Starting phenix.real_space_refine on Fri Mar 1 08:51:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssd_25407/03_2024/7ssd_25407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssd_25407/03_2024/7ssd_25407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssd_25407/03_2024/7ssd_25407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssd_25407/03_2024/7ssd_25407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssd_25407/03_2024/7ssd_25407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssd_25407/03_2024/7ssd_25407_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.111 sd= 0.944 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 176 5.16 5 C 77562 2.51 5 N 28428 2.21 5 O 42153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 ASP 20": "OD1" <-> "OD2" Residue "8 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 94": "OD1" <-> "OD2" Residue "8 GLU 98": "OE1" <-> "OE2" Residue "8 GLU 100": "OE1" <-> "OE2" Residue "8 TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 146": "NH1" <-> "NH2" Residue "8 GLU 205": "OE1" <-> "OE2" Residue "8 ASP 210": "OD1" <-> "OD2" Residue "8 GLU 217": "OE1" <-> "OE2" Residue "8 GLU 224": "OE1" <-> "OE2" Residue "8 GLU 232": "OE1" <-> "OE2" Residue "8 TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 242": "OE1" <-> "OE2" Residue "8 GLU 245": "OE1" <-> "OE2" Residue "8 ASP 291": "OD1" <-> "OD2" Residue "8 ASP 301": "OD1" <-> "OD2" Residue "8 GLU 308": "OE1" <-> "OE2" Residue "8 GLU 315": "OE1" <-> "OE2" Residue "8 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 358": "OE1" <-> "OE2" Residue "8 PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 395": "OD1" <-> "OD2" Residue "8 GLU 429": "OE1" <-> "OE2" Residue "8 GLU 441": "OE1" <-> "OE2" Residue "8 GLU 476": "OE1" <-> "OE2" Residue "8 ASP 500": "OD1" <-> "OD2" Residue "8 ASP 554": "OD1" <-> "OD2" Residue "8 GLU 626": "OE1" <-> "OE2" Residue "8 GLU 683": "OE1" <-> "OE2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b GLU 81": "OE1" <-> "OE2" Residue "b TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 74": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 103": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ASP 176": "OD1" <-> "OD2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d GLU 25": "OE1" <-> "OE2" 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 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ASP 116": "OD1" <-> "OD2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d ASP 140": "OD1" <-> "OD2" Residue "d GLU 144": "OE1" <-> "OE2" Residue "d ASP 145": "OD1" <-> "OD2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 171": "OD1" <-> "OD2" Residue "d ASP 176": "OD1" <-> "OD2" Residue "d PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 9": "OD1" <-> "OD2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 93": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e ASP 146": "OD1" <-> "OD2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g GLU 45": "OE1" <-> "OE2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g GLU 127": "OE1" <-> "OE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 13": "OE1" <-> "OE2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "a GLU 40": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 181": "OD1" <-> "OD2" Residue "a ASP 183": "OD1" <-> "OD2" Residue "a GLU 187": "OE1" <-> "OE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 110": "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 ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ASP 81": "OD1" <-> "OD2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 32": "OE1" <-> "OE2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ASP 72": "OD1" <-> "OD2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 82": "OE1" <-> "OE2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ASP 117": "OD1" <-> "OD2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ASP 2": "OD1" <-> "OD2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ASP 89": "OD1" <-> "OD2" Residue "o PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p GLU 8": "OE1" <-> "OE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "p GLU 111": "OE1" <-> "OE2" 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 ARG 47": "NH1" <-> "NH2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 4": "OE1" <-> "OE2" Residue "t GLU 18": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t GLU 89": "OE1" <-> "OE2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 7": "OE1" <-> "OE2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "v PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 64": "OD1" <-> "OD2" Residue "x GLU 69": "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 ASP 39": "OD1" <-> "OD2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 58": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E PHE 13": "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 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 107": "NH1" <-> "NH2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "S ASP 37": "OD1" <-> "OD2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153049 Number of models: 1 Model: "" Number of chains: 59 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': 101, 'rna2p_pyr': 57, 'rna3p_pur': 773, 'rna3p_pyr': 608} Link IDs: {'rna2p': 158, 'rna3p': 1380} 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': 227, 'rna2p_pyr': 106, 'rna3p_pur': 1447, 'rna3p_pyr': 1123} Link IDs: {'rna2p': 333, 'rna3p': 2569} 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': 2, 'rna3p_pur': 60, 'rna3p_pyr': 53} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "8" Number of atoms: 5157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5157 Classifications: {'peptide': 666} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 633} Chain breaks: 1 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': 6, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 65} 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: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "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: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 355 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 350 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain breaks: 1 Chain: "5" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} 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: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 58.65, per 1000 atoms: 0.38 Number of scatterers: 153049 At special positions: 0 Unit cell: (269.635, 253.093, 241.513, 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 176 16.00 P 4730 15.00 O 42153 8.00 N 28428 7.00 C 77562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 27 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.12 Conformation dependent library (CDL) restraints added in 7.6 seconds 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12120 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: 189 helices and 78 sheets defined 36.7% alpha, 16.8% beta 1203 base pairs and 2671 stacking pairs defined. Time for finding SS restraints: 75.71 Creating SS restraints... Processing helix chain '8' and resid 22 through 36 removed outlier: 3.519A pdb=" N ARG 8 29 " --> pdb=" O THR 8 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 8 33 " --> pdb=" O ARG 8 29 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY 8 35 " --> pdb=" O LEU 8 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL 8 36 " --> pdb=" O PHE 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 92 through 97 removed outlier: 5.412A pdb=" N THR 8 96 " --> pdb=" O HIS 8 92 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE 8 97 " --> pdb=" O VAL 8 93 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 92 through 97' Processing helix chain '8' and resid 98 through 107 removed outlier: 3.642A pdb=" N ARG 8 104 " --> pdb=" O GLU 8 100 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASP 8 107 " --> pdb=" O MET 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 134 removed outlier: 3.546A pdb=" N GLN 8 129 " --> pdb=" O THR 8 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 8 133 " --> pdb=" O GLN 8 129 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 161 removed outlier: 4.208A pdb=" N VAL 8 154 " --> pdb=" O ASN 8 150 " (cutoff:3.500A) Processing helix chain '8' and resid 213 through 227 removed outlier: 3.835A pdb=" N GLU 8 217 " --> pdb=" O GLU 8 213 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP 8 218 " --> pdb=" O LEU 8 214 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS 8 219 " --> pdb=" O ALA 8 215 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE 8 223 " --> pdb=" O HIS 8 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU 8 224 " --> pdb=" O GLN 8 220 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA 8 226 " --> pdb=" O LEU 8 222 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA 8 227 " --> pdb=" O ILE 8 223 " (cutoff:3.500A) Processing helix chain '8' and resid 230 through 240 removed outlier: 3.862A pdb=" N MET 8 234 " --> pdb=" O SER 8 230 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS 8 236 " --> pdb=" O GLU 8 232 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR 8 237 " --> pdb=" O LEU 8 233 " (cutoff:3.500A) Processing helix chain '8' and resid 244 through 259 removed outlier: 3.782A pdb=" N ILE 8 248 " --> pdb=" O THR 8 244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS 8 249 " --> pdb=" O GLU 8 245 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN 8 254 " --> pdb=" O GLY 8 250 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG 8 255 " --> pdb=" O ALA 8 251 " (cutoff:3.500A) Processing helix chain '8' and resid 274 through 285 removed outlier: 3.595A pdb=" N MET 8 278 " --> pdb=" O GLY 8 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU 8 279 " --> pdb=" O VAL 8 275 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP 8 284 " --> pdb=" O ASP 8 280 " (cutoff:3.500A) Processing helix chain '8' and resid 288 through 293 Proline residue: 8 293 - end of helix Processing helix chain '8' and resid 424 through 442 removed outlier: 3.741A pdb=" N LYS 8 430 " --> pdb=" O ALA 8 426 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET 8 431 " --> pdb=" O ASP 8 427 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS 8 440 " --> pdb=" O