Starting phenix.real_space_refine on Mon Mar 25 11:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sso_25411/03_2024/7sso_25411_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sso_25411/03_2024/7sso_25411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sso_25411/03_2024/7sso_25411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sso_25411/03_2024/7sso_25411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sso_25411/03_2024/7sso_25411_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sso_25411/03_2024/7sso_25411_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 sd= 1.142 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 4730 5.49 5 S 160 5.16 5 C 74989 2.51 5 N 27738 2.21 5 O 41363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 65": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 144": "OE1" <-> "OE2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 30": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 39": "OD1" <-> "OD2" Residue "c ASP 43": "OD1" <-> "OD2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "c GLU 99": "OE1" <-> "OE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ASP 7": "OD1" <-> "OD2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ASP 122": "OD1" <-> "OD2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 164": "OE1" <-> "OE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "h GLU 17": "OE1" <-> "OE2" Residue "h TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 114": "OE1" <-> "OE2" Residue "i TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 63": "OD1" <-> "OD2" Residue "i GLU 107": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l GLU 51": "OE1" <-> "OE2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ASP 91": "OD1" <-> "OD2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 70": "OD1" <-> "OD2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n GLU 74": "OE1" <-> "OE2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 55": "OE1" <-> "OE2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 10": "OE1" <-> "OE2" Residue "p PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ASP 81": "OD1" <-> "OD2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 90": "OD1" <-> "OD2" Residue "q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 22": "OD1" <-> "OD2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 68": "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 GLU 25": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 80": "OD1" <-> "OD2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 87": "OE1" <-> "OE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 59": "OE1" <-> "OE2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w GLU 25": "OE1" <-> "OE2" Residue "w ASP 52": "OD1" <-> "OD2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 66": "OE1" <-> "OE2" Residue "w PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 42": "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 5": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 57": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K ASP 13": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ASP 20": "OD1" <-> "OD2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 45": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 19": "OE1" <-> "OE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148980 Number of models: 1 Model: "" Number of chains: 60 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': 93, 'rna2p_pyr': 50, 'rna3p_pur': 781, 'rna3p_pyr': 615} Link IDs: {'rna2p': 143, 'rna3p': 1395} 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': 237, 'rna2p_pyr': 117, 'rna3p_pur': 1437, 'rna3p_pyr': 1112} Link IDs: {'rna2p': 354, 'rna3p': 2548} 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': 5, 'rna2p_pyr': 4, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "h" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 351 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 413 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "6" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "1" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 60.38, per 1000 atoms: 0.41 Number of scatterers: 148980 At special positions: 0 Unit cell: (247.34, 239.87, 253.15, 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 160 16.00 P 4730 15.00 O 41363 8.00 N 27738 7.00 C 74989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 70.77 Conformation dependent library (CDL) restraints added in 7.3 seconds 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11162 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 186 helices and 70 sheets defined 38.5% alpha, 18.1% beta 1401 base pairs and 2374 stacking pairs defined. Time for finding SS restraints: 83.33 Creating SS restraints... Processing helix chain 'b' and resid 9 through 15 removed outlier: 7.352A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.054A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU b 34 " --> pdb=" O ALA b 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 29 through 34' Processing helix chain 'b' and resid 130 through 135 removed outlier: 4.407A pdb=" N ILE b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Proline residue: b 135 - end of helix No H-bonds generated for 'chain 'b' and resid 130 through 135' Processing helix chain 'b' and resid 206 through 214 removed outlier: 4.186A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 4.156A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 267 removed outlier: 6.672A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 201 removed outlier: 3.824A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 5.746A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 removed outlier: 3.577A pdb=" N GLY c 66 " --> pdb=" O LYS c 62 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE c 68 " --> pdb=" O GLU c 64 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 103 removed outlier: 4.763A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 103' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 removed outlier: 4.226A pdb=" N GLY c 44 " --> pdb=" O ASP c 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 39 through 44' Processing helix chain 'd' and resid 15 through 20 removed outlier: 3.601A pdb=" N PHE d 19 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.644A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.573A pdb=" N GLY d 103 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA d 104 " --> pdb=" O MET d 100 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU d 105 " --> pdb=" O TYR d 101 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER d 110 " --> pdb=" O LYS d 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 4.232A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 3.572A pdb=" N LEU d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 4.347A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 4.175A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU d 197 " --> pdb=" O VAL d 193 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 4.165A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR e 6 " --> pdb=" O LYS e 2 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 removed outlier: 3.996A pdb=" N ASP e 45 " --> pdb=" O GLU e 41 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 41 through 46' Processing helix chain 'e' and resid 47 through 61 removed outlier: 3.795A pdb=" N ILE e 59 " --> pdb=" O ASP e 55 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 4.085A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA e 106 " --> pdb=" O LEU e 102 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL e 107 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Proline residue: e 108 - end of helix Processing helix chain 'e' and resid 161 through 173 removed outlier: 3.627A pdb=" N ALA e 170 " --> pdb=" O ARG e 166 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 138 removed outlier: 3.501A pdb=" N ILE e 136 " --> pdb=" O GLU e 133 " (cutoff:3.500A) Proline residue: e 138 - end of helix Processing helix chain 'f' and resid 1 through 6 removed outlier: 5.211A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.511A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET f 74 " --> pdb=" O LEU f 70 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL f 75 " --> pdb=" O LEU f 71 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.516A pdb=" N ILE f 140 " --> pdb=" O ASP f 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG f 148 " --> pdb=" O ALA f 144 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 27 removed outlier: 3.640A pdb=" N ALA g 26 " --> pdb=" O LYS g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 49 removed outlier: 4.442A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE g 47 " --> pdb=" O ASN g 43 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 74 removed outlier: 3.550A pdb=" N ASN g 66 " --> pdb=" O LEU g 62 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA g 74 " --> pdb=" O GLU g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 107 removed outlier: 4.023A pdb=" N ALA g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 3.873A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 111 through 116' Processing helix chain 'a' and resid 6 through 16 removed outlier: 4.444A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 34 removed outlier: 3.775A pdb=" N ALA a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU a 29 " --> pdb=" O GLU a 25 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU a 33 " --> pdb=" O LEU a 29 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 22 through 34' Processing helix chain 'a' and resid 181 through 197 removed outlier: 3.516A pdb=" N LEU a 185 " --> pdb=" O ASP a 181 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL a 194 " --> pdb=" O GLU a 190 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 22 removed outlier: 3.520A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA h 13 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU h 17 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA h 22 " --> pdb=" O VAL h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 48 removed outlier: 3.770A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG h 46 " --> pdb=" O ARG h 42 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA h 48 " --> pdb=" O ALA h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 71 removed outlier: 4.458A pdb=" N GLU h 65 " --> pdb=" O ARG h 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY h 66 " --> pdb=" O ARG h 62 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Proline residue: h 68 - end of helix removed outlier: 4.340A pdb=" N CYS h 71 " --> pdb=" O THR h 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 61 through 71' Processing helix chain 'h' and resid 74 through 79 removed outlier: 4.177A pdb=" N GLY h 78 " --> pdb=" O ASP h 74 " (cutoff:3.500A) Proline residue: h 79 - end of helix No H-bonds generated for 'chain 'h' and resid 74 through 79' Processing helix chain 'h' and resid 94 through 104 removed outlier: 3.752A pdb=" N PHE h 99 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA h 100 " --> pdb=" O PHE h 96 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA h 104 " --> pdb=" O ALA h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 114 removed outlier: 6.179A pdb=" N ALA h 112 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU h 114 " --> pdb=" O ALA h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 31 removed outlier: 3.785A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN i 29 " --> pdb=" O PRO i 25 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY i 31 " --> pdb=" O LEU i 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 23 through 31' Processing helix chain 'i' and resid 33 through 46 removed outlier: 3.560A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE i 41 " --> pdb=" O PHE i 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN i 42 " --> pdb=" O CYS i 38 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 84 removed outlier: 3.987A pdb=" N LEU i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 116 removed outlier: 3.896A pdb=" N ILE i 108 " --> pdb=" O GLN i 104 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN i 110 " --> pdb=" O GLN i 106 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA i 114 " --> pdb=" O GLN i 110 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP i 115 " --> pdb=" O THR i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 121 through 136 removed outlier: 4.349A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER i 134 " --> pdb=" O GLY i 130 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.533A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG j 35 " --> pdb=" O GLU j 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.667A pdb=" N ARG j 96 " --> pdb=" O MET j 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.501A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU j 109 " --> pdb=" O VAL j 105 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 122 removed outlier: 3.793A pdb=" N PHE j 119 " --> pdb=" O GLY j 115 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 119 removed outlier: 6.391A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 42 removed outlier: 5.534A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 removed outlier: 3.624A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.306A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 86 removed outlier: 4.781A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLU l 86 " --> pdb=" O LEU l 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 86' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.470A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.568A pdb=" N ALA l 137 " --> pdb=" O ALA l 133 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY l 139 " --> pdb=" O ILE l 135 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 Processing helix chain 'm' and resid 109 through 125 removed outlier: 4.134A pdb=" N LEU m 119 " --> pdb=" O GLU m 115 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.998A pdb=" N GLY n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER n 27 " --> pdb=" O ASN n 23 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 3.808A pdb=" N GLU n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.304A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 4.903A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 81 removed outlier: 4.172A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 89 removed outlier: 3.779A pdb=" N ARG n 86 " --> pdb=" O GLU n 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA n 88 " --> pdb=" O GLY n 84 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER n 89 " --> pdb=" O PRO n 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 82 through 89' Processing helix chain 'o' and resid 2 through 20 removed outlier: 3.522A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR o 12 " --> pdb=" O ILE o 8 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 3.913A pdb=" N GLU o 60 " --> pdb=" O LYS o 56 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 4.233A pdb=" N ALA o 71 " --> pdb=" O ASN o 67 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA o 72 " --> pdb=" O LYS o 68 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA o 73 " --> pdb=" O ASP o 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL o 74 " --> pdb=" O ALA o 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.888A pdb=" N LEU o 106 " --> pdb=" O ARG o 102 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA o 107 " --> pdb=" O VAL o 103 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU o 112 " --> pdb=" O ASP o 108 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY o 114 " --> pdb=" O ALA o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 12 removed outlier: 4.314A pdb=" N LYS p 5 " --> pdb=" O SER p 1 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 103 removed outlier: 4.766A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) Processing helix chain 'q' and resid 5 through 21 removed outlier: 4.163A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS q 15 " --> pdb=" O ALA q 11 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.409A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL q 30 " --> pdb=" O ALA q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 25 through 30' Processing helix chain 'q' and resid 31 through 36 removed outlier: 4.244A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 72 removed outlier: 3.656A pdb=" N ALA q 45 " --> pdb=" O ALA q 41 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA q 62 " --> pdb=" O GLN q 58 