e+01 angle pdb=" C LYS P 125 " pdb=" N ARG P 126 " pdb=" CA ARG P 126 " ideal model delta sigma weight residual 122.68 131.30 -8.62 1.47e+00 4.63e-01 3.44e+01 ... (remaining 239561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 91850 35.92 - 71.85: 9610 71.85 - 107.77: 1182 107.77 - 143.70: 13 143.70 - 179.62: 19 Dihedral angle restraints: 102674 sinusoidal: 85248 harmonic: 17426 Sorted by residual: dihedral pdb=" CA HIS E 30 " pdb=" C HIS E 30 " pdb=" N ILE E 31 " pdb=" CA ILE E 31 " ideal model delta harmonic sigma weight residual -180.00 -125.42 -54.58 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ALA g 10 " pdb=" C ALA g 10 " pdb=" N ASN g 11 " pdb=" CA ASN g 11 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " pdb=" C1' G 12286 " ideal model delta sinusoidal sigma weight residual -35.00 33.72 -68.72 1 8.00e+00 1.56e-02 9.56e+01 ... (remaining 102671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 22657 0.085 - 0.169: 7640 0.169 - 0.254: 242 0.254 - 0.339: 18 0.339 - 0.423: 2 Chirality restraints: 30559 Sorted by residual: chirality pdb=" CB ILE a 209 " pdb=" CA ILE a 209 " pdb=" CG1 ILE a 209 " pdb=" CG2 ILE a 209 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CB ILE P 30 " pdb=" CA ILE P 30 " pdb=" CG1 ILE P 30 " pdb=" CG2 ILE P 30 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1' U 12259 " pdb=" O4' U 12259 " pdb=" C2' U 12259 " pdb=" N1 U 12259 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 30556 not shown) Planarity restraints: 13074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 31328 " 0.075 2.00e-02 2.50e+03 3.72e-02 3.11e+01 pdb=" N1 C 31328 " -0.008 2.00e-02 2.50e+03 pdb=" C2 C 31328 " -0.016 2.00e-02 2.50e+03 pdb=" O2 C 31328 " -0.030 2.00e-02 2.50e+03 pdb=" N3 C 31328 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C 31328 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C 31328 " 0.054 2.00e-02 2.50e+03 pdb=" C5 C 31328 " -0.032 2.00e-02 2.50e+03 pdb=" C6 C 31328 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 12356 " -0.064 2.00e-02 2.50e+03 3.67e-02 3.02e+01 pdb=" N1 U 12356 " -0.000 2.00e-02 2.50e+03 pdb=" C2 U 12356 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U 12356 " 0.025 2.00e-02 2.50e+03 pdb=" N3 U 12356 " 0.014 2.00e-02 2.50e+03 pdb=" C4 U 12356 " 0.015 2.00e-02 2.50e+03 pdb=" O4 U 12356 " -0.067 2.00e-02 2.50e+03 pdb=" C5 U 12356 " 0.037 2.00e-02 2.50e+03 pdb=" C6 U 12356 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11818 " -0.073 2.00e-02 2.50e+03 3.66e-02 3.01e+01 pdb=" N1 U 11818 " 0.008 2.00e-02 2.50e+03 pdb=" C2 U 11818 " 0.013 2.00e-02 2.50e+03 pdb=" O2 U 11818 " 0.033 2.00e-02 2.50e+03 pdb=" N3 U 11818 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U 11818 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U 11818 " -0.053 2.00e-02 2.50e+03 pdb=" C5 U 11818 " 0.034 2.00e-02 2.50e+03 pdb=" C6 U 11818 " 0.039 2.00e-02 2.50e+03 ... (remaining 13071 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 5827 2.67 - 3.22: 122126 3.22 - 3.78: 263484 3.78 - 4.34: 365124 4.34 - 4.90: 512067 Nonbonded interactions: 1268628 Sorted by model distance: nonbonded pdb=" NZ LYS s 42 " pdb=" O3' G 12010 " model vdw 2.108 2.520 nonbonded pdb=" OG SER t 17 " pdb=" O3' G 11338 " model vdw 2.156 2.440 nonbonded pdb=" OE1 GLU Q 24 " pdb=" O2' A 3 553 " model vdw 2.160 2.440 nonbonded pdb=" NZ LYS d 95 " pdb=" O2' U 1 658 " model vdw 2.170 2.520 nonbonded pdb=" NZ LYS c 114 " pdb=" OP2 C 12681 " model vdw 2.181 2.520 ... (remaining 1268623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 12.470 Check model and map are aligned: 1.600 Set scattering table: 1.010 Process input model: 505.830 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 529.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 0.135 160361 Z= 0.371 Angle : 0.852 14.552 239566 Z= 0.535 Chirality : 0.069 0.423 30559 Planarity : 0.007 0.078 13074 Dihedral : 22.295 179.625 91432 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.58 % Favored : 89.27 % Rotamer: Outliers : 0.56 % Allowed : 10.74 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.88 (0.08), residues: 6011 helix: -3.81 (0.08), residues: 1606 sheet: -3.00 (0.16), residues: 818 loop : -3.13 (0.08), residues: 3587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP G 95 HIS 0.026 0.003 HIS E 42 PHE 0.028 0.003 PHE H 22 TYR 0.031 0.003 TYR 8 244 ARG 0.019 0.001 ARG N 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 663 time to evaluate : 6.324 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: b 160 TYR cc_start: 0.8368 (p90) cc_final: 0.8066 (p90) REVERT: d 115 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8958 (tp40) REVERT: e 25 MET cc_start: 0.7943 (mmt) cc_final: 0.7387 (mmt) REVERT: e 137 PHE cc_start: 0.8091 (m-80) cc_final: 0.7728 (m-80) REVERT: f 136 ASP cc_start: 0.7302 (t0) cc_final: 0.6875 (t0) REVERT: f 150 TYR cc_start: 0.5622 (m-10) cc_final: 0.5287 (m-10) REVERT: g 35 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8262 (mtmt) REVERT: j 108 MET cc_start: 0.7655 (ttm) cc_final: 0.7328 (tpp) REVERT: k 1 MET cc_start: 0.6918 (ttt) cc_final: 0.6203 (ttp) REVERT: k 73 ASP cc_start: 0.8786 (p0) cc_final: 0.8011 (p0) REVERT: k 88 ASN cc_start: 0.9082 (t0) cc_final: 0.8782 (t0) REVERT: k 106 GLU cc_start: 0.8310 (tp30) cc_final: 0.7848 (tp30) REVERT: l 55 MET cc_start: 0.8911 (tpp) cc_final: 0.8699 (tmm) REVERT: l 143 GLU cc_start: 0.7493 (pt0) cc_final: 0.7185 (pp20) REVERT: m 25 ASP cc_start: 0.7509 (t0) cc_final: 0.7171 (t0) REVERT: m 110 GLU cc_start: 0.9050 (tt0) cc_final: 0.8700 (tp30) REVERT: n 20 MET cc_start: 0.8960 (tpp) cc_final: 0.8610 (tpp) REVERT: o 36 TYR cc_start: 0.8323 (m-10) cc_final: 0.7907 (m-10) REVERT: q 43 GLN cc_start: 0.8718 (mt0) cc_final: 0.8410 (pt0) REVERT: q 88 GLU cc_start: 0.8881 (tp30) cc_final: 0.8447 (mp0) REVERT: q 97 ILE cc_start: 0.9678 (mt) cc_final: 0.9470 (tp) REVERT: q 100 PHE cc_start: 0.8862 (m-80) cc_final: 0.8547 (m-10) REVERT: q 109 VAL cc_start: 0.9351 (t) cc_final: 0.9079 (t) REVERT: r 35 PHE cc_start: 0.9045 (m-80) cc_final: 0.8746 (m-80) REVERT: r 98 ILE cc_start: 0.9391 (mm) cc_final: 0.9062 (tt) REVERT: s 52 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8239 (mt-10) REVERT: s 85 ILE cc_start: 0.9108 (mm) cc_final: 0.8766 (tp) REVERT: t 32 LEU cc_start: 0.9228 (tp) cc_final: 0.8833 (tp) REVERT: w 35 ARG cc_start: 0.9008 (ttm170) cc_final: 0.8299 (tpt170) REVERT: x 29 LEU cc_start: 0.9388 (mm) cc_final: 0.9055 (mm) REVERT: x 40 GLU cc_start: 0.8939 (tt0) cc_final: 0.8514 (pm20) REVERT: x 45 PHE cc_start: 0.8789 (m-80) cc_final: 0.8377 (m-10) REVERT: y 7 ARG cc_start: 0.8788 (ptt180) cc_final: 0.8473 (ptt180) REVERT: y 25 GLN cc_start: 0.8950 (tp40) cc_final: 0.8624 (tp-100) REVERT: C 7 LYS cc_start: 0.7073 (mttt) cc_final: 0.6309 (pttp) REVERT: C 24 LYS cc_start: 0.8674 (tppt) cc_final: 0.8079 (tppt) REVERT: C 49 LYS cc_start: 0.9393 (pttm) cc_final: 0.9131 (pttm) REVERT: E 27 ASN cc_start: 0.7839 (p0) cc_final: 0.7319 (t0) REVERT: F 3 VAL cc_start: 0.5381 (m) cc_final: 0.4572 (m) REVERT: G 112 ARG cc_start: 0.6595 (tpt170) cc_final: 0.6119 (ptt-90) REVERT: G 135 MET cc_start: 0.6225 (mmp) cc_final: 0.5711 (ttt) REVERT: G 212 TYR cc_start: 0.7315 (m-10) cc_final: 0.6989 (m-10) REVERT: I 25 ARG cc_start: 0.6985 (ttm170) cc_final: 0.6689 (ttp-170) REVERT: I 74 TYR cc_start: 0.8636 (m-10) cc_final: 0.8155 (m-80) REVERT: M 9 MET cc_start: 0.9510 (ttp) cc_final: 0.9182 (tmm) REVERT: M 47 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8805 (t0) REVERT: N 55 ASP cc_start: 0.6514 (m-30) cc_final: 0.6234 (m-30) REVERT: O 65 TYR cc_start: 0.6117 (m-80) cc_final: 0.5874 (m-80) REVERT: Q 81 ILE cc_start: 0.9364 (pt) cc_final: 0.8944 (mp) REVERT: R 2 ARG cc_start: 0.6575 (ttm-80) cc_final: 0.5939 (mmt180) REVERT: R 7 ASN cc_start: 0.3120 (t0) cc_final: 0.2873 (t0) REVERT: S 23 ARG cc_start: 0.3158 (ttt-90) cc_final: 0.2833 (ttt180) REVERT: U 39 PHE cc_start: 0.9057 (t80) cc_final: 0.8565 (t80) REVERT: U 51 ARG cc_start: 0.8425 (mmt-90) cc_final: 0.7750 (mtt180) REVERT: X 43 MET cc_start: -0.1050 (mtp) cc_final: -0.2496 (mtm) REVERT: Y 31 ILE cc_start: 0.9336 (pt) cc_final: 0.9121 (tp) REVERT: Z 39 LYS cc_start: 0.5672 (tttt) cc_final: 0.4929 (mmtt) REVERT: a 8 MET cc_start: 0.5322 (mmp) cc_final: 0.4531 (ttt) REVERT: a 9 ARG cc_start: 0.5643 (ttp80) cc_final: 0.5306 (mmt-90) REVERT: 8 231 ASP cc_start: 0.3322 (p0) cc_final: 0.2836 (p0) REVERT: 8 310 MET cc_start: 0.6720 (ttm) cc_final: 0.6469 (tpt) outliers start: 28 outliers final: 11 residues processed: 688 average time/residue: 1.3158 time to fit residues: 1554.2747 Evaluate side-chains 433 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 421 time to evaluate : 5.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 889 optimal weight: 30.0000 chunk 798 optimal weight: 20.0000 chunk 442 optimal weight: 40.0000 chunk 272 optimal weight: 30.0000 chunk 538 optimal weight: 6.9990 chunk 426 optimal weight: 20.0000 chunk 825 optimal weight: 20.0000 chunk 319 optimal weight: 50.0000 chunk 501 optimal weight: 8.9990 chunk 614 optimal weight: 30.0000 chunk 956 optimal weight: 30.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 114 GLN b 116 GLN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 126 ASN c 134 HIS c 148 GLN ** c 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 173 GLN c 185 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 HIS ** j 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 131 ASN ** k 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN q 36 GLN q 65 ASN r 6 GLN r 82 HIS s 57 ASN s 102 HIS t 15 HIS ** t 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 HIS u 73 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN x 22 ASN ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN y 31 GLN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 42 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN G 38 HIS ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN H 2 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 88 ASN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN J 147 ASN K 14 GLN K 52 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS O 15 HIS O 99 GLN Q 45 ASN ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 HIS U 18 GLN U 29 ASN ** U 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 74 HIS a 47 ASN 8 38 ASN 8 112 GLN ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 304 ASN 8 313 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 160361 Z= 0.381 Angle : 0.928 19.661 239566 Z= 0.467 Chirality : 0.044 0.327 30559 Planarity : 0.007 0.086 13074 Dihedral : 23.740 179.994 79401 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 36.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.53 % Favored : 88.39 % Rotamer: Outliers : 0.32 % Allowed : 9.11 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.09), residues: 6011 helix: -2.70 (0.09), residues: 1797 sheet: -2.90 (0.16), residues: 841 loop : -2.90 (0.09), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 103 HIS 0.018 0.002 HIS c 140 PHE 0.042 0.003 PHE u 95 TYR 0.024 0.003 TYR m 103 ARG 0.022 0.001 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 555 time to evaluate : 6.347 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: b 160 TYR cc_start: 0.8581 (p90) cc_final: 0.7735 (p90) REVERT: b 180 MET cc_start: 0.8464 (mmm) cc_final: 0.8012 (mmm) REVERT: c 22 ILE cc_start: 0.9413 (pt) cc_final: 0.9206 (mp) REVERT: d 1 MET cc_start: 0.7297 (mtp) cc_final: 0.7075 (mmm) REVERT: d 19 PHE cc_start: 0.8169 (m-80) cc_final: 0.7931 (m-80) REVERT: d 100 MET cc_start: 0.8926 (mmm) cc_final: 0.8508 (mmt) REVERT: e 25 MET cc_start: 0.8198 (mmt) cc_final: 0.7535 (mmt) REVERT: e 137 PHE cc_start: 0.8269 (m-80) cc_final: 0.7919 (m-10) REVERT: f 124 CYS cc_start: 0.3910 (p) cc_final: 0.3263 (m) REVERT: f 150 TYR cc_start: 0.5184 (m-10) cc_final: 0.4834 (m-80) REVERT: k 1 MET cc_start: 0.7367 (ttt) cc_final: 0.6504 (ttt) REVERT: k 45 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7309 (tm-30) REVERT: k 73 ASP cc_start: 0.8891 (p0) cc_final: 0.8320 (p0) REVERT: k 106 GLU cc_start: 0.8445 (tp30) cc_final: 0.8060 (tp30) REVERT: m 25 ASP cc_start: 0.7733 (t0) cc_final: 0.7471 (t0) REVERT: n 20 MET cc_start: 0.9074 (tpp) cc_final: 0.8590 (tpp) REVERT: o 36 TYR cc_start: 0.8829 (m-10) cc_final: 0.8589 (m-10) REVERT: o 93 ASP cc_start: 0.7757 (t70) cc_final: 0.7557 (t0) REVERT: q 88 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8308 (mp0) REVERT: q 100 PHE cc_start: 0.8704 (m-80) cc_final: 0.8457 (m-10) REVERT: r 78 ARG cc_start: 0.8641 (mmt-90) cc_final: 0.8051 (mmt90) REVERT: r 98 ILE cc_start: 0.9422 (mm) cc_final: 0.8761 (tt) REVERT: s 2 GLU cc_start: 0.9099 (pt0) cc_final: 0.8830 (pm20) REVERT: s 19 LEU cc_start: 0.9508 (tp) cc_final: 0.9172 (tp) REVERT: s 52 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8322 (mt-10) REVERT: s 85 ILE cc_start: 0.9128 (mm) cc_final: 0.8782 (tp) REVERT: t 1 MET cc_start: 0.4608 (tpt) cc_final: 0.3303 (mmm) REVERT: w 35 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8312 (mtt180) REVERT: w 62 LYS cc_start: 0.9426 (tptm) cc_final: 0.8733 (tppt) REVERT: x 5 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8228 (mm-40) REVERT: x 24 THR cc_start: 0.9035 (m) cc_final: 0.8531 (m) REVERT: x 29 LEU cc_start: 0.9611 (mm) cc_final: 0.9358 (mm) REVERT: x 40 GLU cc_start: 0.8998 (tt0) cc_final: 0.8676 (pm20) REVERT: x 45 PHE cc_start: 0.8969 (m-80) cc_final: 0.8411 (m-80) REVERT: y 23 ARG cc_start: 0.9535 (mpt180) cc_final: 0.9171 (mpt180) REVERT: B 14 MET cc_start: 0.8607 (mmp) cc_final: 0.8353 (mmp) REVERT: B 51 ARG cc_start: 0.8744 (mtm180) cc_final: 0.8520 (mtm-85) REVERT: B 56 LYS cc_start: 0.7013 (tppt) cc_final: 0.6802 (tppp) REVERT: C 24 LYS cc_start: 0.8867 (tppt) cc_final: 0.8455 (tppt) REVERT: D 29 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8989 (tm-30) REVERT: F 36 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7583 (mmm160) REVERT: G 135 MET cc_start: 0.5532 (mmp) cc_final: 0.5017 (ttt) REVERT: G 199 ILE cc_start: 0.6758 (mp) cc_final: 0.5949 (mp) REVERT: I 13 ARG cc_start: 0.6725 (ttt180) cc_final: 0.4626 (ttt180) REVERT: I 16 THR cc_start: 0.2637 (m) cc_final: 0.2258 (m) REVERT: I 18 LEU cc_start: 0.7484 (mp) cc_final: 0.7175 (tp) REVERT: I 25 ARG cc_start: 0.7418 (ttm170) cc_final: 0.7185 (ttt180) REVERT: I 63 ILE cc_start: 0.8071 (pt) cc_final: 0.7642 (pt) REVERT: J 44 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8506 (mtm-85) REVERT: J 63 MET cc_start: 0.8526 (mtp) cc_final: 0.8281 (mpp) REVERT: M 9 MET cc_start: 0.9335 (ttp) cc_final: 0.9133 (tmm) REVERT: M 13 ILE cc_start: 0.8489 (mt) cc_final: 0.8283 (mt) REVERT: M 47 ASP cc_start: 0.9124 (m-30) cc_final: 0.8848 (t0) REVERT: M 48 PHE cc_start: 0.8143 (p90) cc_final: 0.7553 (p90) REVERT: Q 81 ILE cc_start: 0.9284 (pt) cc_final: 0.8967 (mp) REVERT: R 2 ARG cc_start: 0.6576 (ttm-80) cc_final: 0.5915 (mmp80) REVERT: R 7 ASN cc_start: 0.3207 (t0) cc_final: 0.2585 (m-40) REVERT: T 5 GLU cc_start: 0.9087 (pp20) cc_final: 0.8847 (pm20) REVERT: T 70 LYS cc_start: 0.9250 (tmmt) cc_final: 0.9007 (pttm) REVERT: U 39 PHE cc_start: 0.8951 (t80) cc_final: 0.8563 (t80) REVERT: Z 39 LYS cc_start: 0.5810 (tttt) cc_final: 0.5069 (mmtt) REVERT: a 8 MET cc_start: 0.4867 (mmp) cc_final: 0.4152 (tpp) REVERT: a 9 ARG cc_start: 0.5855 (ttp80) cc_final: 0.5417 (tpp80) REVERT: 8 73 MET cc_start: 0.2506 (ttm) cc_final: 0.2068 (ttm) REVERT: 8 151 MET cc_start: 0.5456 (ttp) cc_final: 0.4761 (tmm) REVERT: 8 172 GLU cc_start: 0.3782 (tt0) cc_final: 0.3515 (tt0) outliers start: 16 outliers final: 9 residues processed: 570 average time/residue: 1.4100 time to fit residues: 1404.7330 Evaluate side-chains 427 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 418 time to evaluate : 6.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 531 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 chunk 795 optimal weight: 40.0000 chunk 651 optimal weight: 50.0000 chunk 263 optimal weight: 30.0000 chunk 957 optimal weight: 20.0000 chunk 1034 optimal weight: 30.0000 chunk 853 optimal weight: 40.0000 chunk 949 optimal weight: 20.0000 chunk 326 optimal weight: 50.0000 chunk 768 optimal weight: 20.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 225 ASN ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN c 185 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 GLN ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 HIS ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 GLN l 104 GLN m 13 HIS ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 ASN ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 89 HIS u 39 ASN ** v 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN L 121 ASN ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 GLN P 21 HIS Q 76 HIS ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN ** W 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 203 GLN 8 8 ASN ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 160361 Z= 0.373 Angle : 0.863 17.829 239566 Z= 0.436 Chirality : 0.044 0.338 30559 Planarity : 0.007 0.296 13074 Dihedral : 24.609 179.725 79401 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 40.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.74 % Favored : 87.14 % Rotamer: Outliers : 0.24 % Allowed : 8.95 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.89 (0.09), residues: 6011 helix: -2.20 (0.10), residues: 1802 sheet: -2.91 (0.16), residues: 874 loop : -2.76 (0.10), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP G 103 HIS 0.017 0.003 HIS r 12 PHE 0.041 0.003 PHE 8 221 TYR 0.048 0.003 TYR I 203 ARG 0.028 0.001 ARG N 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 500 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 160 TYR cc_start: 0.8711 (p90) cc_final: 0.7775 (p90) REVERT: b 224 MET cc_start: 0.7696 (mmt) cc_final: 0.7258 (mmt) REVERT: c 118 PHE cc_start: 0.8464 (t80) cc_final: 0.8254 (t80) REVERT: d 100 MET cc_start: 0.8987 (mmm) cc_final: 0.8537 (mmt) REVERT: d 141 MET cc_start: 0.8972 (mpp) cc_final: 0.8722 (mpp) REVERT: e 137 PHE cc_start: 0.8021 (m-80) cc_final: 0.7576 (m-80) REVERT: f 124 CYS cc_start: 0.3090 (p) cc_final: 0.2779 (m) REVERT: j 108 MET cc_start: 0.7844 (mmm) cc_final: 0.7095 (tpp) REVERT: k 1 MET cc_start: 0.7140 (ttt) cc_final: 0.6141 (tmm) REVERT: k 73 ASP cc_start: 0.8838 (p0) cc_final: 0.8540 (p0) REVERT: k 100 PHE cc_start: 0.8384 (p90) cc_final: 0.8184 (p90) REVERT: k 106 GLU cc_start: 0.8594 (tp30) cc_final: 0.8189 (tp30) REVERT: m 25 ASP cc_start: 0.7631 (t0) cc_final: 0.7412 (t0) REVERT: m 28 PHE cc_start: 0.7872 (m-80) cc_final: 0.7666 (m-80) REVERT: m 130 PHE cc_start: 0.7294 (t80) cc_final: 0.6706 (t80) REVERT: m 136 MET cc_start: 0.5753 (ptt) cc_final: 0.5247 (pmm) REVERT: o 36 TYR cc_start: 0.8662 (m-10) cc_final: 0.8429 (m-10) REVERT: q 88 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8048 (mp0) REVERT: q 100 PHE cc_start: 0.8677 (m-80) cc_final: 0.8401 (m-10) REVERT: r 35 PHE cc_start: 0.9062 (m-80) cc_final: 0.8737 (m-80) REVERT: r 78 ARG cc_start: 0.8411 (mmt-90) cc_final: 0.7770 (mmt90) REVERT: r 95 ASP cc_start: 0.8871 (m-30) cc_final: 0.8617 (m-30) REVERT: r 98 ILE cc_start: 0.9398 (mm) cc_final: 0.8794 (tt) REVERT: s 52 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8413 (mt-10) REVERT: s 78 GLU cc_start: 0.7749 (pt0) cc_final: 0.7528 (pt0) REVERT: s 85 ILE cc_start: 0.8982 (mm) cc_final: 0.8654 (tp) REVERT: t 1 MET cc_start: 0.4962 (tpt) cc_final: 0.4606 (tpt) REVERT: v 48 MET cc_start: 0.8207 (mmm) cc_final: 0.7782 (mmm) REVERT: w 71 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8621 (ttpt) REVERT: x 5 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8369 (mm-40) REVERT: x 29 LEU cc_start: 0.9571 (mm) cc_final: 0.9313 (mm) REVERT: x 40 GLU cc_start: 0.8953 (tt0) cc_final: 0.8685 (pm20) REVERT: y 7 ARG cc_start: 0.8872 (ptt180) cc_final: 0.8427 (ptt-90) REVERT: y 25 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8861 (tp40) REVERT: D 1 MET cc_start: 0.7512 (ptp) cc_final: 0.7299 (ptp) REVERT: D 29 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8845 (tm-30) REVERT: F 1 MET cc_start: 0.4714 (ttm) cc_final: 0.4366 (ppp) REVERT: F 37 GLN cc_start: 0.7685 (tp40) cc_final: 0.7317 (tm-30) REVERT: G 48 MET cc_start: 0.6848 (ppp) cc_final: 0.6268 (ppp) REVERT: G 135 MET cc_start: 0.4840 (mmp) cc_final: 0.4216 (ttt) REVERT: G 212 TYR cc_start: 0.7722 (m-10) cc_final: 0.7475 (m-10) REVERT: I 63 ILE cc_start: 0.8189 (pt) cc_final: 0.7883 (pt) REVERT: I 70 GLN cc_start: 0.8794 (tt0) cc_final: 0.8000 (mm-40) REVERT: I 134 TYR cc_start: 0.9075 (t80) cc_final: 0.8785 (t80) REVERT: J 63 MET cc_start: 0.8031 (mtp) cc_final: 0.7775 (mpp) REVERT: J 110 MET cc_start: 0.8642 (ptp) cc_final: 0.8334 (ptp) REVERT: K 88 MET cc_start: -0.3314 (ptt) cc_final: -0.3518 (ptt) REVERT: M 13 ILE cc_start: 0.8509 (mt) cc_final: 0.8277 (mt) REVERT: M 47 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8678 (t0) REVERT: M 48 PHE cc_start: 0.8423 (p90) cc_final: 0.7821 (p90) REVERT: Q 81 ILE cc_start: 0.9496 (pt) cc_final: 0.9220 (mp) REVERT: R 2 ARG cc_start: 0.6781 (ttm-80) cc_final: 0.6213 (mmp80) REVERT: R 22 TYR cc_start: 0.6295 (t80) cc_final: 0.5311 (t80) REVERT: T 5 GLU cc_start: 0.8865 (pp20) cc_final: 0.8508 (pm20) REVERT: T 70 LYS cc_start: 0.9269 (tmmt) cc_final: 0.8995 (ptpp) REVERT: U 1 MET cc_start: 0.7563 (tpp) cc_final: 0.6854 (mmt) REVERT: U 39 PHE cc_start: 0.8942 (t80) cc_final: 0.8497 (t80) REVERT: U 60 TRP cc_start: 0.9426 (m100) cc_final: 0.9203 (m100) REVERT: W 13 THR cc_start: 0.2111 (OUTLIER) cc_final: 0.1826 (t) REVERT: X 65 MET cc_start: 0.4082 (tmm) cc_final: 0.3838 (tmm) REVERT: Y 35 TYR cc_start: 0.8573 (m-80) cc_final: 0.8130 (m-80) REVERT: Y 74 HIS cc_start: 0.8774 (m-70) cc_final: 0.8220 (m-70) REVERT: Z 39 LYS cc_start: 0.5954 (tttt) cc_final: 0.5291 (tppt) REVERT: a 8 MET cc_start: 0.4599 (mmp) cc_final: 0.3880 (tpt) REVERT: a 9 ARG cc_start: 0.5519 (ttp80) cc_final: 0.5069 (tpp80) REVERT: 8 73 MET cc_start: 0.3008 (ttm) cc_final: 0.2713 (ttm) REVERT: 8 151 MET cc_start: 0.5172 (ttp) cc_final: 0.4787 (tmm) outliers start: 12 outliers final: 2 residues processed: 511 average time/residue: 1.2683 time to fit residues: 1129.6380 Evaluate side-chains 393 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 389 time to evaluate : 6.