GLY 8 436 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP 8 442 " --> pdb=" O LEU 8 438 " (cutoff:3.500A) Processing helix chain '8' and resid 462 through 476 removed outlier: 3.658A pdb=" N LEU 8 466 " --> pdb=" O GLY 8 462 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP 8 467 " --> pdb=" O GLU 8 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE 8 469 " --> pdb=" O HIS 8 465 " (cutoff:3.500A) Processing helix chain '8' and resid 546 through 564 removed outlier: 4.014A pdb=" N ILE 8 550 " --> pdb=" O PRO 8 546 " (cutoff:3.500A) Proline residue: 8 551 - end of helix removed outlier: 3.615A pdb=" N ASP 8 554 " --> pdb=" O ILE 8 550 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS 8 562 " --> pdb=" O GLN 8 558 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA 8 563 " --> pdb=" O GLU 8 559 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY 8 564 " --> pdb=" O GLN 8 560 " (cutoff:3.500A) Processing helix chain '8' and resid 589 through 609 removed outlier: 3.718A pdb=" N PHE 8 593 " --> pdb=" O SER 8 589 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA 8 597 " --> pdb=" O PHE 8 593 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER 8 598 " --> pdb=" O LYS 8 594 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU 8 603 " --> pdb=" O ILE 8 599 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS 8 606 " --> pdb=" O LYS 8 602 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA 8 608 " --> pdb=" O GLY 8 604 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS 8 609 " --> pdb=" O PHE 8 605 " (cutoff:3.500A) Processing helix chain '8' and resid 627 through 639 removed outlier: 3.593A pdb=" N GLY 8 633 " --> pdb=" O GLY 8 629 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG 8 639 " --> pdb=" O LEU 8 635 " (cutoff:3.500A) Processing helix chain '8' and resid 665 through 675 removed outlier: 3.848A pdb=" N GLN 8 669 " --> pdb=" O GLY 8 665 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU 8 673 " --> pdb=" O GLN 8 669 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS 8 675 " --> pdb=" O ARG 8 671 " (cutoff:3.500A) Processing helix chain '8' and resid 691 through 699 removed outlier: 4.049A pdb=" N VAL 8 698 " --> pdb=" O VAL 8 694 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE 8 699 " --> pdb=" O ALA 8 695 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 14 removed outlier: 7.215A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.111A pdb=" N LEU b 33 " --> pdb=" O PHE b 29 " (cutoff:3.500A) removed outlier: 5.971A 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 206 through 214 removed outlier: 3.651A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP b 212 " --> pdb=" O GLY b 208 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.709A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.255A 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: 5.964A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE b 265 " --> pdb=" O ARG b 261 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE b 266 " --> pdb=" O THR b 262 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL b 267 " --> pdb=" O ASP b 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 267' Processing helix chain 'b' and resid 196 through 201 removed outlier: 4.301A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 61 removed outlier: 3.720A pdb=" N VAL c 60 " --> pdb=" O LYS c 56 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 56 through 61' Processing helix chain 'c' and resid 62 through 72 removed outlier: 4.393A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE c 68 " --> pdb=" O GLU c 64 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 105 removed outlier: 4.076A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL c 104 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LYS c 105 " --> pdb=" O PHE c 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 105' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 removed outlier: 3.909A pdb=" N PHE d 19 " --> pdb=" O SER d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.650A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL d 32 " --> pdb=" O VAL d 28 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA d 39 " --> pdb=" O TYR d 35 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.629A pdb=" N GLY d 103 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA d 104 " --> pdb=" O MET d 100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER d 107 " --> pdb=" O GLY d 103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL d 113 " --> pdb=" O LEU d 109 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN d 115 " --> pdb=" O GLU d 111 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.773A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU d 138 " --> pdb=" O LEU d 134 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS d 139 " --> pdb=" O ALA d 135 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 162 removed outlier: 3.536A pdb=" N LEU d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 removed outlier: 3.839A pdb=" N ALA d 182 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 201 removed outlier: 4.622A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN d 195 " --> pdb=" O ASP d 191 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL d 196 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU d 197 " --> pdb=" O VAL d 193 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU d 198 " --> pdb=" O LYS d 194 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET d 199 " --> pdb=" O GLN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.654A pdb=" N ASP e 5 " --> pdb=" O ALA e 1 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET e 16 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE e 19 " --> pdb=" O LEU e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 61 removed outlier: 4.275A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA e 52 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA e 58 " --> pdb=" O ALA e 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER e 60 " --> pdb=" O LEU e 56 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 110 removed outlier: 3.707A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE e 103 " --> pdb=" O PHE e 99 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE e 105 " --> pdb=" O ARG e 101 " (cutoff:3.500A) removed outlier: 4.957A 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: 3.869A pdb=" N LEU e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU e 169 " --> pdb=" O GLY e 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 7 removed outlier: 3.885A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 removed outlier: 3.525A pdb=" N ALA f 64 " --> pdb=" O GLY f 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY f 65 " --> pdb=" O TRP f 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA f 69 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR f 79 " --> pdb=" O VAL f 75 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU f 80 " --> pdb=" O ILE f 76 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 152 removed outlier: 4.462A pdb=" N ILE f 140 " --> pdb=" O ASP f 136 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN f 142 " --> pdb=" O GLN f 138 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP f 146 " --> pdb=" O GLN f 142 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU f 147 " --> pdb=" O VAL f 143 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 27 Processing helix chain 'g' and resid 28 through 33 Proline residue: g 32 - end of helix No H-bonds generated for 'chain 'g' and resid 28 through 33' Processing helix chain 'g' and resid 40 through 50 removed outlier: 3.660A pdb=" N GLU g 48 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 72 removed outlier: 5.520A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA g 59 " --> pdb=" O GLU g 55 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN g 66 " --> pdb=" O LEU g 62 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 5.059A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA g 100 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP g 101 " --> pdb=" O ARG g 97 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL g 103 " --> pdb=" O ILE g 99 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 16 removed outlier: 3.830A pdb=" N ARG a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 33 removed outlier: 4.009A pdb=" N LEU a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 removed outlier: 4.161A pdb=" N LEU a 185 " --> pdb=" O ASP a 181 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS a 186 " --> pdb=" O ALA a 182 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU a 190 " --> pdb=" O LYS a 186 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU a 196 " --> pdb=" O LEU a 192 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA a 199 " --> pdb=" O ALA a 195 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 31 removed outlier: 5.286A pdb=" N LEU i 27 " --> pdb=" O VAL i 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY i 31 " --> pdb=" O LEU i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 49 removed outlier: 4.372A pdb=" N LYS i 39 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN i 42 " --> pdb=" O CYS i 38 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA i 43 " --> pdb=" O LYS i 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU i 49 " --> pdb=" O THR i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 83 removed outlier: 4.572A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.884A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 136 removed outlier: 3.652A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR i 131 " --> pdb=" O SER i 127 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET i 135 " --> pdb=" O THR i 131 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY i 136 " --> pdb=" O ALA i 132 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.631A pdb=" N THR j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY j 38 " --> pdb=" O ARG j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 72 removed outlier: 3.936A pdb=" N ASP j 71 " --> pdb=" O ASN j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 removed outlier: 3.675A pdb=" N ARG j 95 " --> pdb=" O GLU j 91 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG j 96 " --> pdb=" O MET j 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.783A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU j 102 " --> pdb=" O GLU j 98 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 123 removed outlier: 3.746A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS j 123 " --> pdb=" O PHE j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 112 through 119 Processing helix chain 'l' and resid 37 through 42 removed outlier: 4.036A pdb=" N ARG l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER l 42 " --> pdb=" O GLN l 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 37 through 42' Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.026A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 85 removed outlier: 4.031A pdb=" N LEU l 82 " --> pdb=" O ARG l 78 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 78 through 85' Processing helix chain 'l' and resid 91 through 99 removed outlier: 4.504A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 removed outlier: 3.586A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE l 135 " --> pdb=" O ALA l 131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.758A pdb=" N ALA m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG m 51 " --> pdb=" O GLU m 47 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA m 52 " --> pdb=" O ALA m 48 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET m 53 " --> pdb=" O ALA m 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG m 55 " --> pdb=" O ARG m 51 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL m 57 " --> pdb=" O MET m 53 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 124 removed outlier: 3.771A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.760A pdb=" N GLN n 18 " --> pdb=" O SER n 14 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE n 21 " --> pdb=" O ARG n 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL n 29 " --> pdb=" O ALA n 25 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 58 removed outlier: 3.795A pdb=" N ARG n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 3.855A pdb=" N LYS n 56 " --> pdb=" O ILE n 52 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.827A pdb=" N LEU n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE n 67 " --> pdb=" O ARG n 63 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG n 71 " --> pdb=" O PHE n 67 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.366A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU n 82 " --> pdb=" O LYS n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 89 removed outlier: 4.487A pdb=" N PHE n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA n 88 " --> pdb=" O GLY n 84 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER n 89 " --> pdb=" O PRO n 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 83 through 89' Processing helix chain 'o' and resid 2 through 22 removed outlier: 4.032A pdb=" N ALA o 6 " --> pdb=" O ASP o 2 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU o 18 " --> pdb=" O ALA o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 4.849A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.570A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 113 removed outlier: 4.001A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG o 111 " --> pdb=" O ALA o 107 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU o 112 " --> pdb=" O ASP o 108 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 1 through 12 removed outlier: 4.392A pdb=" N LEU p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU p 10 " --> pdb=" O GLN p 6 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET p 12 " --> pdb=" O GLU p 8 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 103 removed outlier: 4.305A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) Processing helix chain 'q' and resid 5 through 21 removed outlier: 3.751A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG q 10 " --> pdb=" O GLY q 6 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG q 12 " --> pdb=" O ILE q 8 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS q 15 " --> pdb=" O ALA q 11 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE q 16 " --> pdb=" O ARG q 12 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.537A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 3.603A 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 35 through 60 removed outlier: 3.504A pdb=" N ILE q 39 " --> pdb=" O PHE q 35 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS q 40 " --> pdb=" O GLN q 36 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR q 44 " --> pdb=" O LYS q 40 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG q 47 " --> pdb=" O GLN q 43 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN q 58 " --> pdb=" O ARG q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 72 Processing helix chain 'q' and resid 74 through 86 removed outlier: 3.517A pdb=" N PHE q 78 " --> pdb=" O SER q 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU q 82 " --> pdb=" O PHE q 78 " (cutoff:3.500A) Processing helix chain 'q' and resid 90 through 101 removed outlier: 3.750A pdb=" N LEU q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA q 98 " --> pdb=" O LEU q 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE q 100 " --> pdb=" O ASP q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 117 removed outlier: 3.662A pdb=" N ALA q 112 " --> pdb=" O LEU q 108 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA q 114 " --> pdb=" O GLU q 110 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA q 115 " --> pdb=" O LYS q 111 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA q 117 " --> pdb=" O LYS q 113 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 25 removed outlier: 4.007A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 4.103A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 4.474A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL s 47 " --> pdb=" O ALA s 43 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA s 56 " --> pdb=" O GLU s 52 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA s 58 " --> pdb=" O ALA s 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN s 61 " --> pdb=" O ASN s 57 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 11 removed outlier: 3.895A pdb=" N ARG t 6 " --> pdb=" O ILE t 2 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU t 7 " --> pdb=" O ARG t 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 2 through 11' Processing helix chain 't' and resid 17 through 27 removed outlier: 4.256A pdb=" N SER t 21 " --> pdb=" O SER t 17 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 50 removed outlier: 3.791A pdb=" N LYS t 44 " --> pdb=" O LYS t 40 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA t 46 " --> pdb=" O GLU t 42 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.774A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.407A 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: 4.025A pdb=" N LEU v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA v 23 " --> pdb=" O ARG v 19 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 53 removed outlier: 3.558A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 removed outlier: 3.610A pdb=" N SER v 58 " --> pdb=" O ALA v 54 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 61 removed outlier: 3.579A pdb=" N LYS x 60 " --> pdb=" O ARG x 56 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.781A pdb=" N ARG x 71 " --> pdb=" O LEU x 67 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY x 74 " --> pdb=" O LEU x 70 " (cutoff:3.500A) Processing helix chain 'y' and resid 1 through 9 removed outlier: 4.785A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS y 9 " --> pdb=" O GLU y 5 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 35 removed outlier: 4.105A pdb=" N GLU y 17 " --> pdb=" O GLU y 13 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU y 18 " --> pdb=" O LEU y 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG y 23 " --> pdb=" O LEU y 19 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN y 25 " --> pdb=" O LEU y 21 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE y 26 " --> pdb=" O LEU y 22 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU y 28 " --> pdb=" O GLU y 24 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA y 32 " --> pdb=" O LEU y 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA y 33 " --> pdb=" O ARG y 29 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY y 35 " --> pdb=" O GLN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 63 removed outlier: 4.363A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS y 44 " --> pdb=" O SER y 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN y 45 " --> pdb=" O HIS y 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP y 49 " --> pdb=" O GLN y 45 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL y 50 " --> pdb=" O VAL y 46 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA y 51 " --> pdb=" O ARG y 47 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU y 56 " --> pdb=" O ARG y 52 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA y 63 " --> pdb=" O GLU y 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 removed outlier: 3.563A pdb=" N THR z 22 " --> pdb=" O LYS z 18 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 51 removed outlier: 3.729A pdb=" N ARG z 44 " --> pdb=" O THR z 40 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE z 47 " --> pdb=" O ILE z 43 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL z 50 " --> pdb=" O MET z 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.557A pdb=" N SER B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 removed outlier: 4.139A pdb=" N ARG D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 3.513A pdb=" N ARG D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 4.415A pdb=" N VAL D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D 33 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.605A pdb=" N ALA E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 6 through 14' Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.776A pdb=" N LYS E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 37 through 45 removed outlier: 4.290A pdb=" N ARG