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG q 69 " --> pdb=" O ASN q 65 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN q 70 " --> pdb=" O ALA q 66 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.515A pdb=" N ASN q 80 " --> pdb=" O SER q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.605A pdb=" N LEU q 108 " --> pdb=" O ALA q 104 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 3.609A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 4.146A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN s 40 " --> pdb=" O LEU s 36 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.719A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA s 56 " --> pdb=" O GLU s 52 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 70 removed outlier: 4.989A pdb=" N LEU s 69 " --> pdb=" O ASP s 65 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS s 70 " --> pdb=" O ILE s 66 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 65 through 70' Processing helix chain 't' and resid 2 through 11 removed outlier: 3.956A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.666A pdb=" N MET t 24 " --> pdb=" O ALA t 20 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 removed outlier: 3.555A pdb=" N ALA t 45 " --> pdb=" O ALA t 41 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.057A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 24 removed outlier: 3.599A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 52 removed outlier: 3.826A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 4.914A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 3.632A pdb=" N ARG x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE x 58 " --> pdb=" O GLY x 54 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS x 60 " --> pdb=" O ARG x 56 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 removed outlier: 4.625A pdb=" N GLU x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU x 70 " --> pdb=" O VAL x 66 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG x 71 " --> pdb=" O LEU x 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 1 through 8 removed outlier: 4.198A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 35 removed outlier: 4.092A pdb=" N ASN y 15 " --> pdb=" O VAL y 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU y 18 " --> pdb=" O LEU y 14 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 61 removed outlier: 6.038A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA y 61 " --> pdb=" O LEU y 57 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.606A pdb=" N THR z 22 " --> pdb=" O LYS z 18 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.674A pdb=" N SER B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 24 removed outlier: 4.402A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.683A pdb=" N GLN D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.764A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.660A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.619A pdb=" N LEU E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 4 through 12 removed outlier: 3.500A pdb=" N MET G 8 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS G 10 " --> pdb=" O ARG G 6 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 63 removed outlier: 4.036A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.558A pdb=" N ILE G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.520A pdb=" N VAL G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 removed outlier: 4.243A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 116 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.988A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 146 removed outlier: 3.673A pdb=" N LEU G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 152 removed outlier: 3.949A pdb=" N LYS G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASP G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 147 through 152' Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.573A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 4.127A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.620A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.570A pdb=" N ASP H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN H 40 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 45 " --> pdb=" O TYR H 41 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 4.362A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 95 removed outlier: 4.157A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.526A pdb=" N VAL H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.838A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.429A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 67 through 82 removed outlier: 4.109A pdb=" N TYR I 74 " --> pdb=" O GLN I 70 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR I 75 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.654A pdb=" N LEU I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 removed outlier: 3.672A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 120 removed outlier: 4.053A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 6.207A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU I 159 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 5.410A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER I 204 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.610A pdb=" N ILE J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.480A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 5.598A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 4.055A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.665A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 removed outlier: 4.503A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.266A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR K 30 " --> pdb=" O THR K 26 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.988A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 34 through 52 Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.523A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 3.703A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET L 100 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.556A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 148 removed outlier: 4.063A pdb=" N ASN L 147 " --> pdb=" O MET L 143 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.896A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.608A pdb=" N ALA M 115 " --> pdb=" O THR M 111 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 Processing helix chain 'N' and resid 43 through 55 removed outlier: 5.102A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.703A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.519A pdb=" N GLY N 76 " --> pdb=" O SER N 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 3.566A pdb=" N ARG N 94 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.606A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 88 removed outlier: 3.654A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.086A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 45 through 50' Processing helix chain 'P' and resid 53 through 58 removed outlier: 4.693A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 73 removed outlier: 3.897A pdb=" N GLN P 63 " --> pdb=" O PRO P 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL P 64 " --> pdb=" O PHE P 60 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 removed outlier: 3.865A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.563A pdb=" N ARG Q 8 " --> pdb=" O ASN Q 4 " (cutoff:3.500A) Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.927A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 22 removed outlier: 3.576A pdb=" N THR R 19 " --> pdb=" O VAL R 15 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.533A pdb=" N LYS R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.251A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 61 removed outlier: 4.388A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 4.234A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET R 80 " --> pdb=" O ILE R 76 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP R 81 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 removed outlier: 3.521A pdb=" N LEU R 88 " --> pdb=" O CYS R 84 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG R 89 " --> pdb=" O TYR R 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.594A pdb=" N GLU S 9 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 28 removed outlier: 3.974A pdb=" N LYS S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 23 through 28' Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.964A pdb=" N ALA S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'S' and resid 79 through 90 removed outlier: 4.170A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU S 85 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.555A pdb=" N ALA T 8 " --> pdb=" O THR T 4 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 46 removed outlier: 3.616A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU T 44 " --> pdb=" O GLY T 40 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 4.340A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS T 70 " --> pdb=" O LEU T 66 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG T 71 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 3.651A pdb=" N GLN T 79 " --> pdb=" O ALA T 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.618A pdb=" N ALA U 72 " --> pdb=" O SER U 68 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 17 removed outlier: 3.888A pdb=" N GLY W 16 " --> pdb=" O PHE W 12 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 33 removed outlier: 3.582A pdb=" N LYS W 29 " --> pdb=" O ILE W 25 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.723A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 65 removed outlier: 3.526A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.702A pdb=" N GLU X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL X 22 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.726A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 5 through 41 removed outlier: 4.367A pdb=" N ARG Y 9 " --> pdb=" O SER Y 5 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS Y 15 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG Y 17 " --> pdb=" O SER Y 13 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS Y 18 " --> pdb=" O GLU Y 14 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 64 Proline residue: Y 55 - end of helix removed outlier: 4.211A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 86 removed outlier: 3.989A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN Y 81 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.358A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 33 removed outlier: 4.330A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 61 Proline residue: Z 40 - end of helix removed outlier: 3.854A pdb=" N LYS Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA Z 51 " --> pdb=" O ALA Z 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'b' and resid 79 through 82 removed outlier: 3.684A pdb=" N ARG b 79 " --> pdb=" O LEU b 92 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.533A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 170 through 174 Processing sheet with id= 5, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.002A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 10 through 16 removed outlier: 3.716A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 13.155A pdb=" N GLY c 198 " --> pdb=" O LYS c 114 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N LYS c 114 " --> pdb=" O GLY c 198 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP c 200 " --> pdb=" O THR c 112 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR c 112 " --> pdb=" O ASP c 200 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 79 through 83 removed outlier: 6.453A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 179 through 182 removed outlier: 3.515A pdb=" N ARG c 179 " --> pdb=" O LEU c 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP c 181 " --> pdb=" O LEU c 186 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 24 through 29 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'c' and resid 105 through 108 removed outlier: 6.333A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'd' and resid 1 through 5 removed outlier: 3.539A pdb=" N LEU d 5 " --> pdb=" O SER d 10 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER d 10 " --> pdb=" O LEU d 5 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'd' and resid 117 through 120 removed outlier: 3.607A pdb=" N LYS d 185 " --> pdb=" O ASP d 145 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU d 147 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.823A pdb=" N LEU e 65 " --> pdb=" O LYS e 87 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY e 85 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS e 86 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE e 33 " --> pdb=" O LEU e 90 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR e 157 " --> pdb=" O GLY e 125 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLY e 125 " --> pdb=" O THR e 157 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'f' and resid 14 through 19 removed outlier: 3.501A pdb=" N ASN f 19 " --> pdb=" O VAL f 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL f 22 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN f 21 " --> pdb=" O LEU f 36 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 40 through 44 removed outlier: 3.500A pdb=" N GLU f 41 " --> pdb=" O GLY f 52 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY f 52 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'f' and resid 93 through 98 removed outlier: 7.246A pdb=" N ASN f 100 " --> pdb=" O LEU f 116 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS f 114 " --> pdb=" O ILE f 102 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'f' and resid 120 through 124 removed outlier: 6.664A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU f 88 " --> pdb=" O THR f 128 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 2 through 6 removed outlier: 6.356A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS g 35 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'g' and resid 76 through 81 removed outlier: 6.999A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= 21, first strand: chain 'a' and resid 60 through 65 removed outlier: 4.536A pdb=" N GLY a 61 " --> pdb=" O TYR a 163 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR a 163 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'h' and resid 23 through 28 removed outlier: 4.060A pdb=" N LEU h 23 " --> pdb=" O GLU h 87 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU h 87 " --> pdb=" O LEU h 23 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'i' and resid 6 through 13 removed outlier: 6.295A pdb=" N ALA i 6 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL i 60 " --> pdb=" O ALA i 6 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU i 10 " --> pdb=" O VAL i 56 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL i 12 " --> pdb=" O ILE i 54 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE i 54 " --> pdb=" O VAL i 12 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER i 65 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'j' and resid 52 through 57 removed outlier: 4.867A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'j' and resid 74 through 78 removed outlier: 7.396A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'k' and resid 56 through 60 removed outlier: 4.911A pdb=" N ASP k 56 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET k 20 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'k' and resid 68 through 71 removed outlier: 4.460A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'm' and resid 37 through 40 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'm' and resid 62 through 66 removed outlier: 3.636A pdb=" N GLU m 104 " --> pdb=" O TRP m 64 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'n' and resid 33 through 37 removed outlier: 4.393A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.734A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS o 29 " --> pdb=" O TYR o 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN o 38 " --> pdb=" O VAL o 27 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU o 26 " --> pdb=" O SER o 91 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'p' and resid 67 through 74 removed outlier: 6.681A pdb=" N THR p 59 " --> pdb=" O ILE p 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE p 47 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE p 63 " --> pdb=" O GLU p 43 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLU p 43 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.558A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LEU r 39 " --> pdb=" O ILE r 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE r 49 " --> pdb=" O LEU r 39 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.907A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'r' and resid 57 through 60 removed outlier: 5.253A pdb=" N VAL r 58 " --> pdb=" O SER r 102 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'r' and resid 65 through 72 removed outlier: 5.772A pdb=" N GLN r 91 " --> pdb=" O GLY r 69 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS r 71 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS r 89 " --> pdb=" O LYS r 71 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 's' and resid 2 through 8 Processing sheet with id= 38, first strand: chain 't' and resid 12 through 15 removed outlier: 3.509A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'u' and resid 39 through 44 removed outlier: 5.186A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'v' and resid 69 through 72 removed outlier: 5.620A pdb=" N ALA v 39 " --> pdb=" O ARG v 9 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'w' and resid 41 through 44 removed outlier: 6.230A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'w' and resid 46 through 50 removed outlier: 8.580A pdb=" N ASN w 46 " --> pdb=" O LYS w 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE w 56 " --> pdb=" O GLY w 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY w 50 " --> pdb=" O THR w 54 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.620A pdb=" N VAL x 12 " --> pdb=" O PHE x 28 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'z' and resid 34 through 38 removed outlier: 7.019A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.633A pdb=" N MET A 22 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS A 16 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN A 20 " --> pdb=" O CYS A 16 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.427A pdb=" N GLU B 35 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 7 through 11 Processing sheet with id= 48, first strand: chain 'C' and resid 33 through 38 removed outlier: 7.095A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 50 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.695A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'F' and resid 1 through 4 removed outlier: 3.551A pdb=" N GLN F 37 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE F 23 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'G' and resid 30 through 33 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.568A pdb=" N ILE G 163 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'H' and resid 52 through 58 removed outlier: 3.595A pdb=" N VAL H 65 " --> pdb=" O GLN H 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'H' and resid 163 through 168 removed outlier: 3.693A pdb=" N ARG H 163 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 196 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL H 199 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN H 184 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'I' and resid 140 through 143 Processing sheet with id= 56, first strand: chain 'J' and resid 10 through 23 removed outlier: 4.216A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY J 39 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL J 17 " --> pdb=" O THR J 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR J 33 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG J 19 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER J 31 " --> pdb=" O ARG J 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER J 21 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE J 29 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR J 23 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY J 27 " --> pdb=" O THR J 23 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY J 46 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'J' and resid 83 through 87 removed outlier: 3.720A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL J 122 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.651A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL K 64 " --> pdb=" O TYR K 4 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'L' and resid 71 through 74 removed outlier: 7.022A pdb=" N THR L 71 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'M' and resid 22 through 27 removed outlier: 5.922A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU M 57 " --> pdb=" O GLU M 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'M' and resid 73 through 76 removed outlier: 4.696A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS M 126 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'N' and resid 5 through 10 removed outlier: 3.608A pdb=" N TYR N 5 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE N 20 " --> pdb=" O TYR N 5 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR N 65 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS N 26 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL N 28 " --> pdb=" O LEU N 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'O' and resid 44 through 52 removed outlier: 3.629A pdb=" N ARG O 45 " --> pdb=" O THR O 69 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG O 7 " --> pdb=" O SER O 101 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'P' and resid 29 through 34 removed outlier: 5.164A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.491A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG Q 53 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG Q 49 " --> pdb=" O THR Q 39 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 80 through 83 removed outlier: 5.088A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.526A pdb=" N TYR U 17 " --> pdb=" O PHE U 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'V' and resid 18 through 29 removed outlier: 4.853A pdb=" N LYS V 18 " --> pdb=" O ASP V 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP V 47 " --> pdb=" O LYS V 18 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'V' and resid 59 through 63 removed outlier: 6.752A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER V 71 " --> pdb=" O CYS V 63 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 29 through 32 removed outlier: 4.463A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) 1561 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3490 hydrogen bonds 5614 hydrogen bond angles 0 basepair planarities 1401 basepair parallelities 2374 stacking parallelities Total time for adding SS restraints: 232.53 Time building geometry restraints manager: 75.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 12351 1.31 - 1.44: 67458 1.44 - 1.57: 72237 1.57 - 1.70: 9466 1.70 - 1.83: 287 Bond restraints: 161799 Sorted by residual: bond pdb=" N PRO 5 101 " pdb=" CD PRO 5 101 " ideal model delta sigma weight residual 1.473 1.293 0.180 1.40e-02 5.10e+03 1.66e+02 bond pdb=" CA PRO 5 101 " pdb=" CB PRO 5 101 " ideal model delta sigma weight residual 1.530 1.311 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" N PRO 5 101 " pdb=" CA PRO 5 101 " ideal model delta sigma weight residual 1.466 1.609 -0.143 1.50e-02 4.44e+03 9.05e+01 bond pdb=" C3' U 1 870 " pdb=" O3' U 1 870 " ideal model delta sigma weight residual 1.417 1.551 -0.134 1.50e-02 4.44e+03 8.02e+01 bond pdb=" O3' U 1 870 " pdb=" P U 1 871 " ideal model delta sigma weight residual 1.607 1.737 -0.130 1.50e-02 4.44e+03 7.52e+01 ... (remaining 161794 not shown) Histogram of bond angle deviations from ideal: 96.02 - 103.86: 14239 103.86 - 111.71: 91410 111.71 - 119.55: 63892 119.55 - 127.39: 62402 127.39 - 135.24: 9972 Bond angle restraints: 241915 Sorted by residual: angle pdb=" C CYS V 63 " pdb=" N ARG V 64 " pdb=" CA ARG V 64 " ideal model delta sigma weight residual 120.39 135.17 -14.78 1.39e+00 5.18e-01 1.13e+02 angle pdb=" C3' A 11057 " pdb=" C2' A 11057 " pdb=" O2' A 11057 " ideal model delta sigma weight residual 110.70 124.72 -14.02 1.50e+00 4.44e-01 8.73e+01 angle pdb=" C4' U 11105 " pdb=" C3' U 11105 " pdb=" O3' U 11105 " ideal model delta sigma weight residual 109.40 96.58 12.82 1.50e+00 4.44e-01 7.30e+01 angle pdb=" N ALA h 44 " pdb=" CA ALA h 44 " pdb=" C ALA h 44 " ideal model delta sigma weight residual 113.23 103.71 9.52 1.24e+00 6.50e-01 5.89e+01 angle pdb=" N VAL L 90 " pdb=" CA VAL L 90 " pdb=" C VAL L 90 " ideal model delta sigma weight residual 110.05 118.24 -8.19 1.09e+00 8.42e-01 5.65e+01 ... (remaining 241910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 91410 35.23 - 70.45: 10943 70.45 - 105.68: 1300 105.68 - 140.90: 17 140.90 - 176.13: 25 Dihedral angle restraints: 103695 sinusoidal: 86402 harmonic: 17293 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 -125.78 -54.22 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA PHE e 174 " pdb=" C PHE e 174 " pdb=" N PRO e 175 " pdb=" CA PRO e 175 " ideal model delta harmonic sigma weight residual 180.00 -128.65 -51.35 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA SER k 91 " pdb=" C SER k 91 " pdb=" N GLU k 92 " pdb=" CA GLU k 92 " ideal model delta harmonic sigma weight residual 180.00 -130.66 -49.34 0 5.00e+00 4.00e-02 9.74e+01 ... (remaining 103692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 30186 0.189 - 0.379: 708 0.379 - 0.568: 19 0.568 - 0.757: 3 0.757 - 0.947: 1 Chirality restraints: 30917 Sorted by residual: chirality pdb=" C2' A 11057 " pdb=" C3' A 11057 " pdb=" O2' A 11057 " pdb=" C1' A 11057 " both_signs ideal model delta sigma weight residual False -2.75 -1.81 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" P U 1 871 " pdb=" OP1 U 1 871 " pdb=" OP2 U 1 871 " pdb=" O5' U 1 871 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" C3' A 11020 " pdb=" C4' A 11020 " pdb=" O3' A 11020 " pdb=" C2' A 11020 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.80e+00 ... (remaining 30914 not shown) Planarity restraints: 13067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 11046 " -0.378 2.00e-02 2.50e+03 1.68e-01 7.74e+02 pdb=" N9 A 11046 " 0.005 2.00e-02 2.50e+03 pdb=" C8 A 11046 " 0.126 2.00e-02 2.50e+03 pdb=" N7 A 11046 " 0.151 2.00e-02 2.50e+03 pdb=" C5 A 11046 " 0.101 2.00e-02 2.50e+03 pdb=" C6 A 11046 " -0.057 2.00e-02 2.50e+03 pdb=" N6 A 11046 " -0.253 2.00e-02 2.50e+03 pdb=" N1 A 11046 " -0.053 2.00e-02 2.50e+03 pdb=" C2 A 11046 " 0.058 2.00e-02 2.50e+03 pdb=" N3 A 11046 " 0.149 2.00e-02 2.50e+03 pdb=" C4 A 11046 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11926 " -0.186 2.00e-02 2.50e+03 9.53e-02 2.04e+02 pdb=" N1 U 11926 " 0.015 2.00e-02 2.50e+03 pdb=" C2 U 11926 " 0.035 2.00e-02 2.50e+03 pdb=" O2 U 11926 " 0.077 2.00e-02 2.50e+03 pdb=" N3 U 11926 " 0.011 2.00e-02 2.50e+03 pdb=" C4 U 11926 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U 11926 " -0.147 2.00e-02 2.50e+03 pdb=" C5 U 11926 " 0.088 2.00e-02 2.50e+03 pdb=" C6 U 11926 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11931 " -0.164 2.00e-02 2.50e+03 9.38e-02 1.98e+02 pdb=" N1 U 11931 " -0.000 2.00e-02 2.50e+03 pdb=" C2 U 11931 " 0.030 2.00e-02 2.50e+03 pdb=" O2 U 11931 " 0.065 2.00e-02 2.50e+03 pdb=" N3 U 11931 " 0.031 2.00e-02 2.50e+03 pdb=" C4 U 11931 " 0.039 2.00e-02 2.50e+03 pdb=" O4 U 11931 " -0.172 2.00e-02 2.50e+03 pdb=" C5 U 11931 " 0.097 2.00e-02 2.50e+03 pdb=" C6 U 11931 " 0.075 2.00e-02 2.50e+03 ... (remaining 13064 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 8 2.06 - 2.77: 25387 2.77 - 3.48: 203046 3.48 - 4.19: 480880 4.19 - 4.90: 638989 Nonbonded interactions: 1348310 Sorted by model distance: nonbonded pdb=" O3' A 5 76 " pdb=" C PRO 5 101 " model vdw 1.353 3.270 nonbonded pdb=" OP1 U 11058 " pdb=" OG1 THR h 34 " model vdw 1.659 2.440 nonbonded pdb=" C2' A 11057 " pdb=" CG2 THR h 34 " model vdw 1.762 3.890 nonbonded pdb=" C3' A 11057 " pdb=" CG2 THR h 34 " model vdw 1.912 3.890 nonbonded pdb=" N3 A 11084 " pdb=" O2' G 11106 " model vdw 1.953 2.520 ... (remaining 1348305 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.370 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: 0.230 Extract box with map and model: 25.740 Check model and map are aligned: 1.710 Set scattering table: 1.060 Process input model: 559.180 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 601.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.010 0.219 161799 Z= 0.572 Angle : 1.023 16.150 241915 Z= 0.651 Chirality : 0.081 0.947 30917 Planarity : 0.014 0.168 13067 Dihedral : 23.203 176.129 92533 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.36 % Favored : 88.09 % Rotamer: Outliers : 0.93 % Allowed : 12.16 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.34 % 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: -4.86 (0.08), residues: 5962 helix: -4.12 (0.07), residues: 1667 sheet: -2.42 (0.15), residues: 990 loop : -3.04 (0.09), residues: 3305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP b 212 HIS 0.021 0.002 HIS b 52 PHE 0.033 0.003 PHE a 38 TYR 0.026 0.003 TYR h 51 ARG 0.013 0.001 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1517 time to evaluate : 6.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 97 ASP cc_start: 0.8172 (p0) cc_final: 0.7947 (p0) REVERT: c 42 ASN cc_start: 0.8264 (p0) cc_final: 0.8021 (m110) REVERT: d 144 GLU cc_start: 0.6854 (tt0) cc_final: 0.6365 (pm20) REVERT: e 11 VAL cc_start: 0.8359 (t) cc_final: 0.8155 (t) REVERT: e 95 MET cc_start: 0.7954 (ptp) cc_final: 0.7553 (ptm) REVERT: e 124 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8620 (mmm160) REVERT: e 149 ARG cc_start: 0.6735 (mpp80) cc_final: 0.6497 (mmp-170) REVERT: f 59 ASP cc_start: 0.8355 (t70) cc_final: 0.8112 (t70) REVERT: f 142 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7924 (mm110) REVERT: i 116 MET cc_start: -0.1908 (ttp) cc_final: -0.2794 (ttt) REVERT: i 135 MET cc_start: 0.2866 (mmp) cc_final: 0.0799 (mtp) REVERT: j 58 ASN cc_start: 0.8003 (m110) cc_final: 0.7736 (m-40) REVERT: k 73 ASP cc_start: 0.8009 (m-30) cc_final: 0.7604 (m-30) REVERT: k 80 ASP cc_start: 0.8258 (m-30) cc_final: 0.8047 (m-30) REVERT: l 85 VAL cc_start: 0.8391 (m) cc_final: 0.8177 (m) REVERT: m 46 ILE cc_start: 0.9373 (mt) cc_final: 0.9157 (mm) REVERT: m 47 GLU cc_start: 0.8145 (tp30) cc_final: 0.7686 (tp30) REVERT: m 112 LEU cc_start: 0.8965 (tp) cc_final: 0.8716 (tp) REVERT: m 133 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8157 (tppt) REVERT: n 9 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7419 (tm-30) REVERT: n 78 LYS cc_start: 0.8975 (tptm) cc_final: 0.8733 (tptm) REVERT: n 115 LEU cc_start: 0.9154 (mt) cc_final: 0.8948 (mt) REVERT: o 43 ASN cc_start: 0.8239 (t0) cc_final: 0.7806 (t0) REVERT: o 108 ASP cc_start: 0.9079 (m-30) cc_final: 0.8812 (m-30) REVERT: o 116 GLN cc_start: 0.8964 (tp40) cc_final: 0.8544 (tm-30) REVERT: o 117 PHE cc_start: 0.8589 (p90) cc_final: 0.8117 (p90) REVERT: q 48 ASP cc_start: 0.7541 (m-30) cc_final: 0.7163 (m-30) REVERT: q 82 LEU cc_start: 0.9511 (mt) cc_final: 0.9295 (mp) REVERT: q 90 ASP cc_start: 0.7832 (p0) cc_final: 0.7566 (p0) REVERT: r 24 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8447 (ttmt) REVERT: r 86 GLN cc_start: 0.7991 (mt0) cc_final: 0.7781 (tt0) REVERT: s 31 GLN cc_start: 0.8367 (mp10) cc_final: 0.8158 (mm110) REVERT: t 42 GLU cc_start: 0.8424 (mp0) cc_final: 0.7805 (mp0) REVERT: t 76 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7145 (ptm-80) REVERT: v 3 THR cc_start: 0.8224 (t) cc_final: 0.7833 (p) REVERT: v 51 GLN cc_start: 0.8866 (pp30) cc_final: 0.8648 (pp30) REVERT: v 71 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8332 (mmmt) REVERT: v 86 LEU cc_start: 0.8683 (pt) cc_final: 0.8040 (mt) REVERT: w 39 THR cc_start: 0.8660 (m) cc_final: 0.8375 (p) REVERT: w 40 LYS cc_start: 0.8984 (mttt) cc_final: 0.8696 (ttmm) REVERT: x 65 THR cc_start: 0.8916 (m) cc_final: 0.8695 (p) REVERT: y 39 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7765 (mm-40) REVERT: z 44 ARG cc_start: 0.8723 (tpp-160) cc_final: 0.8488 (mtt-85) REVERT: A 4 ASP cc_start: 0.8755 (m-30) cc_final: 0.8526 (m-30) REVERT: C 8 ILE cc_start: 0.9179 (pt) cc_final: 0.8709 (pt) REVERT: C 32 LYS cc_start: 0.8234 (mptt) cc_final: 0.7965 (mmtm) REVERT: D 29 GLN cc_start: 0.8598 (mt0) cc_final: 0.8386 (mt0) REVERT: G 73 ARG cc_start: 0.7955 (ptt180) cc_final: 0.7307 (mmm160) REVERT: G 152 ASP cc_start: 0.8459 (p0) cc_final: 0.8150 (p0) REVERT: H 7 ASN cc_start: 0.8772 (t0) cc_final: 0.8510 (t0) REVERT: H 22 PHE cc_start: 0.8918 (t80) cc_final: 0.8694 (t80) REVERT: H 133 MET cc_start: 0.7444 (mtp) cc_final: 0.5461 (mtm) REVERT: H 138 GLN cc_start: 0.8311 (tt0) cc_final: 0.8097 (tt0) REVERT: I 123 MET cc_start: 0.6272 (mmt) cc_final: 0.5991 (tpp) REVERT: J 96 GLN cc_start: 0.7990 (tp40) cc_final: 0.7494 (tm-30) REVERT: K 4 TYR cc_start: 0.8793 (m-80) cc_final: 0.8535 (m-10) REVERT: K 44 ARG cc_start: 0.7965 (ptm160) cc_final: 0.7720 (ptm160) REVERT: K 56 LYS cc_start: 0.8086 (mppt) cc_final: 0.7615 (mmmm) REVERT: L 125 ASP cc_start: 0.8662 (t0) cc_final: 0.8337 (t0) REVERT: L 147 ASN cc_start: 0.8993 (m-40) cc_final: 0.8579 (m-40) REVERT: M 17 GLN cc_start: 0.8324 (mm110) cc_final: 0.8113 (mm-40) REVERT: M 51 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8171 (mm-30) REVERT: M 62 LEU cc_start: 0.9213 (mt) cc_final: 0.8729 (mt) REVERT: M 113 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7866 (ptt90) REVERT: N 6 TYR cc_start: 0.7022 (t80) cc_final: 0.6795 (t80) REVERT: N 56 MET cc_start: 0.7672 (ttt) cc_final: 0.7310 (tmm) REVERT: N 106 ASP cc_start: 0.7843 (t70) cc_final: 0.7567 (t70) REVERT: N 109 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8426 (mp10) REVERT: O 45 ARG cc_start: 0.6210 (mmt180) cc_final: 0.5866 (ttm170) REVERT: O 57 VAL cc_start: 0.8823 (m) cc_final: 0.8499 (m) REVERT: O 67 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8155 (mm) REVERT: P 81 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7127 (pp) REVERT: P 84 MET cc_start: 0.8286 (mmm) cc_final: 0.7990 (mmm) REVERT: P 111 ASP cc_start: 0.7885 (t70) cc_final: 0.7198 (t0) REVERT: Q 60 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: R 38 ILE cc_start: 0.5902 (mm) cc_final: 0.5698 (mm) REVERT: S 5 MET cc_start: 0.8081 (mmm) cc_final: 0.7843 (mmm) REVERT: S 25 GLU cc_start: 0.7299 (pt0) cc_final: 0.6988 (pm20) REVERT: S 61 ASN cc_start: 0.8495 (m-40) cc_final: 0.8258 (m-40) REVERT: S 85 GLU cc_start: 0.8359 (pp20) cc_final: 0.8048 (pp20) REVERT: U 50 THR cc_start: 0.8494 (m) cc_final: 0.8157 (m) REVERT: V 10 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8252 (ttp-170) REVERT: V 46 HIS cc_start: 0.5756 (t70) cc_final: 0.5305 (t-170) REVERT: W 25 ILE cc_start: 0.8210 (pt) cc_final: 0.7872 (mp) REVERT: W 49 LYS cc_start: 0.8920 (ptmt) cc_final: 0.8596 (ttpt) REVERT: X 2 ARG cc_start: 0.6809 (mtt-85) cc_final: 0.6178 (ttp-110) REVERT: X 10 ILE cc_start: 0.8237 (tp) cc_final: 0.7902 (mt) REVERT: X 65 MET cc_start: 0.8282 (mtt) cc_final: 0.8050 (mtp) REVERT: Y 26 MET cc_start: 0.8433 (ppp) cc_final: 0.8189 (ptm) REVERT: Y 47 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8059 (tp-100) REVERT: Z 4 LYS cc_start: 0.7438 (ttpp) cc_final: 0.7163 (mmtt) REVERT: Z 48 LYS cc_start: 0.8996 (tppt) cc_final: 0.8632 (tppt) REVERT: Z 65 ARG cc_start: 0.7071 (mtm110) cc_final: 0.6847 (ttp-110) outliers start: 46 outliers final: 21 residues processed: 1551 average time/residue: 1.3733 time to fit residues: 3636.0051 Evaluate side-chains 1209 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1185 time to evaluate : 6.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 890 optimal weight: 7.9990 chunk 798 optimal weight: 0.5980 chunk 443 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 538 optimal weight: 6.9990 chunk 426 optimal weight: 10.0000 chunk 826 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 502 optimal weight: 1.9990 chunk 614 optimal weight: 20.0000 chunk 957 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 238 ASN c 32 ASN c 49 GLN c 164 GLN d 41 GLN d 97 ASN d 195 GLN e 26 GLN e 51 ASN e 62 GLN f 19 ASN f 44 HIS f 110 HIS ** f 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 GLN g 11 ASN g 33 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN i 30 GLN j 47 HIS j 138 GLN k 3 GLN k 5 GLN k 89 ASN l 4 ASN m 13 HIS m 60 GLN n 9 GLN n 18 GLN n 31 HIS n 81 ASN n 107 ASN o 100 HIS ** q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN q 55 GLN q 71 ASN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 HIS r 89 HIS s 57 ASN t 15 HIS t 59 ASN u 39 ASN ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN v 78 GLN w 8 ASN x 5 GLN y 27 ASN A 20 ASN B 5 ASN B 41 HIS D 6 GLN F 13 ASN G 38 HIS ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN G 177 ASN H 18 ASN H 31 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 GLN J 76 ASN J 77 ASN K 11 HIS K 52 ASN ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 3 ASN O 58 ASN Q 45 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN S 70 HIS T 39 GLN T 79 GLN V 30 HIS V 50 ASN X 42 ASN Y 47 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 161799 Z= 0.243 Angle : 0.700 10.734 241915 Z= 0.365 Chirality : 0.040 0.357 30917 Planarity : 0.006 0.065 13067 Dihedral : 23.435 177.381 80676 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.20 % Favored : 89.50 % Rotamer: Outliers : 4.28 % Allowed : 19.41 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.24 % 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: -3.82 (0.09), residues: 5962 helix: -2.46 (0.10), residues: 1782 sheet: -2.12 (0.15), residues: 995 loop : -2.75 (0.10), residues: 3185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 33 HIS 0.010 0.001 HIS f 114 PHE 0.035 0.002 PHE Z 11 TYR 0.018 0.002 TYR H 41 ARG 0.009 0.001 ARG t 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1333 time to evaluate : 6.861 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: c 30 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7391 (mm-30) REVERT: c 180 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8383 (t) REVERT: d 35 TYR cc_start: 0.8119 (t80) cc_final: 0.7895 (t80) REVERT: d 144 GLU cc_start: 0.6730 (tt0) cc_final: 0.6153 (pm20) REVERT: e 16 MET cc_start: 0.7726 (mtm) cc_final: 0.7141 (tmm) REVERT: e 95 MET cc_start: 0.7736 (ptp) cc_final: 0.7450 (ptm) REVERT: e 120 SER cc_start: 0.4472 (t) cc_final: 0.3773 (p) REVERT: e 124 ARG cc_start: 0.8935 (mtt-85) cc_final: 0.8529 (mmm160) REVERT: f 123 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7769 (tm-30) REVERT: g 5 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6798 (pp) REVERT: h 124 ASP cc_start: 0.3985 (OUTLIER) cc_final: 0.3763 (p0) REVERT: i 116 MET cc_start: -0.1752 (ttp) cc_final: -0.2613 (ttt) REVERT: i 135 MET cc_start: 0.2403 (mmp) cc_final: 0.0474 (mtt) REVERT: j 58 ASN cc_start: 0.8055 (m110) cc_final: 0.7715 (m-40) REVERT: k 73 ASP cc_start: 0.7922 (m-30) cc_final: 0.7649 (m-30) REVERT: l 143 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7197 (tt0) REVERT: m 65 ILE cc_start: 0.8899 (mt) cc_final: 0.8527 (mm) REVERT: n 9 GLN cc_start: 0.7497 (tm130) cc_final: 0.7203 (tm-30) REVERT: n 114 GLU cc_start: 0.7282 (pp20) cc_final: 0.7056 (pp20) REVERT: n 115 LEU cc_start: 0.9047 (mt) cc_final: 0.8558 (mt) REVERT: o 49 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8194 (p) REVERT: p 26 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7177 (tm-30) REVERT: q 48 ASP cc_start: 0.7650 (m-30) cc_final: 0.7240 (m-30) REVERT: q 90 ASP cc_start: 0.7846 (p0) cc_final: 0.7389 (p0) REVERT: q 101 ASP cc_start: 0.7823 (t70) cc_final: 0.7326 (t70) REVERT: r 24 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8210 (ttmm) REVERT: r 39 LEU cc_start: 0.8466 (mm) cc_final: 0.8208 (mm) REVERT: s 65 ASP cc_start: 0.6694 (t0) cc_final: 0.5642 (t70) REVERT: s 67 ASP cc_start: 0.7976 (m-30) cc_final: 0.7653 (p0) REVERT: s 68 ASP cc_start: 0.8162 (p0) cc_final: 0.7365 (p0) REVERT: s 69 LEU cc_start: 0.8883 (mt) cc_final: 0.8591 (mp) REVERT: u 5 ARG cc_start: 0.7691 (ptp-170) cc_final: 0.7438 (ptp-170) REVERT: v 3 THR cc_start: 0.7897 (t) cc_final: 0.7669 (p) REVERT: v 5 ASN cc_start: 0.8327 (m-40) cc_final: 0.7892 (m-40) REVERT: v 86 LEU cc_start: 0.8721 (pt) cc_final: 0.8021 (mt) REVERT: w 13 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7359 (tm-30) REVERT: w 40 LYS cc_start: 0.8948 (mttt) cc_final: 0.8695 (ttmm) REVERT: y 1 MET cc_start: 0.6642 (tpt) cc_final: 0.6440 (tpt) REVERT: y 39 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7821 (mm-40) REVERT: A 4 ASP cc_start: 0.8620 (m-30) cc_final: 0.8411 (m-30) REVERT: C 32 LYS cc_start: 0.8227 (mptt) cc_final: 0.7643 (ttpp) REVERT: D 41 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7388 (tpp80) REVERT: F 1 MET cc_start: 0.7750 (mmt) cc_final: 0.7502 (tpt) REVERT: G 73 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7286 (mmm160) REVERT: G 79 VAL cc_start: 0.7731 (t) cc_final: 0.7442 (p) REVERT: G 152 ASP cc_start: 0.8450 (p0) cc_final: 0.8122 (p0) REVERT: H 22 PHE cc_start: 0.8763 (t80) cc_final: 0.8464 (t80) REVERT: H 138 GLN cc_start: 0.8298 (tt0) cc_final: 0.8042 (tt0) REVERT: H 166 TRP cc_start: 0.8310 (p-90) cc_final: 0.7843 (p-90) REVERT: I 20 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8464 (tt) REVERT: I 123 MET cc_start: 0.6176 (mmt) cc_final: 0.5887 (tpp) REVERT: J 96 GLN cc_start: 0.7878 (tp40) cc_final: 0.7561 (tm-30) REVERT: J 133 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8415 (mp) REVERT: L 109 LYS cc_start: 0.8504 (mmmt) cc_final: 0.7496 (pptt) REVERT: M 17 GLN cc_start: 0.8298 (mm110) cc_final: 0.8049 (mm-40) REVERT: M 46 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7242 (mt-10) REVERT: M 51 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8090 (mm-30) REVERT: M 60 LEU cc_start: 0.8812 (mp) cc_final: 0.8609 (mp) REVERT: M 79 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8367 (ptm-80) REVERT: M 82 LEU cc_start: 0.9587 (tt) cc_final: 0.9153 (tt) REVERT: M 87 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7370 (mtp-110) REVERT: M 113 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7913 (ptt90) REVERT: N 56 MET cc_start: 0.7485 (ttt) cc_final: 0.7211 (tmm) REVERT: N 109 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8316 (mp10) REVERT: O 45 ARG cc_start: 0.6134 (mmt180) cc_final: 0.5760 (ttm170) REVERT: O 46 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8622 (mttp) REVERT: P 63 GLN cc_start: 0.8486 (tp40) cc_final: 0.8251 (tp40) REVERT: Q 60 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: R 68 LEU cc_start: 0.8899 (tp) cc_final: 0.8646 (tp) REVERT: R 71 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6565 (mm-30) REVERT: S 5 MET cc_start: 0.7962 (mmm) cc_final: 0.7707 (mmm) REVERT: S 61 ASN cc_start: 0.8439 (m-40) cc_final: 0.8185 (m-40) REVERT: S 84 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8056 (tmm-80) REVERT: T 37 HIS cc_start: 0.7890 (m90) cc_final: 0.7239 (m90) REVERT: T 79 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: V 8 GLN cc_start: 0.7800 (pp30) cc_final: 0.7331 (pp30) REVERT: V 10 ARG cc_start: 0.8634 (ttm170) cc_final: 0.8330 (ttp-170) REVERT: V 29 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8313 (tptt) REVERT: W 25 ILE cc_start: 0.8207 (pt) cc_final: 0.7859 (mp) REVERT: W 49 LYS cc_start: 0.8864 (ptmt) cc_final: 0.8561 (ttpt) REVERT: X 2 ARG cc_start: 0.6775 (mtt-85) cc_final: 0.6564 (mtp85) REVERT: X 10 ILE cc_start: 0.8063 (tp) cc_final: 0.7788 (mt) REVERT: X 65 MET cc_start: 0.8290 (mtt) cc_final: 0.8040 (mtm) REVERT: X 69 LYS cc_start: 0.7214 (mttt) cc_final: 0.6468 (mtmt) REVERT: Y 27 MET cc_start: 0.9037 (ttm) cc_final: 0.8784 (ttm) REVERT: Y 50 PHE cc_start: 0.8639 (t80) cc_final: 0.8428 (t80) REVERT: Y 73 ARG cc_start: 0.8763 (ttp-110) cc_final: 0.8449 (ttp-110) REVERT: Z 4 LYS cc_start: 0.7485 (ttpp) cc_final: 0.7114 (mmtt) REVERT: Z 48 LYS cc_start: 0.8892 (tppt) cc_final: 0.8622 (mmtt) REVERT: Z 53 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8713 (pttt) REVERT: Z 65 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6452 (ttp-110) outliers start: 212 outliers final: 133 residues processed: 1437 average time/residue: 1.3265 time to fit residues: 3328.6559 Evaluate side-chains 1344 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1201 time to evaluate : 6.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 238 ASN Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 124 ASP Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 88 ASN Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 5 GLU Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain X residue 17 LYS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 531 optimal weight: 40.0000 chunk 297 optimal weight: 20.0000 chunk 796 optimal weight: 7.9990 chunk 651 optimal weight: 20.0000 chunk 264 optimal weight: 30.0000 chunk 958 optimal weight: 9.9990 chunk 1035 optimal weight: 30.0000 chunk 853 optimal weight: 9.9990 chunk 950 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 769 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN e 62 GLN f 19 ASN f 114 HIS ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 80 HIS k 9 ASN ** o 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN y 58 ASN z 8 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS S 65 GLN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 161799 Z= 0.348 Angle : 0.702 11.737 241915 Z= 0.365 Chirality : 0.041 0.350 30917 Planarity : 0.006 0.066 13067 Dihedral : 23.445 178.612 80669 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.61 % Favored : 88.11 % Rotamer: Outliers : 5.84 % Allowed : 21.85 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.22 % 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: -3.38 (0.10), residues: 5962 helix: -1.79 (0.11), residues: 1793 sheet: -1.96 (0.15), residues: 1006 loop : -2.65 (0.10), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 33 HIS 0.012 0.001 HIS W 73 PHE 0.022 0.002 PHE r 5 TYR 0.020 0.002 TYR K 49 ARG 0.009 0.001 ARG R 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1254 time to evaluate : 6.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 145 MET cc_start: 0.7585 (mtt) cc_final: 0.7320 (mtt) REVERT: c 99 GLU cc_start: 0.7975 (tp30) cc_final: 0.7686 (tp30) REVERT: c 167 ASN cc_start: 0.8698 (t0) cc_final: 0.8354 (t0) REVERT: d 197 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: e 16 MET cc_start: 0.7707 (mtm) cc_final: 0.7209 (tmm) REVERT: e 82 TYR cc_start: 0.6889 (m-10) cc_final: 0.6667 (m-10) REVERT: e 120 SER cc_start: 0.4592 (t) cc_final: 0.4141 (p) REVERT: f 123 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7704 (tm-30) REVERT: f 146 ASP cc_start: 0.8477 (t0) cc_final: 0.8029 (t0) REVERT: g 5 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6692 (pp) REVERT: i 116 MET cc_start: -0.1335 (ttp) cc_final: -0.2539 (ttt) REVERT: i 135 MET cc_start: 0.2619 (mmp) cc_final: 0.0498 (mtt) REVERT: j 58 ASN cc_start: 0.8231 (m-40) cc_final: 0.7886 (m-40) REVERT: k 73 ASP cc_start: 0.7934 (m-30) cc_final: 0.7659 (m-30) REVERT: m 65 ILE cc_start: 0.8886 (mt) cc_final: 0.8494 (mm) REVERT: n 114 GLU cc_start: 0.7387 (pp20) cc_final: 0.7141 (pp20) REVERT: n 115 LEU cc_start: 0.9123 (mt) cc_final: 0.8634 (mt) REVERT: q 48 ASP cc_start: 0.7707 (m-30) cc_final: 0.7302 (m-30) REVERT: q 90 ASP cc_start: 0.7977 (p0) cc_final: 0.7373 (p0) REVERT: r 24 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8459 (ttmt) REVERT: s 67 ASP cc_start: 0.8028 (m-30) cc_final: 0.7632 (p0) REVERT: s 69 LEU cc_start: 0.8896 (mt) cc_final: 0.8623 (mp) REVERT: s 85 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8784 (mp) REVERT: t 1 MET cc_start: 0.5808 (mtt) cc_final: 0.5416 (mtt) REVERT: u 5 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7518 (ptp-170) REVERT: v 71 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8262 (mmmt) REVERT: v 86 LEU cc_start: 0.8730 (pt) cc_final: 0.7988 (mt) REVERT: w 13 GLU cc_start: 0.7708 (tm-30) cc_final: 0.6838 (tm-30) REVERT: w 40 LYS cc_start: 0.8969 (mttt) cc_final: 0.8612 (ttmm) REVERT: y 39 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 4 ASP cc_start: 0.8603 (m-30) cc_final: 0.8380 (m-30) REVERT: A 41 HIS cc_start: 0.6690 (t70) cc_final: 0.6253 (t70) REVERT: C 32 LYS cc_start: 0.8205 (mptt) cc_final: 0.7604 (ttpp) REVERT: G 108 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8727 (mp10) REVERT: G 152 ASP cc_start: 0.8602 (p0) cc_final: 0.8267 (p0) REVERT: H 129 PHE cc_start: 0.7968 (p90) cc_final: 0.7673 (p90) REVERT: H 138 GLN cc_start: 0.8399 (tt0) cc_final: 0.8155 (tt0) REVERT: H 166 TRP cc_start: 0.8363 (p-90) cc_final: 0.7738 (p-90) REVERT: I 20 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8483 (tt) REVERT: I 93 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8298 (mm) REVERT: I 123 MET cc_start: 0.6292 (mmt) cc_final: 0.5906 (tpp) REVERT: J 96 GLN cc_start: 0.7877 (tp40) cc_final: 0.7576 (tm-30) REVERT: L 21 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7715 (pp) REVERT: M 79 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8633 (ptm-80) REVERT: M 82 LEU cc_start: 0.9582 (tt) cc_final: 0.9217 (tt) REVERT: M 87 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7302 (mtp-110) REVERT: M 113 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7936 (ptt90) REVERT: O 45 ARG cc_start: 0.6138 (mmt180) cc_final: 0.5825 (ttm170) REVERT: O 67 ILE cc_start: 0.8756 (mm) cc_final: 0.8365 (mm) REVERT: O 97 ASP cc_start: 0.7629 (m-30) cc_final: 0.7416 (m-30) REVERT: P 63 GLN cc_start: 0.8457 (tp40) cc_final: 0.8212 (tp40) REVERT: Q 60 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: R 18 LEU cc_start: 0.7553 (tp) cc_final: 0.7352 (tp) REVERT: R 68 LEU cc_start: 0.8814 (tp) cc_final: 0.8452 (tp) REVERT: R 71 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6390 (mm-30) REVERT: S 48 GLN cc_start: 0.7939 (mp10) cc_final: 0.7550 (mp10) REVERT: S 61 ASN cc_start: 0.8412 (m-40) cc_final: 0.8165 (m-40) REVERT: S 74 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7394 (ttm110) REVERT: S 84 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8052 (tmm-80) REVERT: T 37 HIS cc_start: 0.7829 (m90) cc_final: 0.7217 (m90) REVERT: U 70 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7241 (ttp-170) REVERT: V 8 GLN cc_start: 0.7861 (pp30) cc_final: 0.7470 (pp30) REVERT: V 10 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8295 (ttp-170) REVERT: V 29 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8297 (tptt) REVERT: W 25 ILE cc_start: 0.8206 (pt) cc_final: 0.7795 (mp) REVERT: X 2 ARG cc_start: 0.6918 (mtt-85) cc_final: 0.6456 (mtp85) REVERT: X 10 ILE cc_start: 0.8138 (tp) cc_final: 0.7896 (mt) REVERT: X 43 MET cc_start: 0.4960 (mtt) cc_final: 0.4714 (mtp) REVERT: X 65 MET cc_start: 0.8142 (mtt) cc_final: 0.7821 (mtp) REVERT: X 69 LYS cc_start: 0.7243 (mttm) cc_final: 0.6499 (mttt) REVERT: Y 27 MET cc_start: 0.9095 (ttm) cc_final: 0.8473 (ttm) REVERT: Z 4 LYS cc_start: 0.7440 (ttpp) cc_final: 0.7134 (tptt) REVERT: Z 37 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: Z 48 LYS cc_start: 0.8874 (tppt) cc_final: 0.8606 (mmtt) REVERT: Z 53 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8730 (pttt) outliers start: 289 outliers final: 211 residues processed: 1417 average time/residue: 1.2613 time to fit residues: 3128.7709 Evaluate side-chains 1377 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1156 time to evaluate : 6.