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 946 optimal weight: 30.0000 chunk 720 optimal weight: 30.0000 chunk 497 optimal weight: 0.0870 chunk 106 optimal weight: 6.9990 chunk 457 optimal weight: 8.9990 chunk 643 optimal weight: 20.0000 chunk 961 optimal weight: 20.0000 chunk 1017 optimal weight: 4.9990 chunk 502 optimal weight: 30.0000 chunk 911 optimal weight: 20.0000 chunk 274 optimal weight: 7.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN b 127 ASN ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 28 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 88 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 11 GLN q 71 ASN v 49 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 HIS z 8 GLN ** z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 13 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS I 58 GLN I 73 ASN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN S 61 ASN ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 HIS Y 19 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 203 GLN ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 160361 Z= 0.181 Angle : 0.610 15.585 239566 Z= 0.316 Chirality : 0.035 0.256 30559 Planarity : 0.005 0.119 13074 Dihedral : 24.240 179.844 79401 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.37 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.10), residues: 6011 helix: -1.53 (0.11), residues: 1815 sheet: -2.57 (0.16), residues: 844 loop : -2.56 (0.10), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP q 60 HIS 0.020 0.001 HIS T 45 PHE 0.020 0.002 PHE L 25 TYR 0.044 0.002 TYR I 74 ARG 0.015 0.001 ARG Y 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 6.304 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: b 160 TYR cc_start: 0.8415 (p90) cc_final: 0.7491 (p90) REVERT: c 11 MET cc_start: 0.7248 (pmm) cc_final: 0.6606 (pmm) REVERT: e 25 MET cc_start: 0.9013 (mmp) cc_final: 0.8701 (ttt) REVERT: e 137 PHE cc_start: 0.7982 (m-80) cc_final: 0.7361 (m-80) REVERT: f 124 CYS cc_start: 0.2067 (p) cc_final: 0.1814 (m) REVERT: f 176 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5685 (pttm) REVERT: g 51 ARG cc_start: 0.5517 (mmt-90) cc_final: 0.4981 (mtp180) REVERT: j 108 MET cc_start: 0.7879 (mmm) cc_final: 0.7017 (tpp) REVERT: k 1 MET cc_start: 0.6885 (ttt) cc_final: 0.6168 (tmm) REVERT: k 45 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7623 (tm-30) REVERT: k 73 ASP cc_start: 0.8732 (p0) cc_final: 0.8434 (p0) REVERT: l 90 VAL cc_start: 0.9084 (m) cc_final: 0.8855 (p) REVERT: m 25 ASP cc_start: 0.7457 (t0) cc_final: 0.7239 (t0) REVERT: m 136 MET cc_start: 0.5798 (ptt) cc_final: 0.5121 (pmm) REVERT: n 20 MET cc_start: 0.9192 (tmm) cc_final: 0.8981 (tmm) REVERT: o 36 TYR cc_start: 0.8665 (m-10) cc_final: 0.8401 (m-10) REVERT: q 100 PHE cc_start: 0.8559 (m-80) cc_final: 0.8345 (m-10) REVERT: r 35 PHE cc_start: 0.8979 (m-80) cc_final: 0.8769 (m-80) REVERT: r 78 ARG cc_start: 0.8365 (mmt-90) cc_final: 0.7289 (tpp80) REVERT: r 95 ASP cc_start: 0.8976 (m-30) cc_final: 0.8475 (m-30) REVERT: r 98 ILE cc_start: 0.9477 (mm) cc_final: 0.8963 (tt) REVERT: s 4 ILE cc_start: 0.9096 (pt) cc_final: 0.8841 (pt) REVERT: s 52 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8263 (mt-10) REVERT: t 1 MET cc_start: 0.4675 (tpt) cc_final: 0.3824 (mmm) REVERT: v 48 MET cc_start: 0.8080 (mmm) cc_final: 0.7649 (mmm) REVERT: x 5 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8383 (mm-40) REVERT: x 29 LEU cc_start: 0.9515 (mm) cc_final: 0.9216 (mm) REVERT: x 63 ILE cc_start: 0.6725 (mp) cc_final: 0.6506 (mt) REVERT: y 23 ARG cc_start: 0.9391 (mpt180) cc_final: 0.9069 (mpt180) REVERT: y 25 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8613 (tp40) REVERT: B 14 MET cc_start: 0.8660 (mmp) cc_final: 0.8451 (mmp) REVERT: D 29 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8780 (tm-30) REVERT: F 1 MET cc_start: 0.4699 (ttm) cc_final: 0.4215 (ppp) REVERT: F 37 GLN cc_start: 0.7943 (tp40) cc_final: 0.7464 (tm-30) REVERT: G 135 MET cc_start: 0.4217 (mmp) cc_final: 0.3504 (ttt) REVERT: G 212 TYR cc_start: 0.7471 (m-10) cc_final: 0.7242 (m-10) REVERT: I 134 TYR cc_start: 0.9043 (t80) cc_final: 0.8682 (t80) REVERT: I 135 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8442 (mm-40) REVERT: J 63 MET cc_start: 0.7953 (mtp) cc_final: 0.7650 (mpp) REVERT: J 110 MET cc_start: 0.8700 (ptp) cc_final: 0.8460 (ptp) REVERT: J 133 ILE cc_start: 0.9093 (pt) cc_final: 0.8846 (pt) REVERT: K 21 MET cc_start: 0.4160 (mpp) cc_final: 0.3481 (mpp) REVERT: K 88 MET cc_start: -0.4366 (ptt) cc_final: -0.4840 (ptt) REVERT: M 48 PHE cc_start: 0.8348 (p90) cc_final: 0.7760 (p90) REVERT: O 65 TYR cc_start: 0.5738 (m-80) cc_final: 0.5107 (m-80) REVERT: O 88 MET cc_start: 0.0642 (ppp) cc_final: 0.0367 (mmm) REVERT: Q 35 ARG cc_start: 0.9161 (ttt90) cc_final: 0.8756 (tpm170) REVERT: Q 55 ARG cc_start: 0.9374 (tpt-90) cc_final: 0.8859 (tpt170) REVERT: Q 81 ILE cc_start: 0.9505 (pt) cc_final: 0.9236 (mp) REVERT: T 70 LYS cc_start: 0.9225 (tmmt) cc_final: 0.8991 (ptpp) REVERT: U 39 PHE cc_start: 0.8830 (t80) cc_final: 0.8385 (t80) REVERT: U 60 TRP cc_start: 0.9389 (m100) cc_final: 0.9170 (m100) REVERT: Y 35 TYR cc_start: 0.8481 (m-80) cc_final: 0.8257 (m-80) REVERT: Y 74 HIS cc_start: 0.8749 (m-70) cc_final: 0.8246 (m-70) REVERT: Z 39 LYS cc_start: 0.5619 (tttt) cc_final: 0.5007 (tppt) REVERT: a 8 MET cc_start: 0.5207 (mmp) cc_final: 0.4458 (tpt) REVERT: a 9 ARG cc_start: 0.5466 (ttp80) cc_final: 0.5150 (tpt170) REVERT: 8 73 MET cc_start: 0.2924 (ttm) cc_final: 0.2590 (ttm) REVERT: 8 151 MET cc_start: 0.5373 (ttp) cc_final: 0.4776 (tmm) outliers start: 0 outliers final: 0 residues processed: 574 average time/residue: 1.2793 time to fit residues: 1283.8126 Evaluate side-chains 410 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 6.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 847 optimal weight: 40.0000 chunk 577 optimal weight: 40.0000 chunk 14 optimal weight: 40.0000 chunk 757 optimal weight: 20.0000 chunk 419 optimal weight: 40.0000 chunk 868 optimal weight: 20.0000 chunk 703 optimal weight: 50.0000 chunk 1 optimal weight: 40.0000 chunk 519 optimal weight: 0.0050 chunk 913 optimal weight: 30.0000 chunk 256 optimal weight: 5.9990 overall best weight: 15.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN f 142 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN p 65 ASN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN H 2 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN L 51 GLN ** L 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS V 44 HIS W 30 ASN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 112 GLN ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 160361 Z= 0.373 Angle : 0.844 19.268 239566 Z= 0.425 Chirality : 0.044 0.287 30559 Planarity : 0.006 0.104 13074 Dihedral : 24.879 178.718 79401 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 43.