E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.977A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'G' and resid 42 through 63 removed outlier: 3.542A pdb=" N VAL G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 3.706A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.605A pdb=" N LYS G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 122 removed outlier: 3.525A pdb=" N VAL G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.595A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.931A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 4.816A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 47 removed outlier: 7.107A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN H 40 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 4.263A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 76 " --> pdb=" O PRO H 72 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 77' Processing helix chain 'H' and resid 80 through 95 removed outlier: 3.552A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA H 94 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.607A pdb=" N VAL H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU H 123 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 4.158A pdb=" N MET H 133 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL H 137 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.272A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.645A pdb=" N GLN I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS I 59 " --> pdb=" O ARG I 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG I 62 " --> pdb=" O GLN I 58 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.552A pdb=" N ARG I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR I 74 " --> pdb=" O GLN I 70 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR I 75 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU I 77 " --> pdb=" O ASN I 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.499A pdb=" N GLY I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 removed outlier: 3.696A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 105 " --> pdb=" O VAL I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 120 removed outlier: 4.056A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 165 removed outlier: 4.432A pdb=" N ALA I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.873A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU I 201 " --> pdb=" O HIS I 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU I 202 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.637A pdb=" N ILE J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 5.574A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 3.570A pdb=" N ARG J 137 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE J 140 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'K' and resid 11 through 19 removed outlier: 3.509A pdb=" N SER K 15 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLU K 16 " --> pdb=" O PRO K 12 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 18 " --> pdb=" O GLN K 14 " (cutoff:3.500A) Proline residue: K 19 - end of helix No H-bonds generated for 'chain 'K' and resid 11 through 19' Processing helix chain 'K' and resid 20 through 33 removed outlier: 4.199A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 3.614A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.867A pdb=" N ALA L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL L 31 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 54 removed outlier: 4.467A pdb=" N GLU L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA L 45 " --> pdb=" O ILE L 41 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN L 51 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 69 removed outlier: 4.938A pdb=" N ALA L 60 " --> pdb=" O SER L 56 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 110 removed outlier: 4.996A pdb=" N ASN L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU L 98 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET L 100 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL L 104 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA L 106 " --> pdb=" O TRP L 102 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG L 108 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 removed outlier: 3.626A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP L 125 " --> pdb=" O ASN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 146 removed outlier: 4.255A pdb=" N GLU L 138 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG L 142 " --> pdb=" O GLU L 138 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA L 144 " --> pdb=" O VAL L 140 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 4.095A pdb=" N MET M 9 " --> pdb=" O PRO M 5 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG M 12 " --> pdb=" O ASP M 8 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY M 16 " --> pdb=" O ARG M 12 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 43 removed outlier: 3.591A pdb=" N ALA M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU M 41 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 4.354A pdb=" N ARG M 116 " --> pdb=" O ASP M 112 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 3.543A pdb=" N TYR N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 53 removed outlier: 4.646A pdb=" N VAL N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.312A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 88 removed outlier: 3.612A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE N 82 " --> pdb=" O ILE N 78 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG N 84 " --> pdb=" O HIS N 80 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N MET N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU N 88 " --> pdb=" O ARG N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 101 removed outlier: 4.078A pdb=" N ARG N 94 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU N 97 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 29 removed outlier: 4.003A pdb=" N ILE O 18 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU O 24 " --> pdb=" O GLN O 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 89 removed outlier: 3.756A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.854A pdb=" N SER P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 5.692A 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 59 removed outlier: 4.085A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) Proline residue: P 59 - end of helix No H-bonds generated for 'chain 'P' and resid 53 through 59' Processing helix chain 'P' and resid 60 through 74 removed outlier: 3.512A pdb=" N ALA P 66 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG P 68 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 removed outlier: 4.815A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.615A 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: 4.419A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 22 removed outlier: 3.852A pdb=" N LEU R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.586A pdb=" N ALA R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.924A pdb=" N ILE R 52 " --> pdb=" O SER R 48 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP R 57 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 83 removed outlier: 3.782A pdb=" N ARG R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 removed outlier: 4.784A pdb=" N GLY R 110 " --> pdb=" O ALA R 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 105 through 110' Processing helix chain 'S' and resid 2 through 24 removed outlier: 4.015A pdb=" N VAL S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG S 12 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA S 21 " --> pdb=" O ASP S 17 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 32 removed outlier: 4.794A pdb=" N SER S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 27 through 32' Processing helix chain 'S' and resid 40 through 50 removed outlier: 3.721A pdb=" N VAL S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU S 45 " --> pdb=" O TRP S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.542A pdb=" N VAL S 83 " --> pdb=" O SER S 79 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 removed outlier: 4.271A pdb=" N THR T 7 " --> pdb=" O SER T 3 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA T 8 " --> pdb=" O THR T 4 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL T 11 " --> pdb=" O THR T 7 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 42 removed outlier: 4.154A pdb=" N VAL T 28 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU T 31 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 3.865A pdb=" N ARG T 52 " --> pdb=" O ASP T 48 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG T 53 " --> pdb=" O HIS T 49 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU T 56 " --> pdb=" O ARG T 52 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER T 60 " --> pdb=" O LEU T 56 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP T 67 " --> pdb=" O ARG T 63 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR T 68 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP T 73 " --> pdb=" O LEU T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 85 removed outlier: 4.064A pdb=" N GLN T 79 " --> pdb=" O ALA T 75 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU T 80 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE T 81 " --> pdb=" O TYR T 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY T 85 " --> pdb=" O ILE T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 64 removed outlier: 3.842A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS U 59 " --> pdb=" O ASP U 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL U 61 " --> pdb=" O ILE U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 79 removed outlier: 3.574A pdb=" N ASN U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 16 removed outlier: 3.570A pdb=" N GLU W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 32 removed outlier: 3.756A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS W 29 " --> pdb=" O ILE W 25 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 24 through 32' Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 65 removed outlier: 4.042A pdb=" N GLN W 53 " --> pdb=" O LYS W 49 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE W 