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 24 THR Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 63 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 17 ASP Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 72 ASN Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain x residue 70 LEU Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 947 optimal weight: 30.0000 chunk 720 optimal weight: 9.9990 chunk 497 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 457 optimal weight: 20.0000 chunk 643 optimal weight: 6.9990 chunk 962 optimal weight: 7.9990 chunk 1018 optimal weight: 0.8980 chunk 502 optimal weight: 5.9990 chunk 912 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN f 63 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN n 107 ASN o 100 HIS ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN x 16 ASN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 HIS ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS Y 2 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 161799 Z= 0.225 Angle : 0.614 10.595 241915 Z= 0.321 Chirality : 0.037 0.349 30917 Planarity : 0.005 0.063 13067 Dihedral : 23.415 179.395 80664 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.23 % Favored : 89.55 % Rotamer: Outliers : 5.92 % Allowed : 23.95 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.10), residues: 5962 helix: -1.28 (0.11), residues: 1804 sheet: -1.81 (0.16), residues: 1008 loop : -2.50 (0.10), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 33 HIS 0.037 0.001 HIS Q 71 PHE 0.023 0.002 PHE r 5 TYR 0.024 0.002 TYR Q 65 ARG 0.008 0.001 ARG s 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1264 time to evaluate : 6.757 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: c 99 GLU cc_start: 0.8059 (tp30) cc_final: 0.7806 (tp30) REVERT: c 180 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8357 (t) REVERT: d 111 GLU cc_start: 0.8464 (tp30) cc_final: 0.8233 (tp30) REVERT: d 115 GLN cc_start: 0.8504 (tt0) cc_final: 0.8157 (tm-30) REVERT: d 144 GLU cc_start: 0.6489 (tt0) cc_final: 0.6047 (pm20) REVERT: e 16 MET cc_start: 0.7574 (mtm) cc_final: 0.7240 (tmm) REVERT: e 82 TYR cc_start: 0.6986 (m-10) cc_final: 0.6700 (m-10) REVERT: e 95 MET cc_start: 0.7206 (ptp) cc_final: 0.6564 (ptm) REVERT: e 120 SER cc_start: 0.4439 (t) cc_final: 0.4131 (p) REVERT: f 106 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8107 (pp) REVERT: f 123 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7754 (tm-30) REVERT: f 146 ASP cc_start: 0.8421 (t0) cc_final: 0.7990 (t0) REVERT: f 152 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.8175 (mmm160) REVERT: f 174 LYS cc_start: 0.5187 (OUTLIER) cc_final: 0.4346 (mmtt) REVERT: g 5 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6770 (pp) REVERT: a 33 LEU cc_start: 0.3137 (mt) cc_final: 0.2215 (tt) REVERT: a 50 ILE cc_start: 0.3564 (OUTLIER) cc_final: 0.3260 (tt) REVERT: a 185 LEU cc_start: -0.1110 (mt) cc_final: -0.1412 (tp) REVERT: i 116 MET cc_start: -0.0867 (ttp) cc_final: -0.2138 (ttt) REVERT: i 135 MET cc_start: 0.2528 (mmp) cc_final: 0.0394 (mtt) REVERT: j 58 ASN cc_start: 0.8304 (m-40) cc_final: 0.7940 (m-40) REVERT: k 32 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8425 (p90) REVERT: l 85 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8126 (m) REVERT: l 143 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7272 (tt0) REVERT: m 28 PHE cc_start: 0.8480 (m-10) cc_final: 0.8273 (m-10) REVERT: n 114 GLU cc_start: 0.7453 (pp20) cc_final: 0.7221 (pp20) REVERT: n 115 LEU cc_start: 0.9104 (mt) cc_final: 0.8634 (mt) REVERT: o 116 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7992 (tm-30) REVERT: q 90 ASP cc_start: 0.7907 (p0) cc_final: 0.7395 (p0) REVERT: r 24 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8309 (ttpp) REVERT: s 65 ASP cc_start: 0.6575 (t0) cc_final: 0.5530 (t70) REVERT: s 67 ASP cc_start: 0.7943 (m-30) cc_final: 0.7678 (p0) REVERT: s 68 ASP cc_start: 0.8076 (p0) cc_final: 0.7027 (p0) REVERT: s 85 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8768 (mp) REVERT: s 95 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8028 (mmm-85) REVERT: t 1 MET cc_start: 0.5611 (mtt) cc_final: 0.5253 (mtt) REVERT: u 5 ARG cc_start: 0.7549 (ptp-170) cc_final: 0.7247 (ptp-170) REVERT: u 65 GLN cc_start: 0.7976 (mt0) cc_final: 0.7641 (mt0) REVERT: v 5 ASN cc_start: 0.8322 (m-40) cc_final: 0.7853 (m-40) REVERT: v 86 LEU cc_start: 0.8645 (pt) cc_final: 0.7957 (mt) REVERT: w 13 GLU cc_start: 0.7623 (tm-30) cc_final: 0.6733 (tm-30) REVERT: x 75 GLU cc_start: 0.7906 (mt-10) cc_final: 0.6690 (mt-10) REVERT: y 39 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7831 (mm-40) REVERT: C 6 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7383 (tm-30) REVERT: C 32 LYS cc_start: 0.8236 (mptt) cc_final: 0.7981 (mmtm) REVERT: G 31 PHE cc_start: 0.8676 (t80) cc_final: 0.8460 (t80) REVERT: G 108 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8648 (mp10) REVERT: G 152 ASP cc_start: 0.8518 (p0) cc_final: 0.8184 (p0) REVERT: H 138 GLN cc_start: 0.8405 (tt0) cc_final: 0.8130 (tt0) REVERT: H 166 TRP cc_start: 0.8311 (p-90) cc_final: 0.7775 (p-90) REVERT: I 20 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8460 (tt) REVERT: I 93 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8272 (mm) REVERT: I 115 GLN cc_start: 0.5714 (tp40) cc_final: 0.5199 (mm-40) REVERT: I 123 MET cc_start: 0.6269 (mmt) cc_final: 0.5889 (tpp) REVERT: J 70 MET cc_start: 0.7702 (mmm) cc_final: 0.7393 (mmm) REVERT: J 92 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7894 (mtt90) REVERT: J 96 GLN cc_start: 0.7838 (tp40) cc_final: 0.7581 (tm-30) REVERT: J 133 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8372 (mp) REVERT: L 21 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7872 (pp) REVERT: M 51 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8018 (mm-30) REVERT: M 79 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8526 (ptm-80) REVERT: M 82 LEU cc_start: 0.9556 (tt) cc_final: 0.9248 (tt) REVERT: M 87 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7316 (mtp-110) REVERT: M 110 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8029 (pmm) REVERT: M 113 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7976 (ptt90) REVERT: N 49 GLN cc_start: 0.8267 (mt0) cc_final: 0.7929 (mm110) REVERT: N 56 MET cc_start: 0.7311 (ppp) cc_final: 0.6929 (ppp) REVERT: N 96 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: O 18 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8007 (mt) REVERT: O 31 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.6043 (ptt-90) REVERT: O 67 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8347 (mm) REVERT: O 101 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.6967 (t) REVERT: P 63 GLN cc_start: 0.8378 (tp40) cc_final: 0.8162 (tp40) REVERT: Q 60 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: Q 61 GLU cc_start: 0.7847 (tp30) cc_final: 0.6772 (tp30) REVERT: Q 74 GLN cc_start: 0.8036 (pm20) cc_final: 0.7804 (pm20) REVERT: R 18 LEU cc_start: 0.7555 (tp) cc_final: 0.7338 (tp) REVERT: R 68 LEU cc_start: 0.8738 (tp) cc_final: 0.8467 (tp) REVERT: S 5 MET cc_start: 0.7917 (mmm) cc_final: 0.7674 (mmt) REVERT: S 25 GLU cc_start: 0.7720 (pt0) cc_final: 0.7309 (pm20) REVERT: S 61 ASN cc_start: 0.8357 (m-40) cc_final: 0.8138 (m-40) REVERT: S 74 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7346 (ttm110) REVERT: S 84 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8023 (tmm-80) REVERT: T 37 HIS cc_start: 0.7778 (m90) cc_final: 0.7151 (m90) REVERT: U 70 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7200 (tpp-160) REVERT: V 8 GLN cc_start: 0.7754 (pp30) cc_final: 0.7530 (pp30) REVERT: V 10 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8295 (ttp-170) REVERT: V 29 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8346 (tptt) REVERT: W 25 ILE cc_start: 0.8212 (pt) cc_final: 0.7843 (mp) REVERT: X 2 ARG cc_start: 0.6761 (mtt-85) cc_final: 0.6286 (mtp85) REVERT: X 10 ILE cc_start: 0.8064 (tp) cc_final: 0.7800 (mt) REVERT: X 65 MET cc_start: 0.8120 (mtt) cc_final: 0.7841 (mtm) REVERT: X 69 LYS cc_start: 0.7219 (mttt) cc_final: 0.6570 (mttt) REVERT: Y 27 MET cc_start: 0.9034 (ttm) cc_final: 0.8536 (ttm) REVERT: Z 4 LYS cc_start: 0.7558 (ttpp) cc_final: 0.7125 (mmtt) REVERT: Z 34 ARG cc_start: 0.6996 (ptt-90) cc_final: 0.6754 (ptt-90) REVERT: Z 37 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: Z 48 LYS cc_start: 0.8845 (tppt) cc_final: 0.8603 (mmtt) REVERT: Z 53 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8738 (pttt) outliers start: 293 outliers final: 201 residues processed: 1431 average time/residue: 1.3054 time to fit residues: 3282.3082 Evaluate side-chains 1391 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1168 time to evaluate : 6.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 235 GLU Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 173 GLN Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 85 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 79 ASN Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 848 optimal weight: 7.9990 chunk 578 optimal weight: 0.0770 chunk 14 optimal weight: 30.0000 chunk 758 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 869 optimal weight: 0.9990 chunk 704 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 520 optimal weight: 4.9990 chunk 914 optimal weight: 20.0000 chunk 257 optimal weight: 30.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN f 63 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 ASN o 100 HIS ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN P 37 GLN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS R 13 HIS T 39 GLN Y 19 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 161799 Z= 0.209 Angle : 0.593 12.185 241915 Z= 0.309 Chirality : 0.035 0.286 30917 Planarity : 0.005 0.065 13067 Dihedral : 23.375 179.182 80664 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.80 % Favored : 89.00 % Rotamer: Outliers : 6.28 % Allowed : 25.23 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.72 (0.10), residues: 5962 helix: -0.97 (0.12), residues: 1807 sheet: -1.68 (0.16), residues: 1027 loop : -2.39 (0.10), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 33 HIS 0.012 0.001 HIS W 73 PHE 0.039 0.001 PHE Z 11 TYR 0.021 0.002 TYR K 49 ARG 0.013 0.000 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1548 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1237 time to evaluate : 6.802 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: c 33 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: c 180 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8368 (t) REVERT: d 111 GLU cc_start: 0.8440 (tp30) cc_final: 0.8180 (tp30) REVERT: d 115 GLN cc_start: 0.8519 (tt0) cc_final: 0.8255 (tt0) REVERT: d 144 GLU cc_start: 0.6510 (tt0) cc_final: 0.5981 (pm20) REVERT: e 16 MET cc_start: 0.7560 (mtm) cc_final: 0.7283 (tmm) REVERT: e 82 TYR cc_start: 0.6994 (m-10) cc_final: 0.6642 (m-10) REVERT: e 95 MET cc_start: 0.7159 (ptp) cc_final: 0.6530 (ptm) REVERT: e 120 SER cc_start: 0.4368 (t) cc_final: 0.4147 (p) REVERT: f 106 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8084 (pp) REVERT: f 146 ASP cc_start: 0.8484 (t0) cc_final: 0.8099 (t0) REVERT: f 152 ARG cc_start: 0.8457 (tpp-160) cc_final: 0.8142 (mmm160) REVERT: f 174 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4448 (mmtt) REVERT: g 5 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6814 (pp) REVERT: a 33 LEU cc_start: 0.3130 (mt) cc_final: 0.2219 (tt) REVERT: a 50 ILE cc_start: 0.3295 (OUTLIER) cc_final: 0.2976 (tt) REVERT: i 116 MET cc_start: -0.0599 (ttp) cc_final: -0.1916 (ttt) REVERT: i 135 MET cc_start: 0.2519 (mmp) cc_final: 0.0311 (mtt) REVERT: j 58 ASN cc_start: 0.8302 (m-40) cc_final: 0.7929 (m-40) REVERT: k 32 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8514 (p90) REVERT: l 143 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7292 (tt0) REVERT: m 28 PHE cc_start: 0.8473 (m-10) cc_final: 0.8202 (m-10) REVERT: n 114 GLU cc_start: 0.7506 (pp20) cc_final: 0.7248 (pp20) REVERT: n 115 LEU cc_start: 0.9134 (mt) cc_final: 0.8643 (mt) REVERT: q 90 ASP cc_start: 0.7922 (p0) cc_final: 0.7375 (p0) REVERT: r 24 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8160 (ttpp) REVERT: s 67 ASP cc_start: 0.7957 (m-30) cc_final: 0.7684 (p0) REVERT: s 85 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8796 (mp) REVERT: t 1 MET cc_start: 0.5753 (mtt) cc_final: 0.5440 (mtt) REVERT: u 5 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.7362 (ptp-170) REVERT: u 65 GLN cc_start: 0.8011 (mt0) cc_final: 0.7692 (mt0) REVERT: v 12 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7304 (pp30) REVERT: v 86 LEU cc_start: 0.8722 (pt) cc_final: 0.7958 (mt) REVERT: w 13 GLU cc_start: 0.7662 (tm-30) cc_final: 0.6821 (tm-30) REVERT: y 1 MET cc_start: 0.7161 (mmt) cc_final: 0.4681 (ptt) REVERT: y 39 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7777 (mm-40) REVERT: A 31 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.5940 (t70) REVERT: C 32 LYS cc_start: 0.8283 (mptt) cc_final: 0.7567 (ttpp) REVERT: G 108 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8715 (mp10) REVERT: G 152 ASP cc_start: 0.8497 (p0) cc_final: 0.8160 (p0) REVERT: G 183 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6381 (m-80) REVERT: G 197 PHE cc_start: 0.8601 (m-80) cc_final: 0.8210 (m-80) REVERT: H 138 GLN cc_start: 0.8430 (tt0) cc_final: 0.8154 (tt0) REVERT: H 166 TRP cc_start: 0.8308 (p-90) cc_final: 0.7779 (p-90) REVERT: H 167 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6456 (t80) REVERT: I 115 GLN cc_start: 0.5632 (tp40) cc_final: 0.5165 (mm-40) REVERT: I 123 MET cc_start: 0.6274 (mmt) cc_final: 0.5809 (tpp) REVERT: J 133 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8391 (mp) REVERT: L 21 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7841 (pp) REVERT: L 109 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7371 (pttt) REVERT: M 51 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8095 (mm-30) REVERT: M 79 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8404 (ptm-80) REVERT: M 82 LEU cc_start: 0.9535 (tt) cc_final: 0.9200 (tt) REVERT: M 87 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7317 (mtp-110) REVERT: M 110 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7871 (pmm) REVERT: M 113 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7986 (ptt90) REVERT: N 28 VAL cc_start: 0.7584 (m) cc_final: 