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.51 % Favored : 86.41 % Rotamer: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.49 (0.10), residues: 6011 helix: -1.67 (0.11), residues: 1795 sheet: -2.75 (0.16), residues: 832 loop : -2.63 (0.10), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP q 60 HIS 0.019 0.002 HIS T 45 PHE 0.038 0.003 PHE I 71 TYR 0.041 0.003 TYR I 203 ARG 0.022 0.001 ARG J 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 492 time to evaluate : 6.387 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: b 160 TYR cc_start: 0.8695 (p90) cc_final: 0.7720 (p90) REVERT: b 180 MET cc_start: 0.8243 (mmm) cc_final: 0.7932 (mmm) REVERT: b 239 PHE cc_start: 0.4349 (t80) cc_final: 0.4041 (t80) REVERT: c 11 MET cc_start: 0.7495 (pmm) cc_final: 0.6922 (pmm) REVERT: d 19 PHE cc_start: 0.7958 (m-80) cc_final: 0.7730 (m-80) REVERT: d 141 MET cc_start: 0.8985 (mpp) cc_final: 0.8702 (mpp) REVERT: e 117 SER cc_start: 0.8339 (m) cc_final: 0.8120 (p) REVERT: e 137 PHE cc_start: 0.8110 (m-80) cc_final: 0.7542 (m-80) REVERT: f 124 CYS cc_start: 0.1954 (p) cc_final: 0.1751 (m) REVERT: g 51 ARG cc_start: 0.5833 (mmt-90) cc_final: 0.5386 (mtp180) REVERT: j 108 MET cc_start: 0.7967 (mmm) cc_final: 0.6983 (tpp) REVERT: k 45 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8010 (tm-30) REVERT: n 20 MET cc_start: 0.9279 (tmm) cc_final: 0.9072 (tmm) REVERT: q 100 PHE cc_start: 0.8674 (m-80) cc_final: 0.8429 (m-10) REVERT: r 35 PHE cc_start: 0.9021 (m-80) cc_final: 0.8637 (m-80) REVERT: r 78 ARG cc_start: 0.8400 (mmt-90) cc_final: 0.7775 (mmt90) REVERT: r 98 ILE cc_start: 0.9476 (mm) cc_final: 0.8957 (tt) REVERT: s 2 GLU cc_start: 0.8947 (pp20) cc_final: 0.8649 (pp20) REVERT: s 4 ILE cc_start: 0.8890 (pt) cc_final: 0.8371 (pt) REVERT: s 52 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8297 (mt-10) REVERT: s 94 ASP cc_start: 0.8040 (m-30) cc_final: 0.7495 (t0) REVERT: t 1 MET cc_start: 0.5596 (tpt) cc_final: 0.5221 (mmm) REVERT: t 24 MET cc_start: 0.9471 (mtt) cc_final: 0.9140 (mpp) REVERT: w 71 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8550 (ttpt) REVERT: x 5 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8279 (mm-40) REVERT: y 23 ARG cc_start: 0.9463 (mpt180) cc_final: 0.9082 (mpt180) REVERT: y 25 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8814 (tp40) REVERT: z 46 MET cc_start: 0.7205 (mtt) cc_final: 0.6861 (mtt) REVERT: D 29 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8895 (tm-30) REVERT: F 1 MET cc_start: 0.4637 (ttm) cc_final: 0.3985 (ppp) REVERT: G 135 MET cc_start: 0.4461 (mmp) cc_final: 0.3752 (ttm) REVERT: G 199 ILE cc_start: 0.6357 (mt) cc_final: 0.6052 (mt) REVERT: G 212 TYR cc_start: 0.6514 (m-10) cc_final: 0.6211 (m-10) REVERT: I 134 TYR cc_start: 0.8745 (t80) cc_final: 0.8368 (t80) REVERT: J 63 MET cc_start: 0.7969 (mtp) cc_final: 0.7684 (mpp) REVERT: K 1 MET cc_start: 0.5910 (mmm) cc_final: 0.5702 (mmm) REVERT: K 21 MET cc_start: 0.4289 (mpp) cc_final: 0.4083 (mpp) REVERT: M 48 PHE cc_start: 0.8352 (p90) cc_final: 0.7801 (p90) REVERT: O 65 TYR cc_start: 0.6211 (m-80) cc_final: 0.5711 (m-80) REVERT: Q 81 ILE cc_start: 0.9587 (pt) cc_final: 0.9300 (mp) REVERT: R 2 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.5968 (mmp80) REVERT: U 1 MET cc_start: 0.7398 (tpp) cc_final: 0.6320 (tpp) REVERT: U 39 PHE cc_start: 0.8833 (t80) cc_final: 0.8406 (t80) REVERT: U 60 TRP cc_start: 0.9440 (m100) cc_final: 0.9184 (m100) REVERT: Y 35 TYR cc_start: 0.8406 (m-80) cc_final: 0.7805 (m-80) REVERT: Y 74 HIS cc_start: 0.8825 (m-70) cc_final: 0.8360 (m-70) REVERT: Z 39 LYS cc_start: 0.5884 (tttt) cc_final: 0.5251 (tppt) REVERT: a 8 MET cc_start: 0.4728 (mmp) cc_final: 0.3898 (tmm) REVERT: a 9 ARG cc_start: 0.5408 (ttp80) cc_final: 0.5029 (tpp80) REVERT: 8 73 MET cc_start: 0.2951 (ttm) cc_final: 0.2648 (ttm) REVERT: 8 151 MET cc_start: 0.4930 (ttp) cc_final: 0.4561 (tmm) REVERT: 8 172 GLU cc_start: 0.5911 (tt0) cc_final: 0.4971 (tm-30) outliers start: 2 outliers final: 0 residues processed: 493 average time/residue: 1.2786 time to fit residues: 1105.4893 Evaluate side-chains 380 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 6.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 342 optimal weight: 4.9990 chunk 916 optimal weight: 50.0000 chunk 201 optimal weight: 6.9990 chunk 597 optimal weight: 40.0000 chunk 251 optimal weight: 10.0000 chunk 1018 optimal weight: 6.9990 chunk 845 optimal weight: 30.0000 chunk 471 optimal weight: 10.0000 chunk 84 optimal weight: 50.0000 chunk 337 optimal weight: 5.9990 chunk 534 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 ASN b 116 GLN ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 138 GLN g 135 HIS ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN n 13 ASN ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN o 19 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN J 69 ASN K 52 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN T 39 GLN T 41 HIS V 44 HIS ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 160361 Z= 0.195 Angle : 0.617 16.403 239566 Z= 0.317 Chirality : 0.035 0.283 30559 Planarity : 0.005 0.065 13074 Dihedral : 24.551 178.666 79401 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.16 % Favored : 89.77 % Rotamer: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.10), residues: 6011 helix: -1.22 (0.11), residues: 1812 sheet: -2.52 (0.17), residues: 816 loop : -2.48 (0.10), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP q 60 HIS 0.014 0.001 HIS T 45 PHE 0.021 0.002 PHE 8 221 TYR 0.031 0.002 TYR I 75 ARG 0.026 0.001 ARG b 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 6.339 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: b 160 TYR cc_start: 0.8491 (p90) cc_final: 0.7590 (p90) REVERT: c 11 MET cc_start: 0.7079 (pmm) cc_final: 0.6239 (pmm) REVERT: e 137 PHE cc_start: 0.7908 (m-80) cc_final: 0.7328 (m-80) REVERT: f 61 TRP cc_start: 0.9220 (m-10) cc_final: 0.8805 (m-90) REVERT: f 176 LYS cc_start: 0.6391 (mtpt) cc_final: 0.5914 (pttm) REVERT: g 51 ARG cc_start: 0.5463 (mmt-90) cc_final: 0.5041 (mmm-85) REVERT: j 108 MET cc_start: 0.8048 (mmm) cc_final: 0.7327 (mmt) REVERT: k 45 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7693 (tm-30) REVERT: l 90 VAL cc_start: 0.9111 (m) cc_final: 0.8875 (p) REVERT: n 1 MET cc_start: 0.7502 (ptt) cc_final: 0.6851 (ptp) REVERT: n 20 MET cc_start: 0.9276 (tmm) cc_final: 0.9033 (tmm) REVERT: q 100 PHE cc_start: 0.8583 (m-80) cc_final: 0.8351 (m-10) REVERT: r 35 PHE cc_start: 0.9043 (m-80) cc_final: 0.8709 (m-80) REVERT: r 40 MET cc_start: 0.8551 (tpt) cc_final: 0.8060 (tpp) REVERT: r 78 ARG cc_start: 0.8320 (mmt-90) cc_final: 0.7566 (tpt170) REVERT: r 98 ILE cc_start: 0.9452 (mm) cc_final: 0.8964 (tt) REVERT: s 52 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8169 (mt-10) REVERT: s 94 ASP cc_start: 0.7679 (m-30) cc_final: 0.7221 (t0) REVERT: t 1 MET cc_start: 0.5123 (tpt) cc_final: 0.4584 (mmm) REVERT: v 45 ASP cc_start: 0.8634 (t0) cc_final: 0.8430 (t70) REVERT: w 71 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8704 (ttpt) REVERT: y 23 ARG cc_start: 0.9350 (mpt180) cc_final: 0.9019 (mpt180) REVERT: y 25 