58 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 25 removed outlier: 3.792A pdb=" N LYS X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA X 21 " --> pdb=" O LYS X 17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU X 23 " --> pdb=" O GLU X 19 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 41 removed outlier: 4.477A pdb=" N ALA Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 35 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 64 removed outlier: 3.787A pdb=" N GLU Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Proline residue: Y 55 - end of helix removed outlier: 3.961A pdb=" N ASP Y 58 " --> pdb=" O GLN Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 85 removed outlier: 6.513A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE Y 82 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN Y 83 " --> pdb=" O THR Y 79 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 4.105A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS Z 22 " --> pdb=" O PHE Z 18 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 33 removed outlier: 4.965A pdb=" N LEU Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA Z 29 " --> pdb=" O ALA Z 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.530A pdb=" N THR Z 42 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA Z 49 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA Z 51 " --> pdb=" O ALA Z 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Z 57 " --> pdb=" O LYS Z 53 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU Z 59 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '8' and resid 66 through 73 removed outlier: 6.404A pdb=" N ALA 8 66 " --> pdb=" O ASP 8 88 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ARG 8 9 " --> pdb=" O PRO 8 81 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE 8 15 " --> pdb=" O ILE 8 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL 8 112 " --> pdb=" O SER 8 16 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG 8 137 " --> pdb=" O ILE 8 261 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU 8 263 " --> pdb=" O ARG 8 137 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE 8 262 " --> pdb=" O ASN 8 165 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '8' and resid 170 through 173 removed outlier: 3.815A pdb=" N LEU 8 171 " --> pdb=" O VAL 8 183 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL 8 183 " --> pdb=" O LEU 8 171 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY 8 181 " --> pdb=" O ILE 8 173 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR 8 180 " --> pdb=" O TRP 8 193 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '8' and resid 317 through 321 removed outlier: 7.096A pdb=" N PHE 8 317 " --> pdb=" O ASP 8 399 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP 8 399 " --> pdb=" O PHE 8 317 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP 8 395 " --> pdb=" O ALA 8 321 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '8' and resid 323 through 327 removed outlier: 4.404A pdb=" N LYS 8 323 " --> pdb=" O PHE 8 335 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY 8 331 " --> pdb=" O ASP 8 327 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE 8 386 " --> pdb=" O ARG 8 362 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG 8 362 " --> pdb=" O ILE 8 386 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '8' and resid 348 through 352 removed outlier: 3.799A pdb=" N GLU 8 358 " --> pdb=" O VAL 8 349 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN 8 351 " --> pdb=" O ALA 8 356 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA 8 356 " --> pdb=" O ASN 8 351 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '8' and resid 445 through 449 removed outlier: 4.367A pdb=" N ARG 8 446 " --> pdb=" O ALA 8 459 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA 8 459 " --> pdb=" O ARG 8 446 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR 8 456 " --> pdb=" O VAL 8 420 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE 8 418 " --> pdb=" O ILE 8 458 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY 8 460 " --> pdb=" O ILE 8 416 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '8' and resid 520 through 523 removed outlier: 3.901A pdb=" N GLU 8 535 " --> pdb=" O MET 8 574 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE 8 537 " --> pdb=" O ILE 8 576 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU 8 578 " --> pdb=" O ILE 8 537 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '8' and resid 643 through 647 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'b' and resid 1 through 4 Processing sheet with id= 10, first strand: chain 'b' and resid 79 through 82 removed outlier: 4.052A pdb=" N LEU b 92 " --> pdb=" O ARG b 79 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'b' and resid 137 through 140 removed outlier: 4.274A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE b 163 " --> pdb=" O SER b 138 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'b' and resid 171 through 174 removed outlier: 3.590A pdb=" N ARG b 181 " --> pdb=" O LEU b 173 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'b' and resid 90 through 95 removed outlier: 4.031A pdb=" N TYR b 95 " --> pdb=" O GLU b 99 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'c' and resid 7 through 10 removed outlier: 6.754A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'c' and resid 32 through 35 removed outlier: 6.477A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP c 80 " --> pdb=" O VAL c 50 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'c' and resid 167 through 173 removed outlier: 4.883A pdb=" N GLU c 168 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE c 202 " --> pdb=" O THR c 110 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'd' and resid 2 through 6 removed outlier: 3.902A pdb=" N LEU d 3 " --> pdb=" O LEU d 12 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER d 10 " --> pdb=" O LEU d 5 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.678A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'e' and resid 71 through 74 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'e' and resid 85 through 91 removed outlier: 4.225A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR e 156 " --> pdb=" O LYS e 32 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR e 34 " --> pdb=" O THR e 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR e 154 " --> pdb=" O THR e 34 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'f' and resid 14 through 19 removed outlier: 3.829A pdb=" N THR f 24 " --> pdb=" O LYS f 17 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN f 21 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE f 23 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY f 30 " --> pdb=" O GLY f 27 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'f' and resid 39 through 44 removed outlier: 6.945A pdb=" N ALA f 39 " --> pdb=" O ARG f 54 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG f 54 " --> pdb=" O ALA f 39 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'f' and resid 94 through 98 removed outlier: 6.990A pdb=" N ASN f 100 " --> pdb=" O LEU f 116 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'f' and resid 120 through 124 removed outlier: 3.904A pdb=" N LYS f 133 " --> pdb=" O THR f 121 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL f 131 " --> pdb=" O GLU f 123 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE f 130 " --> pdb=" O LEU f 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU f 86 " --> pdb=" O ILE f 130 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'g' and resid 114 through 117 removed outlier: 5.298A pdb=" N GLU g 114 " --> pdb=" O GLN g 133 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER g 131 " --> pdb=" O ARG g 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL g 144 " --> pdb=" O HIS g 128 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'a' and resid 42 through 46 removed outlier: 3.851A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE a 214 " --> pdb=" O VAL a 222 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'j' and resid 74 through 77 removed outlier: 3.628A pdb=" N ALA j 87 " --> pdb=" O TYR j 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS j 76 " --> pdb=" O LYS j 85 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'k' and resid 6 through 9 removed outlier: 4.644A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS k 21 " --> pdb=" O THR k 6 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET k 20 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP k 56 " --> pdb=" O ILE k 43 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'k' and resid 63 through 66 removed outlier: 3.768A pdb=" N LYS k 66 " --> pdb=" O GLY k 81 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY k 81 " --> pdb=" O LYS k 66 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'k' and resid 68 through 71 removed outlier: 4.103A pdb=" N VAL k 69 " --> pdb=" O ILE k 77 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG k 71 " --> pdb=" O SER k 75 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'm' and resid 38 through 41 Processing sheet with id= 32, first strand: chain 'm' and resid 62 through 66 removed outlier: 6.106A pdb=" N LEU m 102 " --> pdb=" O ARG m 66 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL m 131 " --> pdb=" O GLY m 32 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS m 34 " --> pdb=" O THR m 129 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'n' and resid 33 through 37 removed outlier: 5.642A pdb=" N ALA n 108 " --> pdb=" O PHE n 102 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE n 102 " --> pdb=" O ALA n 108 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.503A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE o 35 " --> pdb=" O THR o 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG o 25 " --> pdb=" O ILE o 40 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'p' and resid 37 through 43 removed outlier: 6.496A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER p 82 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'p' and resid 48 through 52 removed outlier: 4.156A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS p 55 " --> pdb=" O ARG p 52 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'r' and