0.7383 (p) REVERT: N 49 GLN cc_start: 0.8269 (mt0) cc_final: 0.7883 (mm110) REVERT: N 56 MET cc_start: 0.7057 (ppp) cc_final: 0.6757 (ppp) REVERT: N 87 MET cc_start: 0.7735 (mmm) cc_final: 0.7451 (ptt) REVERT: N 96 GLU cc_start: 0.8545 (pm20) cc_final: 0.8153 (pm20) REVERT: O 31 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.6074 (ptt-90) REVERT: O 64 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: O 67 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8333 (mm) REVERT: O 101 SER cc_start: 0.7401 (OUTLIER) cc_final: 0.6946 (t) REVERT: P 13 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.5960 (mmtt) REVERT: P 110 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.6925 (m) REVERT: Q 60 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: R 56 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7214 (tpt-90) REVERT: R 65 GLU cc_start: 0.8183 (pm20) cc_final: 0.7545 (pt0) REVERT: R 71 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7374 (mm-30) REVERT: S 5 MET cc_start: 0.7918 (mmm) cc_final: 0.7611 (mmt) REVERT: S 25 GLU cc_start: 0.7737 (pt0) cc_final: 0.7462 (pm20) REVERT: S 48 GLN cc_start: 0.7802 (mp10) cc_final: 0.7507 (mp10) REVERT: S 53 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6912 (t0) REVERT: S 61 ASN cc_start: 0.8347 (m-40) cc_final: 0.8115 (m-40) REVERT: S 74 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7365 (ttm110) REVERT: S 84 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8003 (tmm-80) REVERT: S 85 GLU cc_start: 0.8255 (pp20) cc_final: 0.7895 (pp20) REVERT: T 37 HIS cc_start: 0.7771 (m90) cc_final: 0.7145 (m90) REVERT: U 47 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: U 70 ARG cc_start: 0.7893 (ttt180) cc_final: 0.7106 (tpp-160) REVERT: V 8 GLN cc_start: 0.7802 (pp30) cc_final: 0.7575 (pp30) REVERT: V 10 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8313 (ttp-170) REVERT: V 29 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8309 (tptt) REVERT: W 11 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5551 (mtm180) REVERT: X 2 ARG cc_start: 0.6780 (mtt-85) cc_final: 0.6313 (mtp85) REVERT: X 10 ILE cc_start: 0.7981 (tp) cc_final: 0.7722 (mt) REVERT: X 20 LYS cc_start: 0.5753 (mttt) cc_final: 0.4533 (tmmt) REVERT: X 65 MET cc_start: 0.8167 (mtt) cc_final: 0.7891 (mtm) REVERT: X 69 LYS cc_start: 0.7215 (mttt) cc_final: 0.6644 (mttt) REVERT: Y 27 MET cc_start: 0.9057 (ttm) cc_final: 0.8519 (ttm) REVERT: Y 29 THR cc_start: 0.8609 (p) cc_final: 0.8339 (p) REVERT: Y 51 ASN cc_start: 0.8529 (m-40) cc_final: 0.8058 (m-40) REVERT: Z 4 LYS cc_start: 0.7528 (ttpp) cc_final: 0.7090 (mmtt) REVERT: Z 37 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: Z 48 LYS cc_start: 0.8868 (tppt) cc_final: 0.8595 (mmtt) REVERT: Z 53 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8761 (pttt) outliers start: 311 outliers final: 220 residues processed: 1421 average time/residue: 1.2692 time to fit residues: 3161.5872 Evaluate side-chains 1422 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1174 time to evaluate : 6.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 71 HIS Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain Z residue 67 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 342 optimal weight: 20.0000 chunk 917 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 598 optimal weight: 0.0040 chunk 251 optimal weight: 10.0000 chunk 1019 optimal weight: 20.0000 chunk 846 optimal weight: 20.0000 chunk 472 optimal weight: 8.9990 chunk 84 optimal weight: 40.0000 chunk 337 optimal weight: 10.0000 chunk 535 optimal weight: 30.0000 overall best weight: 7.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 GLN ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS q 36 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 GLN v 75 GLN v 78 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN M 75 GLN P 37 GLN P 63 GLN Q 4 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 HIS R 13 HIS Y 47 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 161799 Z= 0.303 Angle : 0.648 13.381 241915 Z= 0.335 Chirality : 0.038 0.299 30917 Planarity : 0.005 0.084 13067 Dihedral : 23.406 179.096 80663 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.36 % Favored : 88.43 % Rotamer: Outliers : 6.95 % Allowed : 25.97 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.66 (0.10), residues: 5962 helix: -0.96 (0.12), residues: 1802 sheet: -1.63 (0.16), residues: 1051 loop : -2.33 (0.10), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 33 HIS 0.017 0.001 HIS Q 71 PHE 0.030 0.002 PHE Z 11 TYR 0.023 0.002 TYR K 49 ARG 0.011 0.001 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1203 time to evaluate : 6.838 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: c 33 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7483 (mtm-85) REVERT: c 180 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8362 (t) REVERT: d 111 GLU cc_start: 0.8461 (tp30) cc_final: 0.8238 (tp30) REVERT: d 115 GLN cc_start: 0.8585 (tt0) cc_final: 0.8375 (tt0) REVERT: d 144 GLU cc_start: 0.6647 (tt0) cc_final: 0.6157 (pm20) REVERT: e 16 MET cc_start: 0.7508 (mtm) cc_final: 0.7228 (tmm) REVERT: e 82 TYR cc_start: 0.6987 (m-10) cc_final: 0.6624 (m-10) REVERT: e 120 SER cc_start: 0.4409 (t) cc_final: 0.4163 (p) REVERT: f 106 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8109 (pp) REVERT: f 123 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7514 (tm-30) REVERT: f 146 ASP cc_start: 0.8543 (t0) cc_final: 0.8155 (t0) REVERT: f 152 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8141 (mmm160) REVERT: f 174 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4319 (mmtt) REVERT: g 5 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6844 (pp) REVERT: a 33 LEU cc_start: 0.3136 (mt) cc_final: 0.2173 (tt) REVERT: a 50 ILE cc_start: 0.3332 (OUTLIER) cc_final: 0.3038 (tt) REVERT: i 116 MET cc_start: -0.0586 (ttp) cc_final: -0.1875 (ttt) REVERT: i 135 MET cc_start: 0.2577 (mmp) cc_final: 0.0401 (mtt) REVERT: j 58 ASN cc_start: 0.8311 (m-40) cc_final: 0.7941 (m-40) REVERT: k 32 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8449 (p90) REVERT: l 86 GLU cc_start: 0.7648 (pm20) cc_final: 0.7392 (pm20) REVERT: l 143 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7213 (tt0) REVERT: n 114 GLU cc_start: 0.7482 (pp20) cc_final: 0.7141 (pp20) REVERT: n 115 LEU cc_start: 0.9152 (mt) cc_final: 0.8591 (mt) REVERT: n 116 VAL cc_start: 0.8920 (t) cc_final: 0.8669 (p) REVERT: o 34 HIS cc_start: 0.7565 (m-70) cc_final: 0.7120 (m-70) REVERT: q 90 ASP cc_start: 0.8047 (p0) cc_final: 0.7423 (p0) REVERT: r 24 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8195 (ttpp) REVERT: s 67 ASP cc_start: 0.7937 (m-30) cc_final: 0.7671 (p0) REVERT: s 85 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8777 (mp) REVERT: t 1 MET cc_start: 0.6028 (mtt) cc_final: 0.5768 (mtt) REVERT: u 5 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.7427 (ptp-170) REVERT: u 65 GLN cc_start: 0.8047 (mt0) cc_final: 0.7697 (mt0) REVERT: v 12 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7212 (pp30) REVERT: v 86 LEU cc_start: 0.8830 (pt) cc_final: 0.8049 (mt) REVERT: w 13 GLU cc_start: 0.7650 (tm-30) cc_final: 0.6878 (tm-30) REVERT: w 36 GLN cc_start: 0.8466 (pt0) cc_final: 0.8266 (pt0) REVERT: w 60 ASP cc_start: 0.8456 (m-30) cc_final: 0.8199 (m-30) REVERT: y 1 MET cc_start: 0.6954 (mmt) cc_final: 0.5071 (ptt) REVERT: y 39 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7852 (mm-40) REVERT: y 59 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: A 31 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6327 (t70) REVERT: C 6 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 32 LYS cc_start: 0.8242 (mptt) cc_final: 0.7605 (ttpp) REVERT: G 108 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8716 (mp10) REVERT: G 152 ASP cc_start: 0.8639 (p0) cc_final: 0.8298 (p0) REVERT: H 138 GLN cc_start: 0.8449 (tt0) cc_final: 0.8167 (tt0) REVERT: H 167 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6389 (t80) REVERT: L 4 ARG cc_start: 0.6715 (mtm180) cc_final: 0.6303 (mtp180) REVERT: L 21 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7813 (pp) REVERT: L 109 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7444 (pttt) REVERT: M 9 MET cc_start: 0.8425 (ttt) cc_final: 0.8223 (ttt) REVERT: M 51 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8106 (mm-30) REVERT: M 87 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7289 (mtp-110) REVERT: M 110 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8063 (pmm) REVERT: M 113 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7989 (ptt90) REVERT: N 45 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7129 (ptp) REVERT: N 49 GLN cc_start: 0.8326 (mt0) cc_final: 0.7957 (mm110) REVERT: N 56 MET cc_start: 0.6949 (ppp) cc_final: 0.6672 (ppp) REVERT: N 96 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: O 31 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.6150 (ptt-90) REVERT: O 64 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7426 (mm-40) REVERT: O 67 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8409 (mm) REVERT: O 71 LEU cc_start: 0.7911 (mt) cc_final: 0.7704 (mt) REVERT: O 101 SER cc_start: 0.7375 (OUTLIER) cc_final: 0.6921 (t) REVERT: P 13 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6147 (mmtt) REVERT: P 110 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.6898 (p) REVERT: Q 23 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5920 (mt) REVERT: Q 60 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: Q 74 GLN cc_start: 0.7883 (pm20) cc_final: 0.7608 (pm20) REVERT: R 65 GLU cc_start: 0.8296 (pm20) cc_final: 0.7578 (pt0) REVERT: R 71 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7366 (mm-30) REVERT: S 3 GLN cc_start: 0.7974 (mm110) cc_final: 0.7762 (mm-40) REVERT: S 5 MET cc_start: 0.7970 (mmm) cc_final: 0.7636 (mmt) REVERT: S 25 GLU cc_start: 0.7788 (pt0) cc_final: 0.7485 (pm20) REVERT: S 53 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6885 (t0) REVERT: S 61 ASN cc_start: 0.8361 (m-40) cc_final: 0.8137 (m-40) REVERT: S 74 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7302 (ttm110) REVERT: S 85 GLU cc_start: 0.8336 (pp20) cc_final: 0.7965 (pp20) REVERT: T 37 HIS cc_start: 0.7834 (m90) cc_final: 0.7230 (m90) REVERT: U 47 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6134 (pm20) REVERT: V 8 GLN cc_start: 0.7872 (pp30) cc_final: 0.7545 (pp30) REVERT: V 10 ARG cc_start: 0.8721 (ttm170) cc_final: 0.8370 (ttp-170) REVERT: V 29 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8318 (tptt) REVERT: W 11 ARG cc_start: 0.5962 (OUTLIER) cc_final: 0.5535 (mtm180) REVERT: X 2 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6535 (mtp85) REVERT: X 10 ILE cc_start: 0.8031 (tp) cc_final: 0.7756 (mt) REVERT: X 20 LYS cc_start: 0.5665 (mttt) cc_final: 0.4388 (tmmt) REVERT: X 33 TRP cc_start: 0.7753 (m-90) cc_final: 0.7086 (m-90) REVERT: X 65 MET cc_start: 0.8210 (mtt) cc_final: 0.7870 (mtp) REVERT: X 69 LYS cc_start: 0.7210 (mttt) cc_final: 0.6623 (mttt) REVERT: Y 26 MET cc_start: 0.8538 (ptm) cc_final: 0.7895 (ptp) REVERT: Y 27 MET cc_start: 0.9105 (ttm) cc_final: 0.8580 (ttm) REVERT: Y 51 ASN cc_start: 0.8578 (m-40) cc_final: 0.7927 (m-40) REVERT: Y 54 GLN cc_start: 0.8420 (mt0) cc_final: 0.7910 (tt0) REVERT: Y 73 ARG cc_start: 0.8715 (ttp-110) cc_final: 0.8296 (ttp-170) REVERT: Z 4 LYS cc_start: 0.7463 (ttpp) cc_final: 0.7115 (mmtt) REVERT: Z 37 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6360 (m-80) REVERT: Z 48 LYS cc_start: 0.8889 (tppt) cc_final: 0.8659 (mmtt) REVERT: Z 53 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8765 (pttt) outliers start: 344 outliers final: 264 residues processed: 1408 average time/residue: 1.2479 time to fit residues: 3100.1247 Evaluate side-chains 1455 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1163 time to evaluate : 6.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 52 HIS Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 134 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 235 GLU Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 100 MET Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 135 HIS Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain i residue 138 VAL Chi-restraints excluded: chain i residue 139 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 71 ASP Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain m residue 129 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 60 GLU Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 84 SER Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 23 LEU Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 17 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 12 GLN Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain w residue 78 ILE Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 50 VAL Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 21 TYR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 96 ASN Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 73 HIS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain Z residue 67 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 983 optimal weight: 1.9990 chunk 114 optimal weight: 50.0000 chunk 581 optimal weight: 50.0000 chunk 744 optimal weight: 9.9990 chunk 577 optimal weight: 30.0000 chunk 858 optimal weight: 4.9990 chunk 569 optimal weight: 7.9990 chunk 1015 optimal weight: 1.9990 chunk 635 optimal weight: 10.0000 chunk 619 optimal weight: 0.6980 chunk 469 optimal weight: 0.0570 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 HIS o 100 HIS ** p 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN v 51 GLN v 78 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Q 4 ASN ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN Y 47 GLN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 161799 Z= 0.132 Angle : 0.560 13.759 241915 Z= 0.288 Chirality : 0.033 0.574 30917 Planarity : 0.004 0.086 13067 Dihedral : 23.367 179.506 80663 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.99 % Favored : 90.84 % Rotamer: Outliers : 4.54 % Allowed : 29.00 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.32 (0.10), residues: 5962 helix: -0.62 (0.12), residues: 1806 sheet: -1.44 (0.16), residues: 1035 loop : -2.17 (0.10), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 33 HIS 0.005 0.001 HIS I 119 PHE 0.025 0.001 PHE Z 11 TYR 0.026 0.002 TYR H 41 ARG 0.024 0.001 ARG k 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1285 time to evaluate : 6.897 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: c 11 MET cc_start: 0.8469 (mtp) cc_final: 0.8210 (mtm) REVERT: c 33 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7354 (mtm-85) REVERT: c 180 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8279 (t) REVERT: d 111 GLU cc_start: 0.8294 (tp30) cc_final: 0.7467 (pt0) REVERT: d 144 GLU cc_start: 0.6469 (tt0) cc_final: 0.5942 (pm20) REVERT: e 80 GLN cc_start: 0.7714 (tp40) cc_final: 0.7434 (tm-30) REVERT: e 82 TYR cc_start: 0.7069 (m-10) cc_final: 0.6691 (m-10) REVERT: e 95 MET cc_start: 0.6868 (ptp) cc_final: 0.6405 (ptm) REVERT: e 124 ARG cc_start: 0.8845 (mtt-85) cc_final: 0.8414 (mmm160) REVERT: f 106 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8002 (pp) REVERT: f 123 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7696 (tm-30) REVERT: f 146 ASP cc_start: 0.8434 (t0) cc_final: 0.8134 (t0) REVERT: f 174 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.4510 (mmtt) REVERT: g 5 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6857 (pp) REVERT: g 135 HIS cc_start: 0.2963 (OUTLIER) cc_final: 0.2229 (m-70) REVERT: a 33 LEU cc_start: 0.3035 (mt) cc_final: 0.2120 (tt) REVERT: a 50 ILE cc_start: 0.3125 (OUTLIER) cc_final: 0.2797 (tt) REVERT: i 116 MET cc_start: -0.0853 (ttp) cc_final: -0.1567 (mtp) REVERT: i 135 MET cc_start: 0.2377 (mmp) cc_final: 0.0141 (mtt) REVERT: j 58 ASN cc_start: 0.8301 (m-40) cc_final: 0.7939 (m-40) REVERT: j 86 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: l 143 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7296 (tt0) REVERT: m 28 PHE cc_start: 0.8402 (m-10) cc_final: 0.8111 (m-10) REVERT: m 47 GLU cc_start: 0.7220 (tp30) cc_final: 0.7012 (tp30) REVERT: n 114 GLU cc_start: 0.7518 (pp20) cc_final: 0.7253 (pp20) REVERT: n 115 LEU cc_start: 0.9125 (mt) cc_final: 0.8606 (mt) REVERT: q 48 ASP cc_start: 0.7647 (m-30) cc_final: 0.7263 (m-30) REVERT: q 90 ASP cc_start: 0.7822 (p0) cc_final: 0.7258 (p0) REVERT: r 24 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8242 (ttpp) REVERT: r 48 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7851 (ptpp) REVERT: s 68 ASP cc_start: 0.8224 (p0) cc_final: 0.8022 (p0) REVERT: u 5 ARG cc_start: 0.7624 (ptp-170) cc_final: 0.7332 (ptp-170) REVERT: u 38 ILE cc_start: 0.7380 (mm) cc_final: 0.7177 (tp) REVERT: u 65 GLN cc_start: 0.7903 (mt0) cc_final: 0.7598 (mt0) REVERT: u 95 PHE cc_start: 0.8634 (m-80) cc_final: 0.8323 (m-80) REVERT: v 86 LEU cc_start: 0.8640 (pt) cc_final: 0.7952 (mt) REVERT: w 13 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6737 (tm-30) REVERT: x 21 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8796 (mp) REVERT: y 1 MET cc_start: 0.6829 (mmt) cc_final: 0.4974 (ptt) REVERT: y 39 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7687 (mm-40) REVERT: y 59 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: A 31 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6049 (t70) REVERT: D 3 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7685 (mmm160) REVERT: G 26 MET cc_start: 0.7493 (mmm) cc_final: 0.7264 (mmm) REVERT: G 108 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8761 (mp10) REVERT: G 152 ASP cc_start: 0.8401 (p0) cc_final: 0.8058 (p0) REVERT: G 183 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: H 138 GLN cc_start: 0.8415 (tt0) cc_final: 0.8148 (tt0) REVERT: H 166 TRP cc_start: 0.8131 (p-90) cc_final: 0.7867 (p-90) REVERT: H 167 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6341 (t80) REVERT: I 123 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5726 (tpp) REVERT: J 133 ILE cc_start: 0.8912 (mp) cc_final: 0.8671 (tp) REVERT: J 145 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8068 (m-40) REVERT: K 78 PHE cc_start: 0.7911 (m-80) cc_final: 0.7676 (m-80) REVERT: K 88 MET cc_start: 0.8011 (tmm) cc_final: 0.7375 (tmm) REVERT: K 90 MET cc_start: 0.7843 (mmm) cc_final: 0.7388 (mmm) REVERT: K 98 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: L 21 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7951 (pp) REVERT: L 109 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7405 (pttt) REVERT: M 79 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8159 (ptm-80) REVERT: M 87 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7286 (mtp-110) REVERT: M 110 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7846 (pmm) REVERT: M 113 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7967 (ptt90) REVERT: N 56 MET cc_start: 0.6919 (ppp) cc_final: 0.6717 (ppp) REVERT: N 96 GLU cc_start: 0.8508 (pm20) cc_final: 0.8139 (pm20) REVERT: O 11 LYS cc_start: 0.7182 (mtpt) cc_final: 0.6730 (mtpt) REVERT: O 31 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6241 (ptt-90) REVERT: O 64 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7367 (mm-40) REVERT: O 67 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8334 (mm) REVERT: O 101 SER cc_start: 0.7433 (OUTLIER) cc_final: 0.7043 (t) REVERT: P 84 MET cc_start: 0.8238 (mmm) cc_final: 0.7979 (mmp) REVERT: P 110 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.6619 (p) REVERT: Q 60 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: R 65 GLU cc_start: 0.8146 (pm20) cc_final: 0.7513 (pt0) REVERT: R 67 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7374 (t70) REVERT: R 71 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7124 (mm-30) REVERT: S 5 MET cc_start: 0.7925 (mmm) cc_final: 0.7562 (mmp) REVERT: S 25 GLU cc_start: 0.7802 (pt0) cc_final: 0.7484 (pm20) REVERT: S 53 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6898 (t0) REVERT: S 61 ASN cc_start: 0.8372 (m-40) cc_final: 0.8053 (m110) REVERT: S 74 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7094 (ttp80) REVERT: S 84 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7049 (tmm-80) REVERT: S 85 GLU cc_start: 0.8199 (pp20) cc_final: 0.7975 (pp20) REVERT: U 15 PRO cc_start: 0.8846 (Cg_endo) cc_final: 0.8142 (Cg_exo) REVERT: U 46 LYS cc_start: 0.5572 (pttm) cc_final: 0.3616 (mtmm) REVERT: U 48 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6184 (tm-30) REVERT: V 10 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8374 (ttp-170) REVERT: W 11 ARG cc_start: 0.5862 (ptt90) cc_final: 0.5579 (mtm180) REVERT: X 2 ARG cc_start: 0.6537 (mtt-85) cc_final: 0.6074 (mtp85) REVERT: X 10 ILE cc_start: 0.7961 (tp) cc_final: 0.7706 (mt) REVERT: X 20 LYS cc_start: 0.5541 (mttt) cc_final: 0.4491 (tmmt) REVERT: X 33 TRP cc_start: 0.7522 (m-90) cc_final: 0.6484 (m-90) REVERT: X 65 MET cc_start: 0.8140 (mtt) cc_final: 0.7801 (mtp) REVERT: X 69 LYS cc_start: 0.7204 (mttt) cc_final: 0.6725 (mttt) REVERT: Y 26 MET cc_start: 0.8494 (ptm) cc_final: 0.7875 (ptp) REVERT: Y 27 MET cc_start: 0.8953 (ttm) cc_final: 0.8516 (ttm) REVERT: Y 47 GLN cc_start: 0.8099 (tp40) cc_final: 0.7874 (tp-100) REVERT: Y 51 ASN cc_start: 0.8527 (m-40) cc_final: 0.7895 (m-40) REVERT: Y 54 GLN cc_start: 0.8373 (mt0) cc_final: 0.7867 (tt0) REVERT: Y 81 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8094 (tm-30) REVERT: Z 4 LYS cc_start: 0.7494 (ttpp) cc_final: 0.7133 (mmtt) REVERT: Z 37 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: Z 53 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8756 (pttt) outliers start: 225 outliers final: 140 residues processed: 1416 average time/residue: 1.3081 time to fit residues: 3250.9661 Evaluate side-chains 1361 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1191 time to evaluate : 6.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 135 HIS Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Chi-restraints excluded: chain Z residue 67 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 628 optimal weight: 2.9990 chunk 405 optimal weight: 10.0000 chunk 606 optimal weight: 0.5980 chunk 306 optimal weight: 40.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 645 optimal weight: 0.0970 chunk 692 optimal weight: 9.9990 chunk 502 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 798 optimal weight: 20.0000 overall best weight: 4.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN o 100 HIS ** p 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 49 ASN v 75 GLN v 78 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN L 27 ASN M 75 GLN P 37 GLN Q 4 ASN Q 58 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 161799 Z= 0.207 Angle : 0.581 13.087 241915 Z= 0.299 Chirality : 0.034 0.335 30917 Planarity : 0.005 0.093 13067 Dihedral : 23.301 179.992 80658 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.47 % Favored : 89.38 % Rotamer: Outliers : 4.73 % Allowed : 29.21 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.25 (0.10), residues: 5962 helix: -0.57 (0.12), residues: 1828 sheet: -1.38 (0.16), residues: 1061 loop : -2.14 (0.11), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 33 HIS 0.007 0.001 HIS E 30 PHE 0.024 0.001 PHE r 5 TYR 0.029 0.002 TYR J 49 ARG 0.022 0.000 ARG U 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1199 time to evaluate : 6.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 180 MET cc_start: 0.8028 (mmm) cc_final: 0.7712 (mmt) REVERT: c 180 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8316 (t) REVERT: d 111 GLU cc_start: 0.8400 (tp30) cc_final: 0.7884 (tp30) REVERT: d 115 GLN cc_start: 0.8701 (tt0) cc_final: 0.7461 (tm-30) REVERT: d 144 GLU cc_start: 0.6539 (tt0) cc_final: 0.6091 (pm20) REVERT: e 80 GLN cc_start: 0.7735 (tp40) cc_final: 0.7422 (tm-30) REVERT: e 95 MET cc_start: 0.6992 (ptp) cc_final: 0.6459 (ptm) REVERT: f 106 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7972 (pp) REVERT: f 146 ASP cc_start: 0.8507 (t0) cc_final: 0.8163 (t0) REVERT: f 152 ARG cc_start: 0.8580 (tpp-160) cc_final: 0.8308 (mmm160) REVERT: f 174 LYS cc_start: 0.5194 (OUTLIER) cc_final: 0.4371 (mmtt) REVERT: g 5 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6815 (pp) REVERT: a 33 LEU cc_start: 0.3047 (mt) cc_final: 0.2147 (tt) REVERT: a 50 ILE cc_start: 0.3185 (OUTLIER) cc_final: 0.2847 (tt) REVERT: i 116 MET cc_start: -0.0849 (ttp) cc_final: -0.1667 (mtp) REVERT: i 135 MET cc_start: 0.2246 (mmp) cc_final: 0.0027 (mtt) REVERT: j 58 ASN cc_start: 0.8232 (m-40) cc_final: 0.7895 (m-40) REVERT: j 86 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: k 66 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8551 (ttmm) REVERT: k 114 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7592 (mmmm) REVERT: l 143 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7280 (tt0) REVERT: n 114 GLU cc_start: 0.7553 (pp20) cc_final: 0.7254 (pp20) REVERT: n 115 LEU cc_start: 0.9127 (mt) cc_final: 0.8594 (mt) REVERT: q 70 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8000 (mm-40) REVERT: q 90 ASP cc_start: 0.7955 (p0) cc_final: 0.7372 (p0) REVERT: r 24 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8149 (ttpp) REVERT: r 48 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7843 (ptpp) REVERT: s 85 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8797 (mp) REVERT: t 1 MET cc_start: 0.5660 (mtt) cc_final: 0.4791 (mmm) REVERT: u 5 ARG cc_start: 0.7770 (ptp-170) cc_final: 0.7507 (ptp-170) REVERT: u 65 GLN cc_start: 0.7953 (mt0) cc_final: 0.7627 (mt0) REVERT: v 86 LEU cc_start: 0.8741 (pt) cc_final: 0.7993 (mt) REVERT: w 13 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6796 (tm-30) REVERT: x 21 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8827 (mp) REVERT: y 1 MET cc_start: 0.6762 (mmt) cc_final: 0.5013 (ptt) REVERT: y 39 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7747 (mm-40) REVERT: y 59 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: A 31 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6092 (t70) REVERT: C 32 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7735 (ttpp) REVERT: G 108 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8757 (mp10) REVERT: G 152 ASP cc_start: 0.8403 (p0) cc_final: 0.8072 (p0) REVERT: G 183 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: G 197 PHE cc_start: 0.8639 (m-80) cc_final: 0.8158 (m-80) REVERT: H 138 GLN cc_start: 0.8429 (tt0) cc_final: 0.8162 (tt0) REVERT: H 166 TRP cc_start: 0.8259 (p-90) cc_final: 0.7793 (p-90) REVERT: H 167 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6133 (t80) REVERT: K 88 MET cc_start: 0.8068 (tmm) cc_final: 0.7227 (tmm) REVERT: K 90 MET cc_start: 0.7927 (mmm) cc_final: 0.7443 (mmm) REVERT: K 98 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: L 109 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7441 (pttt) REVERT: M 79 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8143 (ptm-80) REVERT: M 87 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7241 (mtp-110) REVERT: M 110 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7801 (pmm) REVERT: M 113 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7976 (ptt90) REVERT: N 6 TYR cc_start: 0.7760 (t80) cc_final: 0.7553 (t80) REVERT: N 56 MET cc_start: 0.6981 (ppp) cc_final: 0.6740 (ppp) REVERT: N 88 GLU cc_start: 0.8347 (pt0) cc_final: 0.8129 (pm20) REVERT: N 96 GLU cc_start: 0.8518 (pm20) cc_final: 0.8159 (pm20) REVERT: O 64 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7311 (mm-40) REVERT: O 67 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8149 (mm) REVERT: O 101 SER cc_start: 0.7423 (OUTLIER) cc_final: 0.7042 (t) REVERT: P 110 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7144 (p) REVERT: Q 60 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: R 65 GLU cc_start: 0.8238 (pm20) cc_final: 0.7517 (pt0) REVERT: S 5 MET cc_start: 0.7950 (mmm) cc_final: 0.7672 (mmm) REVERT: S 25 GLU cc_start: 0.7801 (pt0) cc_final: 0.7475 (pm20) REVERT: S 53 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6960 (t0) REVERT: S 61 ASN cc_start: 0.8340 (m-40) cc_final: 0.8124 (m-40) REVERT: S 74 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7310 (ttm110) REVERT: S 85 GLU cc_start: 0.8290 (pp20) cc_final: 0.7922 (pp20) REVERT: T 37 HIS cc_start: 0.7756 (m90) cc_final: 0.7155 (m90) REVERT: U 46 LYS cc_start: 0.5570 (pttm) cc_final: 0.3692 (mtpp) REVERT: U 48 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6342 (tm-30) REVERT: V 10 ARG cc_start: 0.8685 (ttm170) cc_final: 0.8403 (ttp-170) REVERT: V 29 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8327 (tptt) REVERT: W 11 ARG cc_start: 0.5815 (ptt90) cc_final: 0.5466 (mtm180) REVERT: X 2 ARG cc_start: 0.6716 (mtt-85) cc_final: 0.6263 (mtp85) REVERT: X 10 ILE cc_start: 0.7937 (tp) cc_final: 0.7673 (mt) REVERT: X 20 LYS cc_start: 0.5472 (mttt) cc_final: 0.4428 (tmmt) REVERT: X 33 TRP cc_start: 0.7628 (m-90) cc_final: 0.6779 (m-90) REVERT: X 65 MET cc_start: 0.8335 (mtt) cc_final: 0.8011 (mtp) REVERT: X 69 LYS cc_start: 0.7211 (mttt) cc_final: 0.6726 (mttt) REVERT: Y 26 MET cc_start: 0.8524 (ptm) cc_final: 0.7883 (ptp) REVERT: Y 27 MET cc_start: 0.9063 (ttm) cc_final: 0.8820 (ttm) REVERT: Y 47 GLN cc_start: 0.8095 (tp40) cc_final: 0.7874 (tp-100) REVERT: Y 51 ASN cc_start: 0.8534 (m-40) cc_final: 0.7897 (m110) REVERT: Y 54 GLN cc_start: 0.8407 (mt0) cc_final: 0.7922 (tt0) REVERT: Z 4 LYS cc_start: 0.7497 (ttpp) cc_final: 0.7125 (mmtt) REVERT: Z 37 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: Z 53 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8752 (pttt) outliers start: 234 outliers final: 179 residues processed: 1330 average time/residue: 1.3366 time to fit residues: 3169.2645 Evaluate side-chains 1366 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1164 time to evaluate : 6.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 198 GLU Chi-restraints excluded: chain b residue 222 THR Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 135 HIS Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 117 SER Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 11 ILE Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 60 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 108 ASN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 924 optimal weight: 7.9990 chunk 973 optimal weight: 0.9990 chunk 887 optimal weight: 20.0000 chunk 946 optimal weight: 20.0000 chunk 972 optimal weight: 1.9990 chunk 569 optimal weight: 5.9990 chunk 412 optimal weight: 10.0000 chunk 743 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 855 optimal weight: 0.8980 chunk 895 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS ** p 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN P 37 GLN Q 4 ASN ** Y 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 161799 Z= 0.159 Angle : 0.560 13.155 241915 Z= 0.288 Chirality : 0.033 0.260 30917 Planarity : 0.004 0.111 13067 Dihedral : 23.296 179.646 80658 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.00 % Favored : 89.85 % Rotamer: Outliers : 4.58 % Allowed : 29.51 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.16 (0.11), residues: 5962 helix: -0.48 (0.12), residues: 1825 sheet: -1.35 (0.16), residues: 1062 loop : -2.07 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 80 HIS 0.006 0.001 HIS E 30 PHE 0.021 0.001 PHE Z 11 TYR 0.024 0.002 TYR H 183 ARG 0.010 0.000 ARG J 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1202 time to evaluate : 6.791 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: c 180 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8390 (t) REVERT: d 144 GLU cc_start: 0.6456 (tt0) cc_final: 0.5985 (pm20) REVERT: e 80 GLN cc_start: 0.7763 (tp40) cc_final: 0.7412 (tm-30) REVERT: e 95 MET cc_start: 0.6986 (ptp) cc_final: 0.6465 (ptm) REVERT: f 106 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7950 (pp) REVERT: f 146 ASP cc_start: 0.8471 (t0) cc_final: 0.8137 (t0) REVERT: f 152 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.8256 (mmm160) REVERT: f 174 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4436 (mmtt) REVERT: g 5 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6884 (pp) REVERT: a 33 LEU cc_start: 0.2975 (mt) cc_final: 0.2168 (tt) REVERT: a 50 ILE cc_start: 0.3107 (OUTLIER) cc_final: 0.2783 (tt) REVERT: i 116 MET cc_start: -0.0781 (ttp) cc_final: -0.1611 (mtp) REVERT: i 135 MET cc_start: 0.2235 (mmp) cc_final: -0.0038 (mtt) REVERT: j 58 ASN cc_start: 0.8244 (m-40) cc_final: 0.7918 (m-40) REVERT: j 86 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: k 66 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8535 (ttmm) REVERT: k 114 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7525 (mmmm) REVERT: l 143 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7336 (tt0) REVERT: m 59 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.5896 (mmt180) REVERT: n 29 VAL cc_start: 0.9025 (t) cc_final: 0.8820 (m) REVERT: n 114 GLU cc_start: 0.7578 (pp20) cc_final: 0.7291 (pp20) REVERT: n 115 LEU cc_start: 0.9144 (mt) cc_final: 0.8612 (mt) REVERT: p 37 LYS cc_start: 0.7620 (tptp) cc_final: 0.7402 (tppt) REVERT: q 90 ASP cc_start: 0.7903 (p0) cc_final: 0.7339 (p0) REVERT: r 24 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8152 (ttpp) REVERT: r 48 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7774 (ptpp) REVERT: s 85 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8720 (mt) REVERT: t 1 MET cc_start: 0.5634 (mtt) cc_final: 0.4934 (mmm) REVERT: u 5 ARG cc_start: 0.7744 (ptp-170) cc_final: 0.7523 (ptp-170) REVERT: u 38 ILE cc_start: 0.7399 (mm) cc_final: 0.7134 (tp) REVERT: u 65 GLN cc_start: 0.7929 (mt0) cc_final: 0.7613 (mt0) REVERT: v 86 LEU cc_start: 0.8658 (pt) cc_final: 0.7950 (mt) REVERT: w 13 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6715 (tm-30) REVERT: x 21 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8809 (mp) REVERT: y 1 MET cc_start: 0.6844 (mmt) cc_final: 0.5152 (ptt) REVERT: y 39 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7634 (mm-40) REVERT: y 59 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: A 31 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6092 (t70) REVERT: C 32 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7714 (ttpp) REVERT: G 108 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8787 (mp10) REVERT: G 152 ASP cc_start: 0.8334 (p0) cc_final: 0.7984 (p0) REVERT: G 183 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: G 197 PHE cc_start: 0.8635 (m-80) cc_final: 0.8215 (m-80) REVERT: H 138 GLN cc_start: 0.8418 (tt0) cc_final: 0.8147 (tt0) REVERT: H 166 TRP cc_start: 0.8209 (p-90) cc_final: 0.7779 (p-90) REVERT: H 167 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6052 (t80) REVERT: I 123 MET cc_start: 0.6333 (mtt) cc_final: 0.5665 (ttm) REVERT: K 88 MET cc_start: 0.8008 (tmm) cc_final: 0.7087 (tmm) REVERT: K 90 MET cc_start: 0.7833 (mmm) cc_final: 0.7402 (mmm) REVERT: K 98 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: L 109 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7393 (pttt) REVERT: M 79 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8151 (ptm-80) REVERT: M 87 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7245 (mtp-110) REVERT: M 110 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7790 (pmm) REVERT: M 113 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7962 (ptt90) REVERT: N 56 MET cc_start: 0.7012 (ppp) cc_final: 0.6774 (ppp) REVERT: N 96 GLU cc_start: 0.8507 (pm20) cc_final: 0.8147 (pm20) REVERT: O 64 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7278 (mm-40) REVERT: O 101 SER cc_start: 0.7447 (OUTLIER) cc_final: 0.7024 (t) REVERT: P 110 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7120 (m) REVERT: Q 60 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6610 (m-80) REVERT: R 65 GLU cc_start: 0.8241 (pm20) cc_final: 0.7457 (pt0) REVERT: S 5 MET cc_start: 0.7968 (mmm) cc_final: 0.7616 (mmp) REVERT: S 25 GLU cc_start: 0.7788 (pt0) cc_final: 0.7466 (pm20) REVERT: S 53 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6992 (t0) REVERT: S 61 ASN cc_start: 0.8367 (m-40) cc_final: 0.8076 (m110) REVERT: S 85 GLU cc_start: 0.8258 (pp20) cc_final: 0.7905 (pp20) REVERT: T 37 HIS cc_start: 0.7730 (m90) cc_final: 0.7121 (m90) REVERT: U 15 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8686 (Cg_endo) REVERT: U 46 LYS cc_start: 0.5331 (pttm) cc_final: 0.3640 (mtpp) REVERT: U 48 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6378 (tm-30) REVERT: V 10 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8397 (ttp-170) REVERT: V 29 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8369 (tptt) REVERT: W 11 ARG cc_start: 0.5778 (ptt90) cc_final: 0.5420 (mtm180) REVERT: X 2 ARG cc_start: 0.6635 (mtt-85) cc_final: 0.6186 (mtp85) REVERT: X 10 ILE cc_start: 0.7914 (tp) cc_final: 0.7638 (mt) REVERT: X 20 LYS cc_start: 0.5573 (mttt) cc_final: 0.4559 (tmmt) REVERT: X 33 TRP cc_start: 0.7616 (m-90) cc_final: 0.6789 (m-90) REVERT: X 65 MET cc_start: 0.8389 (mtt) cc_final: 0.8171 (mtm) REVERT: X 69 LYS cc_start: 0.7182 (mttt) cc_final: 0.6715 (mttt) REVERT: Y 26 MET cc_start: 0.8525 (ptm) cc_final: 0.7880 (ptp) REVERT: Y 27 MET cc_start: 0.9009 (ttm) cc_final: 0.8771 (ttm) REVERT: Y 47 GLN cc_start: 0.8078 (tp40) cc_final: 0.7844 (tp-100) REVERT: Y 51 ASN cc_start: 0.8533 (m-40) cc_final: 0.7904 (m110) REVERT: Y 54 GLN cc_start: 0.8392 (mt0) cc_final: 0.7898 (tt0) REVERT: Z 4 LYS cc_start: 0.7486 (ttpp) cc_final: 0.7054 (mmtt) REVERT: Z 37 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6289 (m-80) REVERT: Z 53 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8746 (pttt) outliers start: 227 outliers final: 177 residues processed: 1330 average time/residue: 1.2729 time to fit residues: 2988.5320 Evaluate side-chains 1369 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1169 time to evaluate : 6.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 251 THR Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 27 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 135 HIS Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain h residue 123 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain j residue 131 ASN Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 86 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain n residue 74 GLU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 10 GLU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 76 SER Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 48 LYS Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain T residue 45 HIS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 943 optimal weight: 2.9990 chunk 621 optimal weight: 2.9990 chunk 1001 optimal weight: 20.0000 chunk 610 optimal weight: 0.8980 chunk 474 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 1050 optimal weight: 0.2980 chunk 966 optimal weight: 7.9990 chunk 836 optimal weight: 0.3980 chunk 86 optimal weight: 10.0000 chunk 645 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 11 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS ** p 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 36 GLN r 18 GLN v 75 GLN v 78 GLN ** y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN P 37 GLN Q 4 ASN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 161799 Z= 0.128 Angle : 0.541 13.497 241915 Z= 0.276 Chirality : 0.031 0.256 30917 Planarity : 0.004 0.085 13067 Dihedral : 23.232 179.763 80656 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.36 % Favored : 90.49 % Rotamer: Outliers : 3.66 % Allowed : 30.48 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.06 (0.11), residues: 5962 helix: -0.38 (0.12), residues: 1831 sheet: -1.32 (0.16), residues: 1056 loop : -2.01 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 103 HIS 0.016 0.001 HIS A 6 PHE 0.020 0.001 PHE Z 36 TYR 0.030 0.002 TYR J 49 ARG 0.017 0.000 ARG D 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1249 time to evaluate : 6.747 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: c 180 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8329 (t) REVERT: d 111 GLU cc_start: 0.8317 (tp30) cc_final: 0.8024 (tp30) REVERT: e 80 GLN cc_start: 0.7719 (tp40) cc_final: 0.6946 (tm-30) REVERT: e 95 MET cc_start: 0.6858 (ptp) cc_final: 0.6356 (ptm) REVERT: e 124 ARG cc_start: 0.8820 (mtt-85) cc_final: 0.8366 (mmm160) REVERT: f 106 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (pp) REVERT: f 133 LYS cc_start: 0.8751 (mttp) cc_final: 0.8426 (tptp) REVERT: f 146 ASP cc_start: 0.8368 (t0) cc_final: 0.8082 (t0) REVERT: f 174 LYS cc_start: 0.5211 (OUTLIER) cc_final: 0.4285 (mmtt) REVERT: g 5 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6883 (pp) REVERT: g 135 HIS cc_start: 0.3019 (OUTLIER) cc_final: 0.2342 (m-70) REVERT: a 33 LEU cc_start: 0.2921 (mt) cc_final: 0.2186 (tt) REVERT: a 37 LYS cc_start: 0.6316 (tppt) cc_final: 0.5852 (pttm) REVERT: a 50 ILE cc_start: 0.2974 (OUTLIER) cc_final: 0.2687 (tt) REVERT: i 116 MET cc_start: -0.0528 (ttp) cc_final: -0.1158 (mtp) REVERT: i 135 MET cc_start: 0.2061 (mmp) cc_final: -0.0225 (mtt) REVERT: j 58 ASN cc_start: 0.8193 (m-40) cc_final: 0.7873 (m-40) REVERT: j 71 ASP cc_start: 0.8317 (t0) cc_final: 0.7395 (t0) REVERT: j 86 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: k 114 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7345 (mmtp) REVERT: l 129 LYS cc_start: 0.8573 (mttt) cc_final: 0.8362 (ptpt) REVERT: l 143 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7491 (tt0) REVERT: m 59 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.5823 (mmt180) REVERT: n 114 GLU cc_start: 0.7625 (pp20) cc_final: 0.7335 (pp20) REVERT: n 115 LEU cc_start: 0.9139 (mt) cc_final: 0.8520 (mt) REVERT: o 38 GLN cc_start: 0.8360 (mt0) cc_final: 0.8127 (mt0) REVERT: p 37 LYS cc_start: 0.7649 (tptp) cc_final: 0.7381 (tppt) REVERT: q 90 ASP cc_start: 0.7826 (p0) cc_final: 0.7287 (p0) REVERT: r 24 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8210 (ttpp) REVERT: s 85 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8702 (mt) REVERT: t 1 MET cc_start: 0.5567 (mtt) cc_final: 0.5094 (mmp) REVERT: u 95 PHE cc_start: 0.8334 (m-80) cc_final: 0.8064 (m-80) REVERT: v 86 LEU cc_start: 0.8539 (pt) cc_final: 0.7892 (mt) REVERT: w 73 ARG cc_start: 0.6725 (mtt180) cc_final: 0.6276 (mtt180) REVERT: y 1 MET cc_start: 0.6634 (mmt) cc_final: 0.5309 (ptt) REVERT: y 39 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7547 (mm-40) REVERT: y 59 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: z 13 ILE cc_start: 0.9001 (mm) cc_final: 0.8623 (mm) REVERT: z 43 ILE cc_start: 0.9193 (mm) cc_final: 0.8985 (mm) REVERT: A 1 MET cc_start: 0.7653 (tpp) cc_final: 0.7140 (tpt) REVERT: A 31 ASP cc_start: 0.6576 (OUTLIER) cc_final: 0.6053 (t70) REVERT: B 36 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8114 (tttp) REVERT: C 32 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7731 (ttpp) REVERT: G 108 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8797 (mp10) REVERT: G 152 ASP cc_start: 0.8143 (p0) cc_final: 0.7857 (p0) REVERT: G 183 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: H 138 GLN cc_start: 0.8374 (tt0) cc_final: 0.8107 (tt0) REVERT: I 123 MET cc_start: 0.6412 (mtt) cc_final: 0.5893 (ttm) REVERT: I 177 MET cc_start: 0.6331 (mtt) cc_final: 0.5617 (mtm) REVERT: K 40 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7040 (tt0) REVERT: K 88 MET cc_start: 0.8013 (tmm) cc_final: 0.7053 (tmm) REVERT: K 90 MET cc_start: 0.7737 (mmm) cc_final: 0.7479 (mmm) REVERT: K 98 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: L 24 LYS cc_start: 0.7925 (tptt) cc_final: 0.7669 (ttmt) REVERT: L 30 MET cc_start: 0.8093 (tpp) cc_final: 0.7809 (ttt) REVERT: L 109 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7498 (pttt) REVERT: M 79 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8177 (ptm-80) REVERT: M 87 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7236 (mtp-110) REVERT: M 113 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7929 (ptt90) REVERT: N 56 MET cc_start: 0.6998 (ppp) cc_final: 0.6780 (ppp) REVERT: N 94 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7391 (mtt90) REVERT: O 64 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7265 (mm-40) REVERT: O 101 SER cc_start: 0.7400 (OUTLIER) cc_final: 0.6974 (t) REVERT: P 81 LEU cc_start: 0.7544 (mt) cc_final: 0.7330 (mt) REVERT: Q 60 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: R 65 GLU cc_start: 0.8158 (pm20) cc_final: 0.7419 (pt0) REVERT: R 71 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7281 (mm-30) REVERT: S 5 MET cc_start: 0.7870 (mmm) cc_final: 0.7529 (mmp) REVERT: S 25 GLU cc_start: 0.7787 (pt0) cc_final: 0.7440 (pm20) REVERT: S 53 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6876 (t0) REVERT: S 61 ASN cc_start: 0.8296 (m-40) cc_final: 0.8039 (m110) REVERT: S 85 GLU cc_start: 0.8182 (pp20) cc_final: 0.7822 (pp20) REVERT: U 8 ARG cc_start: 0.8156 (tmt-80) cc_final: 0.7898 (tpt90) REVERT: U 15 PRO cc_start: 0.8931 (Cg_exo) cc_final: 0.8702 (Cg_endo) REVERT: U 46 LYS cc_start: 0.5029 (pttm) cc_final: 0.3592 (mtpp) REVERT: U 77 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8517 (tm-30) REVERT: V 10 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8361 (ttp-170) REVERT: V 59 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7596 (tm-30) REVERT: V 60 ILE cc_start: 0.9186 (pt) cc_final: 0.8807 (pt) REVERT: X 10 ILE cc_start: 0.7822 (tp) cc_final: 0.7535 (mt) REVERT: X 69 LYS cc_start: 0.7143 (mttt) cc_final: 0.6714 (mttt) REVERT: Y 8 LYS cc_start: 0.7161 (mptt) cc_final: 0.6191 (tttt) REVERT: Y 26 MET cc_start: 0.8451 (ptm) cc_final: 0.7791 (ptp) REVERT: Y 27 MET cc_start: 0.8924 (ttm) cc_final: 0.8709 (ttm) REVERT: Y 47 GLN cc_start: 0.8012 (tp40) cc_final: 0.7753 (tp-100) REVERT: Y 51 ASN cc_start: 0.8486 (m-40) cc_final: 0.7815 (m110) REVERT: Y 54 GLN cc_start: 0.8400 (mt0) cc_final: 0.7932 (tt0) REVERT: Z 4 LYS cc_start: 0.7422 (ttpp) cc_final: 0.7010 (mmtt) REVERT: Z 37 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: Z 53 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8761 (pttt) outliers start: 181 outliers final: 138 residues processed: 1347 average time/residue: 1.3119 time to fit residues: 3118.8733 Evaluate side-chains 1341 residues out of total 4951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1184 time to evaluate : 6.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 ASP Chi-restraints excluded: chain b residue 267 VAL Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 207 VAL Chi-restraints excluded: chain d residue 88 ARG Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 57 TYR Chi-restraints excluded: chain f residue 61 TRP Chi-restraints excluded: chain f residue 86 LEU Chi-restraints excluded: chain f residue 100 ASN Chi-restraints excluded: chain f residue 106 LEU Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 150 TYR Chi-restraints excluded: chain f residue 174 LYS Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 11 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 135 HIS Chi-restraints excluded: chain g residue 142 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain h residue 82 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 117 THR Chi-restraints excluded: chain j residue 86 GLN Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 61 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 42 SER Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 59 ARG Chi-restraints excluded: chain m residue 104 GLU Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 85 ILE Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 11 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain u residue 8 ASP Chi-restraints excluded: chain u residue 40 LEU Chi-restraints excluded: chain u residue 69 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 59 GLU Chi-restraints excluded: chain z residue 23 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 79 ARG Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain Q residue 60 PHE Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain T residue 21 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 38 THR Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 24 LYS Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 37 TYR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 512 optimal weight: 6.9990 chunk 664 optimal weight: 5.9990 chunk 890 optimal weight: 1.9990 chunk 256 optimal weight: 20.0000 chunk 770 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 232 optimal weight: 10.0000 chunk 837 optimal weight: 8.9990 chunk 350 optimal weight: 10.0000 chunk 859 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 GLN g 11 ASN ** a 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 ASN o 100 HIS ** p 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 51 ASN q 36 GLN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN N 49 GLN P 37 GLN P 63 GLN Q 4 ASN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.081985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.064589 restraints weight = 580675.611| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.74 r_work: 0.3223 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 161799 Z= 0.210 Angle : 0.578 16.438 241915 Z= 0.294 Chirality : 0.033 0.311 30917 Planarity : 0.005 0.088 13067 Dihedral : 23.193 179.715 80654 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.18 % Favored : 89.68 % Rotamer: Outliers : 3.80 % Allowed : 31.10 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -2.04 (0.11), residues: 5962 helix: -0.42 (0.12), residues: 1845 sheet: -1.23 (0.16), residues: 1054 loop : -2.01 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 103 HIS 0.007 0.001 HIS E 30 PHE 0.027 0.002 PHE d 183 TYR 0.027 0.002 TYR H 183 ARG 0.018 0.001 ARG P 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47179.74 seconds wall clock time: 820 minutes 29.30 seconds (49229.30 seconds total)