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8682 (tp40) REVERT: C 31 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6409 (pm20) REVERT: D 29 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8778 (tm-30) REVERT: F 1 MET cc_start: 0.4405 (ttm) cc_final: 0.3794 (ppp) REVERT: F 37 GLN cc_start: 0.8083 (tp40) cc_final: 0.7494 (tm-30) REVERT: G 103 TRP cc_start: 0.7950 (t-100) cc_final: 0.7483 (t-100) REVERT: G 135 MET cc_start: 0.4471 (mmp) cc_final: 0.3744 (ttm) REVERT: G 212 TYR cc_start: 0.6420 (m-10) cc_final: 0.6216 (m-10) REVERT: I 134 TYR cc_start: 0.8974 (t80) cc_final: 0.8662 (t80) REVERT: J 63 MET cc_start: 0.7860 (mtp) cc_final: 0.7626 (mpp) REVERT: K 90 MET cc_start: 0.3817 (tpt) cc_final: 0.3435 (tmm) REVERT: M 9 MET cc_start: 0.9387 (tmm) cc_final: 0.9088 (ppp) REVERT: M 48 PHE cc_start: 0.8268 (p90) cc_final: 0.7786 (p90) REVERT: M 75 GLN cc_start: 0.8068 (pm20) cc_final: 0.7494 (pp30) REVERT: O 65 TYR cc_start: 0.6064 (m-80) cc_final: 0.5699 (m-80) REVERT: O 88 MET cc_start: 0.0588 (ppp) cc_final: 0.0385 (mmm) REVERT: Q 55 ARG cc_start: 0.9353 (tpt-90) cc_final: 0.8871 (tpt170) REVERT: Q 81 ILE cc_start: 0.9507 (pt) cc_final: 0.9235 (mp) REVERT: R 2 ARG cc_start: 0.6657 (ttm-80) cc_final: 0.5885 (mmp80) REVERT: U 1 MET cc_start: 0.7393 (tpp) cc_final: 0.6258 (tpp) REVERT: U 39 PHE cc_start: 0.8771 (t80) cc_final: 0.8375 (t80) REVERT: U 60 TRP cc_start: 0.9437 (m100) cc_final: 0.9208 (m100) REVERT: Y 35 TYR cc_start: 0.8410 (m-80) cc_final: 0.7755 (m-80) REVERT: Y 74 HIS cc_start: 0.8786 (m-70) cc_final: 0.8255 (m-70) REVERT: Z 39 LYS cc_start: 0.5647 (tttt) cc_final: 0.5028 (tppt) REVERT: a 8 MET cc_start: 0.4790 (mmp) cc_final: 0.4205 (tmm) REVERT: a 9 ARG cc_start: 0.5412 (ttp80) cc_final: 0.5062 (tpp80) REVERT: 8 116 ARG cc_start: 0.8921 (tpm170) cc_final: 0.8428 (mmt90) REVERT: 8 151 MET cc_start: 0.4716 (ttp) cc_final: 0.4449 (tmm) REVERT: 8 172 GLU cc_start: 0.5504 (tt0) cc_final: 0.4726 (tm-30) outliers start: 1 outliers final: 0 residues processed: 536 average time/residue: 1.2814 time to fit residues: 1201.9483 Evaluate side-chains 398 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 6.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 982 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 580 optimal weight: 40.0000 chunk 744 optimal weight: 30.0000 chunk 576 optimal weight: 30.0000 chunk 857 optimal weight: 40.0000 chunk 568 optimal weight: 40.0000 chunk 1014 optimal weight: 50.0000 chunk 635 optimal weight: 50.0000 chunk 618 optimal weight: 50.0000 chunk 468 optimal weight: 0.6980 overall best weight: 19.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** b 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 52 ASN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN I 88 ASN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN J 82 HIS K 52 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.8918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 160361 Z= 0.447 Angle : 0.947 22.538 239566 Z= 0.471 Chirality : 0.047 0.374 30559 Planarity : 0.007 0.087 13074 Dihedral : 25.354 179.100 79401 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 51.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.94 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.10), residues: 6011 helix: -1.75 (0.11), residues: 1764 sheet: -2.66 (0.17), residues: 812 loop : -2.67 (0.10), residues: 3435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP G 95 HIS 0.020 0.003 HIS T 45 PHE 0.036 0.003 PHE I 71 TYR 0.031 0.003 TYR I 203 ARG 0.034 0.001 ARG J 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 6.373 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: b 160 TYR cc_start: 0.8648 (p90) cc_final: 0.7586 (p90) REVERT: c 11 MET cc_start: 0.7742 (pmm) cc_final: 0.7178 (pmm) REVERT: d 19 PHE cc_start: 0.8291 (m-80) cc_final: 0.7990 (m-80) REVERT: e 137 PHE cc_start: 0.8028 (m-80) cc_final: 0.7461 (m-80) REVERT: g 51 ARG cc_start: 0.5638 (mmt-90) cc_final: 0.5250 (mmm-85) REVERT: j 108 MET cc_start: 0.8033 (mmm) cc_final: 0.7730 (mmt) REVERT: k 45 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7678 (tm-30) REVERT: n 1 MET cc_start: 0.7412 (ptt) cc_final: 0.6774 (ptp) REVERT: q 24 TYR cc_start: 0.7773 (t80) cc_final: 0.7565 (t80) REVERT: q 100 PHE cc_start: 0.8680 (m-80) cc_final: 0.8405 (m-10) REVERT: r 60 LYS cc_start: 0.9684 (pttp) cc_final: 0.9444 (pttp) REVERT: r 78 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.7982 (mmt-90) REVERT: s 94 ASP cc_start: 0.7977 (m-30) cc_final: 0.7217 (t0) REVERT: t 1 MET cc_start: 0.6021 (tpt) cc_final: 0.5748 (mmm) REVERT: v 48 MET cc_start: 0.7849 (mmm) cc_final: 0.7496 (mmm) REVERT: x 55 MET cc_start: 0.9527 (mmp) cc_final: 0.9268 (tpt) REVERT: D 29 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8944 (tm-30) REVERT: F 1 MET cc_start: 0.4552 (ttm) cc_final: 0.4029 (ppp) REVERT: G 135 MET cc_start: 0.4405 (mmp) cc_final: 0.3647 (ttm) REVERT: G 212 TYR cc_start: 0.6280 (m-10) cc_final: 0.6055 (m-10) REVERT: I 75 TYR cc_start: 0.8775 (t80) cc_final: 0.8549 (t80) REVERT: I 134 TYR cc_start: 0.8683 (t80) cc_final: 0.8370 (t80) REVERT: J 59 ILE cc_start: 0.8323 (pt) cc_final: 0.8086 (pt) REVERT: K 21 MET cc_start: 0.4778 (mpp) cc_final: 0.4148 (mpp) REVERT: M 48 PHE cc_start: 0.8222 (p90) cc_final: 0.7647 (p90) REVERT: O 65 TYR cc_start: 0.6236 (m-80) cc_final: 0.5814 (m-80) REVERT: Q 81 ILE cc_start: 0.9595 (pt) cc_final: 0.9231 (mp) REVERT: R 2 ARG cc_start: 0.6632 (ttm-80) cc_final: 0.5952 (mmp80) REVERT: R 22 TYR cc_start: 0.6030 (t80) cc_final: 0.5769 (t80) REVERT: U 1 MET cc_start: 0.7602 (tpp) cc_final: 0.6705 (tpp) REVERT: U 39 PHE cc_start: 0.8893 (t80) cc_final: 0.8487 (t80) REVERT: Y 35 TYR cc_start: 0.8361 (m-80) cc_final: 0.8075 (m-80) REVERT: Y 74 HIS cc_start: 0.8870 (m-70) cc_final: 0.8317 (m-70) REVERT: a 9 ARG cc_start: 0.5122 (ttp80) cc_final: 0.4807 (tpp80) REVERT: 8 151 MET cc_start: 0.4654 (ttp) cc_final: 0.4308 (tmm) REVERT: 8 172 GLU cc_start: 0.6012 (tt0) cc_final: 0.5230 (tm-30) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 1.2863 time to fit residues: 1024.5912 Evaluate side-chains 367 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 6.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 627 optimal weight: 40.0000 chunk 405 optimal weight: 40.0000 chunk 606 optimal weight: 30.0000 chunk 305 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 645 optimal weight: 30.0000 chunk 691 optimal weight: 30.0000 chunk 501 optimal weight: 30.0000 chunk 94 optimal weight: 40.0000 chunk 797 optimal weight: 30.0000 overall best weight: 22.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 ASN b 116 GLN ** b 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 ASN ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 ASN j 47 HIS ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN ** x 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 1.0242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.175 160361 Z= 0.487 Angle : 1.034 26.769 239566 Z= 0.517 Chirality : 0.052 0.381 30559 Planarity : 0.007 0.105 13074 Dihedral : 26.046 177.657 79401 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 59.