resid 3 through 6 Processing sheet with id= 38, first strand: chain 'r' and resid 18 through 23 removed outlier: 4.794A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'r' and resid 71 through 78 removed outlier: 3.674A pdb=" N VAL r 72 " --> pdb=" O HIS r 89 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 's' and resid 2 through 8 removed outlier: 4.313A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL s 107 " --> pdb=" O THR s 3 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY s 79 " --> pdb=" O THR s 100 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 's' and resid 80 through 88 removed outlier: 3.895A pdb=" N ARG s 88 " --> pdb=" O ARG s 92 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 't' and resid 12 through 15 removed outlier: 3.659A pdb=" N ALA t 13 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN t 28 " --> pdb=" O LEU t 87 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA t 83 " --> pdb=" O LEU t 32 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'u' and resid 39 through 44 removed outlier: 5.866A pdb=" N ASN u 39 " --> pdb=" O ALA u 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL u 41 " --> pdb=" O LYS u 60 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS u 60 " --> pdb=" O VAL u 41 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS u 43 " --> pdb=" O VAL u 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL u 58 " --> pdb=" O LYS u 43 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'u' and resid 82 through 86 Processing sheet with id= 45, first strand: chain 'v' and resid 6 through 9 removed outlier: 3.518A pdb=" N ARG v 9 " --> pdb=" O ALA v 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA v 39 " --> pdb=" O ARG v 9 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE v 30 " --> pdb=" O LEU v 38 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'v' and resid 60 through 64 Processing sheet with id= 47, first strand: chain 'w' and resid 41 through 44 removed outlier: 6.377A pdb=" N ILE w 78 " --> pdb=" O GLY w 44 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS w 62 " --> pdb=" O GLU w 79 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'w' and resid 46 through 50 removed outlier: 6.871A pdb=" N ASN w 46 " --> pdb=" O LYS w 58 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'x' and resid 11 through 18 removed outlier: 3.574A pdb=" N VAL x 12 " --> pdb=" O PHE x 28 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG x 26 " --> pdb=" O GLY x 14 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'x' and resid 34 through 38 Processing sheet with id= 51, first strand: chain 'z' and resid 32 through 38 removed outlier: 4.134A pdb=" N HIS z 33 " --> pdb=" O GLN z 8 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE z 6 " --> pdb=" O VAL z 35 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG z 37 " --> pdb=" O ILE z 4 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE z 4 " --> pdb=" O ARG z 37 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'A' and resid 21 through 25 removed outlier: 4.139A pdb=" N MET A 22 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 32 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 28 through 31 removed outlier: 5.300A pdb=" N GLU B 35 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.884A pdb=" N LEU C 10 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 20 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.830A pdb=" N LEU C 35 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.680A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 24 through 27 removed outlier: 5.310A pdb=" N CYS F 27 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS F 33 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 29 through 33 removed outlier: 7.796A pdb=" N PHE G 29 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN G 41 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 89 through 92 removed outlier: 3.524A pdb=" N LEU G 160 " --> pdb=" O PRO G 181 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE G 183 " --> pdb=" O LEU G 160 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'H' and resid 53 through 58 removed outlier: 3.602A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 66 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 67 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 105 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'H' and resid 163 through 170 removed outlier: 3.580A pdb=" N GLU H 165 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 148 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 140 through 143 removed outlier: 3.848A pdb=" N ASP I 140 " --> pdb=" O PHE I 181 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 11 through 15 removed outlier: 7.023A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE J 29 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 83 through 87 removed outlier: 4.231A pdb=" N MET J 95 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL J 93 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG J 92 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA J 98 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASN J 121 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'J' and resid 31 through 39 removed outlier: 4.338A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'K' and resid 37 through 43 removed outlier: 3.607A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL K 10 " --> pdb=" O HIS K 58 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL K 64 " --> pdb=" O TYR K 4 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR K 92 " --> pdb=" O HIS K 3 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 72 through 75 removed outlier: 3.971A pdb=" N LYS L 75 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL L 86 " --> pdb=" O LYS L 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'M' and resid 23 through 27 removed outlier: 3.844A pdb=" N VAL M 24 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU M 60 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR M 61 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP M 47 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'M' and resid 122 through 125 removed outlier: 3.597A pdb=" N VAL M 102 " --> pdb=" O CYS M 126 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS M 126 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.510A pdb=" N ILE N 20 " --> pdb=" O TYR N 5 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA N 15 " --> pdb=" O LYS N 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'O' and resid 42 through 52 removed outlier: 4.975A pdb=" N LEU O 71 " --> pdb=" O PRO O 43 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR O 69 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL O 51 " --> pdb=" O ASP O 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA O 12 " --> pdb=" O HIS O 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU O 10 " --> pdb=" O ARG O 72 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE O 8 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE O 76 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG O 9 " --> pdb=" O GLN O 99 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'P' and resid 29 through 35 Processing sheet with id= 73, first strand: chain 'Q' and resid 28 through 32 removed outlier: 5.478A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL Q 97 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Q' and resid 36 through 40 removed outlier: 3.911A pdb=" N TYR Q 37 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 51 " --> pdb=" O TYR Q 37 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR Q 39 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL Q 62 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU Q 56 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.534A pdb=" N VAL U 20 " --> pdb=" O ARG U 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL U 19 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY U 49 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'V' and resid 6 through 9 removed outlier: 3.843A pdb=" N GLY V 9 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'V' and resid 18 through 29 No H-bonds generated for sheet with id= 77 Processing sheet with id= 78, first strand: chain 'X' and resid 29 through 33 removed outlier: 3.738A pdb=" N HIS X 51 " --> pdb=" O THR X 32 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) 1399 hydrogen bonds defined for protein. 4116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2942 hydrogen bonds 4822 hydrogen bond angles 0 basepair planarities 1203 basepair parallelities 2671 stacking parallelities Total time for adding SS restraints: 221.51 Time building geometry restraints manager: 63.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27311 1.33 - 1.46: 71818 1.46 - 1.59: 57046 1.59 - 1.71: 9453 1.71 - 1.84: 316 Bond restraints: 165944 Sorted by residual: bond pdb=" CB THR b 49 " pdb=" CG2 THR b 49 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.03e+01 bond pdb=" CA GLN I 151 " pdb=" CB GLN I 151 " ideal model delta sigma weight residual 1.536 1.635 -0.099 3.46e-02 8.35e+02 8.14e+00 bond pdb=" C ASP 8 88 " pdb=" N THR 8 89 " ideal model delta sigma weight residual 1.331 1.247 0.084 3.12e-02 1.03e+03 7.22e+00 bond pdb=" CA THR G 124 " pdb=" CB THR G 124 " ideal model delta sigma weight residual 1.525 1.558 -0.033 1.25e-02 6.40e+03 7.15e+00 bond pdb=" O5' U 31308 " pdb=" C5' U 31308 " ideal model delta sigma weight residual 1.420 1.460 -0.040 1.50e-02 4.44e+03 7.07e+00 ... (remaining 165939 not shown) Histogram of bond angle deviations from ideal: 96.16 - 104.20: 17183 104.20 - 112.24: 95518 112.24 - 120.28: 77513 120.28 - 128.32: 49629 128.32 - 136.35: 7676 Bond angle restraints: 247519 Sorted by residual: angle pdb=" C ASN 8 194 " pdb=" N ASP 8 195 " pdb=" CA ASP 8 195 " ideal model delta sigma weight residual 121.54 136.35 -14.81 1.91e+00 2.74e-01 6.02e+01 angle pdb=" C ILE K 51 " pdb=" N ASN K 52 " pdb=" CA ASN K 52 " ideal model delta sigma weight residual 121.54 134.93 -13.39 1.91e+00 2.74e-01 4.92e+01 angle pdb=" C HIS E 30 " pdb=" N ILE E 31 " pdb=" CA ILE E 31 " ideal model delta sigma weight residual 121.97 134.06 -12.09 1.80e+00 3.09e-01 4.51e+01 angle pdb=" N VAL 8 353 " pdb=" CA VAL 8 353 " pdb=" C