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.07 % Favored : 84.78 % Rotamer: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.97 (0.10), residues: 6011 helix: -2.20 (0.11), residues: 1702 sheet: -2.97 (0.16), residues: 865 loop : -2.85 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP G 95 HIS 0.023 0.003 HIS T 45 PHE 0.053 0.004 PHE 8 221 TYR 0.056 0.004 TYR 8 296 ARG 0.019 0.001 ARG q 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 430 time to evaluate : 6.465 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: b 160 TYR cc_start: 0.8808 (p90) cc_final: 0.7846 (p90) REVERT: b 239 PHE cc_start: 0.4284 (t80) cc_final: 0.3748 (t80) REVERT: c 11 MET cc_start: 0.8026 (pmm) cc_final: 0.7370 (pmm) REVERT: c 118 PHE cc_start: 0.8505 (t80) cc_final: 0.8254 (t80) REVERT: e 137 PHE cc_start: 0.7888 (m-80) cc_final: 0.7359 (m-80) REVERT: f 176 LYS cc_start: 0.6185 (mtpt) cc_final: 0.5907 (pttm) REVERT: j 108 MET cc_start: 0.8341 (mmm) cc_final: 0.7898 (mmt) REVERT: k 45 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7667 (tm-30) REVERT: m 25 ASP cc_start: 0.7445 (t0) cc_final: 0.7216 (t0) REVERT: m 91 TYR cc_start: 0.8235 (p90) cc_final: 0.7908 (p90) REVERT: q 100 PHE cc_start: 0.8569 (m-80) cc_final: 0.8342 (m-10) REVERT: r 40 MET cc_start: 0.8495 (tpt) cc_final: 0.7724 (tpp) REVERT: r 48 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8159 (mmtt) REVERT: r 78 ARG cc_start: 0.8568 (mmt180) cc_final: 0.8098 (mmt90) REVERT: s 94 ASP cc_start: 0.8512 (m-30) cc_final: 0.7205 (t0) REVERT: t 11 LEU cc_start: 0.9163 (mt) cc_final: 0.8960 (mt) REVERT: x 55 MET cc_start: 0.9613 (mmp) cc_final: 0.9394 (tpp) REVERT: z 46 MET cc_start: 0.7685 (mtt) cc_final: 0.7447 (mtt) REVERT: D 29 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8981 (tm-30) REVERT: F 1 MET cc_start: 0.4987 (ttm) cc_final: 0.4310 (ppp) REVERT: G 95 TRP cc_start: 0.5573 (t-100) cc_final: 0.5181 (t-100) REVERT: G 135 MET cc_start: 0.4223 (mmp) cc_final: 0.3335 (ttm) REVERT: J 110 MET cc_start: 0.8530 (ptt) cc_final: 0.8272 (ptt) REVERT: Q 81 ILE cc_start: 0.9575 (pt) cc_final: 0.9209 (mp) REVERT: R 2 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.5987 (mmp80) REVERT: T 14 PHE cc_start: 0.7499 (m-80) cc_final: 0.7102 (m-80) REVERT: U 1 MET cc_start: 0.7692 (tpp) cc_final: 0.6843 (tpp) REVERT: X 65 MET cc_start: 0.3367 (tmm) cc_final: 0.2914 (tmm) REVERT: Y 35 TYR cc_start: 0.8441 (m-80) cc_final: 0.8174 (m-80) REVERT: Y 74 HIS cc_start: 0.8907 (m-70) cc_final: 0.8467 (m-70) REVERT: Z 36 PHE cc_start: 0.5309 (m-10) cc_final: 0.4958 (m-10) REVERT: Z 39 LYS cc_start: 0.6301 (tttt) cc_final: 0.5466 (mmtt) REVERT: a 9 ARG cc_start: 0.5046 (ttp80) cc_final: 0.4633 (tpt170) REVERT: 8 73 MET cc_start: 0.2913 (ttp) cc_final: 0.2631 (ptm) REVERT: 8 151 MET cc_start: 0.4923 (ttp) cc_final: 0.4568 (tmm) REVERT: 8 172 GLU cc_start: 0.6009 (tt0) cc_final: 0.5419 (tm-30) outliers start: 2 outliers final: 0 residues processed: 432 average time/residue: 1.2925 time to fit residues: 980.4653 Evaluate side-chains 346 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 8.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 923 optimal weight: 50.0000 chunk 972 optimal weight: 30.0000 chunk 887 optimal weight: 20.0000 chunk 945 optimal weight: 20.0000 chunk 569 optimal weight: 30.0000 chunk 412 optimal weight: 7.9990 chunk 742 optimal weight: 40.0000 chunk 290 optimal weight: 3.9990 chunk 854 optimal weight: 50.0000 chunk 894 optimal weight: 50.0000 chunk 942 optimal weight: 20.0000 overall best weight: 14.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN b 259 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Z 55 HIS 8 48 ASN ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 346 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 1.0132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 160361 Z= 0.338 Angle : 0.824 22.162 239566 Z= 0.416 Chirality : 0.044 0.327 30559 Planarity : 0.006 0.080 13074 Dihedral : 25.665 179.275 79401 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 44.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.04 % Favored : 85.89 % Rotamer: Outliers : 0.02 % Allowed : 1.16 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.10), residues: 6011 helix: -1.82 (0.11), residues: 1737 sheet: -2.83 (0.16), residues: 879 loop : -2.73 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 95 HIS 0.021 0.002 HIS T 45 PHE 0.037 0.003 PHE I 19 TYR 0.039 0.003 TYR I 75 ARG 0.019 0.001 ARG 8 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 6.361 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: b 160 TYR cc_start: 0.8692 (p90) cc_final: 0.7610 (p90) REVERT: b 239 PHE cc_start: 0.3856 (t80) cc_final: 0.3515 (t80) REVERT: c 11 MET cc_start: 0.7967 (pmm) cc_final: 0.7269 (pmm) REVERT: d 19 PHE cc_start: 0.8269 (m-80) cc_final: 0.8006 (m-80) REVERT: d 119 ILE cc_start: 0.9100 (tp) cc_final: 0.8846 (mp) REVERT: e 137 PHE cc_start: 0.7824 (m-80) cc_final: 0.7301 (m-80) REVERT: f 176 LYS cc_start: 0.6252 (mtpt) cc_final: 0.5921 (pttm) REVERT: g 51 ARG cc_start: 0.5623 (mmt-90) cc_final: 0.5067 (mtp180) REVERT: j 43 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8559 (tp30) REVERT: j 108 MET cc_start: 0.8440 (mmm) cc_final: 0.7324 (mmt) REVERT: m 65 ILE cc_start: 0.8842 (mm) cc_final: 0.8628 (mm) REVERT: n 20 MET cc_start: 0.9322 (tmm) cc_final: 0.9122 (tmm) REVERT: p 12 MET cc_start: 0.9157 (mmt) cc_final: 0.8710 (mmt) REVERT: q 100 PHE cc_start: 0.8601 (m-80) cc_final: 0.8319 (m-10) REVERT: q 108 LEU cc_start: 0.9467 (tp) cc_final: 0.9213 (tp) REVERT: q 109 VAL cc_start: 0.9142 (t) cc_final: 0.8800 (t) REVERT: q 110 GLU cc_start: 0.8869 (mp0) cc_final: 0.8623 (mp0) REVERT: r 35 PHE cc_start: 0.9118 (m-80) cc_final: 0.8412 (m-80) REVERT: r 40 MET cc_start: 0.8439 (tpt) cc_final: 0.7835 (tpp) REVERT: r 48 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8140 (tptp) REVERT: r 78 ARG cc_start: 0.8548 (mmt180) cc_final: 0.8132 (mmt90) REVERT: r 98 ILE cc_start: 0.9441 (mp) cc_final: 0.9087 (tt) REVERT: s 52 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8285 (mt-10) REVERT: s 94 ASP cc_start: 0.8385 (m-30) cc_final: 0.7219 (t0) REVERT: v 45 ASP cc_start: 0.8598 (t0) cc_final: 0.8260 (t0) REVERT: v 48 MET cc_start: 0.7671 (mmp) cc_final: 0.7212 (mmm) REVERT: x 55 MET cc_start: 0.9558 (mmp) cc_final: 0.9313 (tpt) REVERT: y 23 ARG cc_start: 0.9466 (mpt180) cc_final: 0.9119 (mpt180) REVERT: z 46 MET cc_start: 0.8010 (mtt) cc_final: 0.7722 (mtt) REVERT: D 29 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9037 (tm-30) REVERT: F 1 MET cc_start: 0.4924 (ttm) cc_final: 0.4338 (ppp) REVERT: G 95 TRP cc_start: 0.5360 (t-100) cc_final: 0.4837 (t-100) REVERT: G 112 ARG cc_start: 0.5912 (tpt170) cc_final: 0.5091 (ttm170) REVERT: I 44 LYS cc_start: 0.6785 (tmmt) cc_final: 0.6562 (mtpp) REVERT: I 75 TYR cc_start: 0.8835 (t80) cc_final: 0.8552 (t80) REVERT: J 146 MET cc_start: 0.8117 (ppp) cc_final: 0.7759 (ppp) REVERT: K 88 MET cc_start: -0.4098 (ptt) cc_final: -0.4633 (ptt) REVERT: M 48 PHE cc_start: 0.8079 (p90) cc_final: 0.7567 (p90) REVERT: M 75 GLN cc_start: 0.7847 (pm20) cc_final: 0.7326 (pp30) REVERT: Q 55 ARG cc_start: 0.9368 (tpt-90) cc_final: 0.8958 (tpt170) REVERT: Q 81 ILE cc_start: 0.9594 (pt) cc_final: 0.9281 (mp) REVERT: R 2 ARG cc_start: 0.7181 (ttm-80) cc_final: 0.6081 (mmp80) REVERT: T 14 PHE cc_start: 0.7246 (m-80) cc_final: 0.6763 (m-80) REVERT: U 1 MET cc_start: 0.7555 (tpp) cc_final: 0.6670 (tpp) REVERT: Y 35 TYR cc_start: 0.8399 (m-80) cc_final: 0.8120 (m-80) REVERT: Z 39 LYS cc_start: 0.6401 (tttt) cc_final: 0.5580 (mmtt) REVERT: a 8 MET cc_start: 0.3778 (tpp) cc_final: 0.3572 (ttt) REVERT: 8 151 MET cc_start: 0.4722 (ttp) cc_final: 0.4118 (tmm) REVERT: 8 172 GLU cc_start: 0.6038 (tt0) cc_final: 0.5565 (tm-30) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 1.2722 time to fit residues: 1011.4531 Evaluate side-chains 357 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 6.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 621 optimal weight: 50.0000 chunk 1000 optimal weight: 40.0000 chunk 610 optimal weight: 30.0000 chunk 474 optimal weight: 0.0040 chunk 695 optimal weight: 20.0000 chunk 1049 optimal weight: 7.9990 chunk 965 optimal weight: 20.0000 chunk 835 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 645 optimal weight: 40.0000 chunk 512 optimal weight: 20.0000 overall best weight: 11.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN s 31 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN O 15 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 1.0193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 160361 Z= 0.293 Angle : 0.768 20.953 239566 Z= 0.389 Chirality : 0.041 0.306 30559 Planarity : 0.006 0.064 13074 Dihedral : 25.569 179.714 79401 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 41.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.16 % Favored : 86.74 % Rotamer: Outliers : 0.02 % Allowed : 0.48 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.49 (0.10), residues: 6011 helix: -1.61 (0.11), residues: 1738 sheet: -2.75 (0.16), residues: 862 loop : -2.65 (0.10), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 95 HIS 0.021 0.002 HIS T 45 PHE 0.037 0.002 PHE Y 30 TYR 0.032 0.003 TYR I 75 ARG 0.009 0.001 ARG B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12022 Ramachandran restraints generated. 6011 Oldfield, 0 Emsley, 6011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 454 time to evaluate : 6.458 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: b 160 TYR cc_start: 0.8669 (p90) cc_final: 0.7626 (p90) REVERT: b 239 PHE cc_start: 0.3895 (t80) cc_final: 0.3622 (t80) REVERT: c 11 MET cc_start: 0.7776 (pmm) cc_final: 0.7061 (pmm) REVERT: d 19 PHE cc_start: 0.8204 (m-80) cc_final: 0.7926 (m-80) REVERT: d 119 ILE cc_start: 0.9107 (tp) cc_final: 0.8842 (mp) REVERT: e 137 PHE cc_start: 0.7860 (m-80) cc_final: 0.7412 (m-80) REVERT: f 176 LYS cc_start: 0.6494 (mtpt) cc_final: 0.6250 (pttm) REVERT: g 51 ARG cc_start: 0.5926 (mmt-90) cc_final: 0.5591 (mmm-85) REVERT: j 108 MET cc_start: 0.8350 (mmm) cc_final: 0.7978 (mmt) REVERT: j 118 MET cc_start: 0.8721 (pmm) cc_final: 0.8332 (pmm) REVERT: m 65 ILE cc_start: 0.8721 (mm) cc_final: 0.8510 (mm) REVERT: n 1 MET cc_start: 0.7324 (ptp) cc_final: 0.7104 (ptp) REVERT: n 20 MET cc_start: 0.9315 (tmm) cc_final: 0.9091 (tmm) REVERT: p 12 MET cc_start: 0.9227 (mmt) cc_final: 0.8737 (mmt) REVERT: q 100 PHE cc_start: 0.8574 (m-80) cc_final: 0.8289 (m-10) REVERT: q 109 VAL cc_start: 0.9114 (t) cc_final: 0.8843 (t) REVERT: q 110 GLU cc_start: 0.8914 (mp0) cc_final: 0.8674 (mp0) REVERT: r 40 MET cc_start: 0.8473 (tpt) cc_final: 0.7736 (tpp) REVERT: r 78 ARG cc_start: 0.8524 (mmt180) cc_final: 0.7386 (tpp80) REVERT: r 98 ILE cc_start: 0.9494 (mp) cc_final: 0.9183 (tt) REVERT: s 52 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8245 (mt-10) REVERT: s 94 ASP cc_start: 0.8433 (m-30) cc_final: 0.7258 (t70) REVERT: t 1 MET cc_start: 0.4703 (mmp) cc_final: 0.2697 (mtt) REVERT: v 3 THR cc_start: 0.8241 (p) cc_final: 0.7917 (p) REVERT: v 48 MET cc_start: 0.7857 (mmp) cc_final: 0.7556 (mmm) REVERT: x 55 MET cc_start: 0.9523 (mmp) cc_final: 0.9280 (tpt) REVERT: y 23 ARG cc_start: 0.9426 (mpt180) cc_final: 0.9122 (mpt180) REVERT: z 46 MET cc_start: 0.8018 (mtt) cc_final: 0.7781 (mtt) REVERT: B 14 MET cc_start: 0.8570 (mmp) cc_final: 0.8346 (mmp) REVERT: C 7 LYS cc_start: 0.7899 (mttt) cc_final: 0.6908 (pttt) REVERT: F 1 MET cc_start: 0.4564 (ttm) cc_final: 0.4139 (ppp) REVERT: G 95 TRP cc_start: 0.5909 (t-100) cc_final: 0.5548 (t-100) REVERT: G 112 ARG cc_start: 0.5864 (tpt170) cc_final: 0.5047 (ttm170) REVERT: G 135 MET cc_start: 0.3753 (mmp) cc_final: 0.3099 (ttm) REVERT: G 199 ILE cc_start: 0.5384 (mt) cc_final: 0.5126 (mt) REVERT: I 75 TYR cc_start: 0.8832 (t80) cc_final: 0.8567 (t80) REVERT: I 134 TYR cc_start: 0.8873 (t80) cc_final: 0.8507 (t80) REVERT: K 88 MET cc_start: -0.4270 (ptt) cc_final: -0.4842 (ptm) REVERT: M 48 PHE cc_start: 0.7950 (p90) cc_final: 0.7489 (p90) REVERT: M 75 GLN cc_start: 0.7860 (pm20) cc_final: 0.7518 (pm20) REVERT: O 76 ILE cc_start: 0.4577 (mm) cc_final: 0.4375 (mm) REVERT: Q 81 ILE cc_start: 0.9587 (pt) cc_final: 0.9300 (mp) REVERT: T 14 PHE cc_start: 0.7273 (m-80) cc_final: 0.6873 (m-80) REVERT: U 1 MET cc_start: 0.7577 (tpp) cc_final: 0.6880 (tpp) REVERT: Y 35 TYR cc_start: 0.8396 (m-80) cc_final: 0.8119 (m-80) REVERT: Z 39 LYS cc_start: 0.6275 (tttt) cc_final: 0.5444 (mmtt) REVERT: 8 151 MET cc_start: 0.4616 (ttp) cc_final: 0.4090 (tmm) REVERT: 8 172 GLU cc_start: 0.5942 (tt0) cc_final: 0.5294 (tm-30) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 1.2616 time to fit residues: 1013.3492 Evaluate side-chains 366 residues out of total 5007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 6.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1053 random chunks: chunk 663 optimal weight: 50.0000 chunk 889 optimal weight: 30.0000 chunk 255 optimal weight: 9.9990 chunk 770 optimal weight: 40.0000 chunk 123 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 836 optimal weight: 20.0000 chunk 350 optimal weight: 10.0000 chunk 859 optimal weight: 50.0000 chunk 105 optimal weight: 30.0000 chunk 154 optimal weight: 6.9990 overall best weight: 7.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 GLN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN f 63 GLN f 72 ASN ** k 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 19 HIS ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** 8 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.055636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.038270 restraints weight = 1701537.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.038792 restraints weight = 833476.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.038944 restraints weight = 573391.845| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 160361 Z= 0.212 Angle : 0.666 17.150 239566 Z= 0.339 Chirality : 0.037 0.382 30559 Planarity : 0.005 0.067 13074 Dihedral : 25.252 179.973 79401 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 33.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.63 % Favored : 88.34 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.10), residues: 6011 helix: -1.34 (0.11), residues: 1761 sheet: -2.63 (0.16), residues: 846 loop : -2.48 (0.10), residues: 3404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 95 HIS 0.020 0.002 HIS T 45 PHE 0.041 0.002 PHE U 39 TYR 0.030 0.002 TYR I 75 ARG 0.029 0.001 ARG f 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22100.20 seconds wall clock time: 399 minutes 53.16 seconds (23993.16 seconds total)