VAL 8 353 " ideal model delta sigma weight residual 113.71 107.44 6.27 9.50e-01 1.11e+00 4.35e+01 angle pdb=" N ARG G 20 " pdb=" CA ARG G 20 " pdb=" C ARG G 20 " ideal model delta sigma weight residual 114.75 106.64 8.11 1.26e+00 6.30e-01 4.14e+01 ... (remaining 247514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 94659 35.90 - 71.79: 10288 71.79 - 107.69: 1213 107.69 - 143.59: 19 143.59 - 179.49: 22 Dihedral angle restraints: 106201 sinusoidal: 87405 harmonic: 18796 Sorted by residual: dihedral pdb=" CA THR c 133 " pdb=" C THR c 133 " pdb=" N HIS c 134 " pdb=" CA HIS c 134 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA GLY d 82 " pdb=" C GLY d 82 " pdb=" N VAL d 83 " pdb=" CA VAL d 83 " ideal model delta harmonic sigma weight residual -180.00 -131.74 -48.26 0 5.00e+00 4.00e-02 9.31e+01 dihedral pdb=" CA MET m 82 " pdb=" C MET m 82 " pdb=" N GLY m 83 " pdb=" CA GLY m 83 " ideal model delta harmonic sigma weight residual -180.00 -133.78 -46.22 0 5.00e+00 4.00e-02 8.54e+01 ... (remaining 106198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 28072 0.114 - 0.229: 3302 0.229 - 0.343: 146 0.343 - 0.457: 6 0.457 - 0.571: 4 Chirality restraints: 31530 Sorted by residual: chirality pdb=" P A 4 5 " pdb=" OP1 A 4 5 " pdb=" OP2 A 4 5 " pdb=" O5' A 4 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P C 5 1 " pdb=" OP1 C 5 1 " pdb=" OP2 C 5 1 " pdb=" O5' C 5 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE K 51 " pdb=" CA ILE K 51 " pdb=" CG1 ILE K 51 " pdb=" CG2 ILE K 51 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 31527 not shown) Planarity restraints: 13817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 11779 " 0.125 2.00e-02 2.50e+03 7.06e-02 1.12e+02 pdb=" N1 U 11779 " -0.002 2.00e-02 2.50e+03 pdb=" C2 U 11779 " -0.024 2.00e-02 2.50e+03 pdb=" O2 U 11779 " -0.047 2.00e-02 2.50e+03 pdb=" N3 U 11779 " -0.027 2.00e-02 2.50e+03 pdb=" C4 U 11779 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U 11779 " 0.129 2.00e-02 2.50e+03 pdb=" C5 U 11779 " -0.070 2.00e-02 2.50e+03 pdb=" C6 U 11779 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 4 9 " -0.144 2.00e-02 2.50e+03 6.02e-02 1.09e+02 pdb=" N9 G 4 9 " 0.010 2.00e-02 2.50e+03 pdb=" C8 G 4 9 " 0.052 2.00e-02 2.50e+03 pdb=" N7 G 4 9 " 0.046 2.00e-02 2.50e+03 pdb=" C5 G 4 9 " 0.033 2.00e-02 2.50e+03 pdb=" C6 G 4 9 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G 4 9 " -0.101 2.00e-02 2.50e+03 pdb=" N1 G 4 9 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 4 9 " 0.021 2.00e-02 2.50e+03 pdb=" N2 G 4 9 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 4 9 " 0.055 2.00e-02 2.50e+03 pdb=" C4 G 4 9 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 1 511 " -0.114 2.00e-02 2.50e+03 6.46e-02 9.38e+01 pdb=" N1 U 1 511 " 0.003 2.00e-02 2.50e+03 pdb=" C2 U 1 511 " 0.022 2.00e-02 2.50e+03 pdb=" O2 U 1 511 " 0.039 2.00e-02 2.50e+03 pdb=" N3 U 1 511 " 0.026 2.00e-02 2.50e+03 pdb=" C4 U 1 511 " 0.028 2.00e-02 2.50e+03 pdb=" O4 U 1 511 " -0.120 2.00e-02 2.50e+03 pdb=" C5 U 1 511 " 0.063 2.00e-02 2.50e+03 pdb=" C6 U 1 511 " 0.051 2.00e-02 2.50e+03 ... (remaining 13814 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 391 2.51 - 3.11: 98991 3.11 - 3.70: 276340 3.70 - 4.30: 408587 4.30 - 4.90: 568397 Nonbonded interactions: 1352706 Sorted by model distance: nonbonded pdb=" N1 A 4 21 " pdb=" O4 U 5 34 " model vdw 1.912 2.496 nonbonded pdb=" OE2 GLU 8 590 " pdb=" N2 G 4 23 " model vdw 2.034 2.520 nonbonded pdb=" O VAL 8 586 " pdb=" N6 A 4 22 " model vdw 2.108 2.520 nonbonded pdb=" CD ARG 8 512 " pdb=" OP2 A 4 22 " model vdw 2.159 3.440 nonbonded pdb=" O GLY J 86 " pdb=" N HIS J 88 " model vdw 2.215 2.520 ... (remaining 1352701 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 23.560 Check model and map are aligned: 1.880 Set scattering table: 1.110 Process input model: 522.530 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 559.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 : 0.007 0.106 165944 Z= 0.427 Angle : 0.905 14.814 247519 Z= 0.554 Chirality : 0.074 0.571 31530 Planarity : 0.010 0.096 13817 Dihedral : 22.652 179.485 94078 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.69 % Allowed : 11.59 % Favored : 87.72 % Rotamer: Outliers : 1.08 % Allowed : 9.40 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.52 % 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: -5.26 (0.08), residues: 6489 helix: -4.35 (0.06), residues: 1654 sheet: -3.04 (0.14), residues: 1028 loop : -3.33 (0.08), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP b 212 HIS 0.017 0.002 HIS P 117 PHE 0.046 0.003 PHE G 89 TYR 0.046 0.003 TYR N 37 ARG 0.016 0.001 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1603 time to evaluate : 6.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7213 (tttt) REVERT: 8 83 ARG cc_start: 0.5899 (ttm170) cc_final: 0.4796 (ttm110) REVERT: 8 147 MET cc_start: 0.5113 (ptt) cc_final: 0.4635 (ptp) REVERT: 8 211 MET cc_start: 0.5361 (ptm) cc_final: 0.4787 (mmm) REVERT: 8 603 GLU cc_start: 0.5262 (tp30) cc_final: 0.4805 (tp30) REVERT: 8 635 LEU cc_start: 0.8631 (mp) cc_final: 0.8298 (mp) REVERT: 8 682 MET cc_start: 0.6431 (ptt) cc_final: 0.5771 (ptm) REVERT: 8 700 GLU cc_start: 0.4825 (pt0) cc_final: 0.4523 (mt-10) REVERT: b 24 HIS cc_start: 0.5805 (t70) cc_final: 0.5550 (t-170) REVERT: b 199 HIS cc_start: 0.7985 (t-90) cc_final: 0.6526 (t-170) REVERT: b 260 LYS cc_start: 0.7930 (mttt) cc_final: 0.7678 (ttmm) REVERT: c 1 MET cc_start: 0.4236 (ppp) cc_final: 0.2965 (mmm) REVERT: d 134 LEU cc_start: 0.8348 (mp) cc_final: 0.7919 (tt) REVERT: d 159 LEU cc_start: 0.8538 (mt) cc_final: 0.8283 (mt) REVERT: e 4 HIS cc_start: 0.7910 (t-170) cc_final: 0.7476 (t-170) REVERT: e 25 MET cc_start: 0.7268 (mmt) cc_final: 0.7047 (mmm) REVERT: e 33 ILE cc_start: 0.7657 (tt) cc_final: 0.7398 (tt) REVERT: f 142 GLN cc_start: 0.8336 (mm110) cc_final: 0.8003 (mm-40) REVERT: g 1 MET cc_start: 0.3972 (pmm) cc_final: 0.3729 (pmm) REVERT: a 8 MET cc_start: 0.4926 (mtm) cc_final: 0.3604 (pmm) REVERT: l 4 ASN cc_start: 0.7931 (p0) cc_final: 0.7548 (p0) REVERT: n 99 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8466 (mtmt) REVERT: o 15 ARG cc_start: 0.6811 (mmt90) cc_final: 0.6541 (mtp180) REVERT: o 65 THR cc_start: 0.8662 (t) cc_final: 0.8445 (t) REVERT: o 104 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8055 (tm-30) REVERT: q 65 ASN cc_start: 0.8727 (t0) cc_final: 0.8361 (t0) REVERT: r 21 ARG cc_start: 0.7359 (ttm110) cc_final: 0.7147 (mtp85) REVERT: u 81 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7811 (mtm110) REVERT: v 63 ILE cc_start: 0.5760 (mt) cc_final: 0.5483 (mm) REVERT: w 25 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7303 (mt-10) REVERT: x 31 ASN cc_start: 0.7983 (t0) cc_final: 0.7399 (t0) REVERT: y 6 LEU cc_start: 0.7600 (tp) cc_final: 0.7242 (tt) REVERT: y 7 ARG cc_start: 0.6461 (ppt170) cc_final: 0.5385 (ttm110) REVERT: y 8 GLU cc_start: 0.6281 (mt-10) cc_final: 0.5973 (mt-10) REVERT: y 30 MET cc_start: 0.6826 (tmm) cc_final: 0.6581 (mmt) REVERT: y 39 GLN cc_start: 0.7928 (mp10) cc_final: 0.7606 (mt0) REVERT: A 22 MET cc_start: 0.5985 (ptt) cc_final: 0.5737 (ptt) REVERT: B 47 TYR cc_start: 0.8020 (m-80) cc_final: 0.7093 (m-10) REVERT: B 48 TYR cc_start: 0.8184 (t80) cc_final: 0.7894 (t80) REVERT: C 38 PHE cc_start: 0.7242 (t80) cc_final: 0.7011 (t80) REVERT: D 2 LYS cc_start: 0.8129 (tttm) cc_final: 0.7793 (tmtt) REVERT: E 14 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8065 (mmtp) REVERT: E 44 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.6776 (ttp80) REVERT: G 44 LYS cc_start: 0.5870 (tttt) cc_final: 0.5235 (mmmt) REVERT: G 99 MET cc_start: 0.4903 (mmm) cc_final: 0.4624 (mmm) REVERT: G 107 ARG cc_start: 0.7278 (tmm-80) cc_final: 0.6959 (ttm-80) REVERT: G 142 LYS cc_start: 0.6833 (tttt) cc_final: 0.6119 (tptm) REVERT: G 212 TYR cc_start: 0.6731 (m-80) cc_final: 0.6366 (m-80) REVERT: H 131 ARG cc_start: 0.7758 (ttt90) cc_final: 0.7547 (tpm170) REVERT: H 200 TRP cc_start: 0.5368 (m-10) cc_final: 0.5147 (m-10) REVERT: I 61 ARG cc_start: 0.6235 (mtm110) cc_final: 0.5894 (ttm110) REVERT: I 70 GLN cc_start: 0.8165 (mt0) cc_final: 0.7619 (tm-30) REVERT: I 71 PHE cc_start: 0.8228 (t80) cc_final: 0.7869 (t80) REVERT: I 82 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7327 (mttt) REVERT: I 169 TRP cc_start: 0.6493 (p90) cc_final: 0.6261 (p90) REVERT: I 205 LYS cc_start: 0.7384 (ptmt) cc_final: 0.6496 (tptp) REVERT: J 25 LYS cc_start: 0.6443 (ttpt) cc_final: 0.5886 (tttp) REVERT: J 96 GLN cc_start: 0.8273 (mt0) cc_final: 0.8045 (mt0) REVERT: K 1 MET cc_start: 0.5107 (mtm) cc_final: 0.4830 (ttp) REVERT: K 35 LYS cc_start: 0.7038 (mttm) cc_final: 0.6796 (mttt) REVERT: L 100 MET cc_start: 0.5182 (mtm) cc_final: 0.3335 (mmt) REVERT: L 108 ARG cc_start: 0.4707 (mpp80) cc_final: 0.4362 (mtt90) REVERT: L 112 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6966 (p0) REVERT: M 113 ARG cc_start: 0.7259 (tpm170) cc_final: 0.6973 (ptm-80) REVERT: N 84 ARG cc_start: 0.4714 (mpt180) cc_final: 0.2850 (tpt-90) REVERT: N 87 MET cc_start: 0.6187 (tpt) cc_final: 0.5592 (mmm) REVERT: P 86 LYS cc_start: 0.7346 (ttpt) cc_final: 0.6860 (tttp) REVERT: Q 82 ARG cc_start: 0.7383 (ptt90) cc_final: 0.7125 (ptt180) REVERT: Q 119 LYS cc_start: 0.6325 (tptp) cc_final: 0.5512 (mttp) REVERT: R 69 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7773 (mtt180) REVERT: S 12 ARG cc_start: 0.7019 (ttm170) cc_final: 0.6448 (ttp-170) REVERT: S 39 ASP cc_start: 0.7332 (m-30) cc_final: 0.7119 (p0) REVERT: T 63 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7450 (mmm160) REVERT: T 66 LEU cc_start: 0.7948 (mt) cc_final: 0.7707 (mm) REVERT: U 51 ARG cc_start: 0.7337 (ttp-170) cc_final: 0.6976 (ttp-170) REVERT: V 80 LYS cc_start: 0.6401 (mmtm) cc_final: 0.5309 (tmtt) REVERT: W 22 TYR cc_start: 0.5665 (p90) cc_final: 0.5430 (p90) REVERT: W 52 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7276 (mtm-85) REVERT: X 35 ARG cc_start: 0.6637 (ptm160) cc_final: 0.6420 (ptm-80) REVERT: X 79 TYR cc_start: 0.5748 (t80) cc_final: 0.5453 (t80) REVERT: Y 50 PHE cc_start: 0.7616 (t80) cc_final: 0.7163 (t80) outliers start: 58 outliers final: 21 residues processed: 1649 average time/residue: 1.3991 time to fit residues: 3872.5153 Evaluate side-chains 1302 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1280 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain a residue 42 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain X residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 933 optimal weight: 30.0000 chunk 838 optimal weight: 0.4980 chunk 465 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 565 optimal weight: 5.9990 chunk 447 optimal weight: 9.9990 chunk 866 optimal weight: 3.9990 chunk 335 optimal weight: 5.9990 chunk 527 optimal weight: 20.0000 chunk 645 optimal weight: 6.9990 chunk 1004 optimal weight: 20.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 92 HIS 8 129 GLN 8 192 ASN ** 8 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 496 GLN 8 505 HIS ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 HIS ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 250 GLN c 58 ASN c 94 GLN ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 GLN d 97 ASN e 26 GLN e 51 ASN f 19 ASN ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 GLN g 2 GLN g 119 ASN a 47 ASN a 172 HIS a 188 ASN ** i 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 GLN j 132 HIS j 135 GLN ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 3 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 61 GLN p 2 ASN p 6 GLN p 9 GLN q 43 GLN q 51 GLN r 11 GLN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 82 HIS s 7 HIS ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 HIS t 72 GLN u 39 ASN u 65 GLN ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN w 8 ASN y 20 ASN y 25 GLN y 36 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS F 33 HIS G 38 HIS ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN I 39 GLN I 40 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 GLN I 197 HIS ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN M 3 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN T 36 ASN T 45 HIS V 8 GLN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN X 51 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 165944 Z= 0.289 Angle : 0.753 13.553 247519 Z= 0.386 Chirality : 0.042 0.314 31530 Planarity : 0.006 0.091 13817 Dihedral : 23.294 179.197 81208 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.65 % Favored : 88.10 % Rotamer: Outliers : 3.97 % Allowed : 18.18 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.66 (0.08), residues: 6489 helix: -3.33 (0.09), residues: 1812 sheet: -2.80 (0.14), residues: 1055 loop : -3.12 (0.09), residues: 3622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 8 127 HIS 0.019 0.002 HIS m 13 PHE 0.045 0.002 PHE Z 36 TYR 0.020 0.002 TYR e 7 ARG 0.006 0.001 ARG N 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1340 time to evaluate : 6.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 83 ARG cc_start: 0.5795 (ttm170) cc_final: 0.4644 (ttm110) REVERT: 8 603 GLU cc_start: 0.5116 (tp30) cc_final: 0.4408 (tp30) REVERT: 8 630 ASP cc_start: 0.6434 (m-30) cc_final: 0.6180 (m-30) REVERT: 8 635 LEU cc_start: 0.8753 (mp) cc_final: 0.8501 (mp) REVERT: c 1 MET cc_start: 0.4489 (ppp) cc_final: 0.3051 (tmm) REVERT: d 117 ARG cc_start: 0.6885 (mtp180) cc_final: 0.6572 (mtp180) REVERT: d 134 LEU cc_start: 0.8380 (mp) cc_final: 0.8169 (mp) REVERT: d 195 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7908 (mm-40) REVERT: e 129 MET cc_start: 0.5374 (mtp) cc_final: 0.5140 (mtp) REVERT: f 57 TYR cc_start: 0.6524 (m-80) cc_final: 0.6227 (m-80) REVERT: f 142 GLN cc_start: 0.8244 (mm110) cc_final: 0.7812 (mm110) REVERT: a 8 MET cc_start: 0.5181 (mtm) cc_final: 0.3859 (pmm) REVERT: j 25 LEU cc_start: 0.8640 (tp) cc_final: 0.8388 (tp) REVERT: j 96 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6435 (ttp80) REVERT: j 129 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: l 4 ASN cc_start: 0.7874 (p0) cc_final: 0.7660 (p0) REVERT: o 29 HIS cc_start: 0.7917 (t-170) cc_final: 0.7538 (t-170) REVERT: o 104 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7856 (tm-30) REVERT: u 81 ARG cc_start: 0.8323 (mtm110) cc_final: 0.7557 (mtm110) REVERT: v 43 ASP cc_start: 0.7228 (t0) cc_final: 0.6890 (t0) REVERT: w 25 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7328 (mt-10) REVERT: w 75 PHE cc_start: 0.8227 (m-80) cc_final: 0.7832 (m-80) REVERT: x 31 ASN cc_start: 0.7989 (t0) cc_final: 0.7449 (t0) REVERT: x 73 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6939 (ttp-110) REVERT: y 7 ARG cc_start: 0.6412 (ppt170) cc_final: 0.5401 (ttm110) REVERT: y 8 GLU cc_start: 0.6300 (mt-10) cc_final: 0.5330 (mt-10) REVERT: y 12 GLU cc_start: 0.7094 (tt0) cc_final: 0.6262 (tm-30) REVERT: y 20 ASN cc_start: 0.7925 (m-40) cc_final: 0.7560 (m110) REVERT: y 26 PHE cc_start: 0.8356 (t80) cc_final: 0.8090 (t80) REVERT: y 30 MET cc_start: 0.6966 (tmm) cc_final: 0.6623 (mmt) REVERT: B 47 TYR cc_start: 0.7975 (m-80) cc_final: 0.7241 (m-10) REVERT: D 22 MET cc_start: 0.7473 (tpp) cc_final: 0.7220 (tpt) REVERT: E 14 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8025 (mmtp) REVERT: E 44 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6888 (ttp80) REVERT: F 15 LYS cc_start: 0.7231 (ttmt) cc_final: 0.6989 (mppt) REVERT: F 24 ARG cc_start: 0.6934 (mtp85) cc_final: 0.6644 (mtt90) REVERT: G 44 LYS cc_start: 0.5430 (tttt) cc_final: 0.5191 (mmmt) REVERT: G 99 MET cc_start: 0.5124 (mmm) cc_final: 0.4739 (mmm) REVERT: G 142 LYS cc_start: 0.6795 (tttt) cc_final: 0.6213 (tptm) REVERT: G 212 TYR cc_start: 0.6357 (m-80) cc_final: 0.6044 (m-80) REVERT: H 131 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7629 (tpm170) REVERT: H 141 MET cc_start: 0.5582 (mmt) cc_final: 0.5198 (mmt) REVERT: H 187 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7175 (mm-30) REVERT: I 34 GLU cc_start: 0.6317 (pm20) cc_final: 0.6114 (pm20) REVERT: I 70 GLN cc_start: 0.8038 (mt0) cc_final: 0.7606 (tm-30) REVERT: I 71 PHE cc_start: 0.8194 (t80) cc_final: 0.7865 (t80) REVERT: I 82 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7087 (mttt) REVERT: I 199 ILE cc_start: 0.5814 (mm) cc_final: 0.5603 (mt) REVERT: I 205 LYS cc_start: 0.7355 (ptmt) cc_final: 0.6549 (tptp) REVERT: J 25 LYS cc_start: 0.6473 (ttpt) cc_final: 0.5890 (tttp) REVERT: J 72 ASN cc_start: 0.8067 (m-40) cc_final: 0.7577 (p0) REVERT: J 85 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5695 (mmtt) REVERT: J 110 MET cc_start: 0.7026 (mpp) cc_final: 0.6794 (mpp) REVERT: K 35 LYS cc_start: 0.7051 (mttm) cc_final: 0.6816 (mttt) REVERT: K 90 MET cc_start: 0.6196 (ttt) cc_final: 0.5611 (ttp) REVERT: L 100 MET cc_start: 0.4981 (mtm) cc_final: 0.2907 (mmt) REVERT: L 140 VAL cc_start: 0.5182 (m) cc_final: 0.4921 (t) REVERT: M 60 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5560 (pp) REVERT: M 113 ARG cc_start: 0.7342 (tpm170) cc_final: 0.6834 (ptm-80) REVERT: N 84 ARG cc_start: 0.4303 (mpt180) cc_final: 0.2463 (tpt-90) REVERT: N 97 LEU cc_start: 0.3641 (OUTLIER) cc_final: 0.2935 (mt) REVERT: P 86 LYS cc_start: 0.7000 (ttpt) cc_final: 0.6511 (tttt) REVERT: Q 94 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: Q 119 LYS cc_start: 0.6266 (tptp) cc_final: 0.5352 (mttp) REVERT: R 69 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7662 (mtt180) REVERT: R 86 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7674 (mtm-85) REVERT: S 12 ARG cc_start: 0.6952 (ttm170) cc_final: 0.6505 (ttp-170) REVERT: S 39 ASP cc_start: 0.7281 (m-30) cc_final: 0.7047 (p0) REVERT: T 63 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7422 (mmm160) REVERT: T 69 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6763 (mp) REVERT: U 1 MET cc_start: 0.3007 (ttp) cc_final: 0.2549 (tpt) REVERT: U 59 HIS cc_start: 0.3394 (OUTLIER) cc_final: 0.2564 (t70) REVERT: V 30 HIS cc_start: 0.7522 (t70) cc_final: 0.7280 (t70) REVERT: W 22 TYR cc_start: 0.5413 (p90) cc_final: 0.4868 (p90) REVERT: W 52 ARG cc_start: 0.7467 (mtp85) cc_final: 0.7181 (mtm-85) REVERT: X 35 ARG cc_start: 0.6763 (ptm160) cc_final: 0.6461 (ptm160) REVERT: Y 4 LYS cc_start: 0.6850 (ptmm) cc_final: 0.6325 (pttm) REVERT: Y 28 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7551 (mtt90) REVERT: Z 9 GLU cc_start: 0.6732 (mp0) cc_final: 0.6357 (mm-30) outliers start: 214 outliers final: 140 residues processed: 1449 average time/residue: 1.4146 time to fit residues: 3503.9744 Evaluate side-chains 1379 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1231 time to evaluate : 6.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 155 VAL Chi-restraints excluded: chain 8 residue 182 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 245 GLU Chi-restraints excluded: chain 8 residue 256 VAL Chi-restraints excluded: chain 8 residue 391 VAL Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 212 TRP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 87 GLN Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 129 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 41 VAL Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 65 PHE Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain z residue 46 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 94 TYR Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 42 PHE Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 558 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 835 optimal weight: 0.1980 chunk 683 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 1006 optimal weight: 4.9990 chunk 1086 optimal weight: 7.9990 chunk 896 optimal weight: 7.9990 chunk 997 optimal weight: 20.0000 chunk 343 optimal weight: 10.0000 chunk 807 optimal weight: 7.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 120 GLN 8 178 HIS ** 8 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 152 GLN ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 ASN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 5 GLN y 27 ASN y 31 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN G 41 ASN G 57 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 40 HIS I 70 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN J 69 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 5 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 HIS T 45 HIS U 9 HIS V 44 HIS ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 165944 Z= 0.344 Angle : 0.791 15.323 247519 Z= 0.400 Chirality : 0.044 0.369 31530 Planarity : 0.006 0.099 13817 Dihedral : 23.593 179.023 81199 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.41 % Favored : 86.35 % Rotamer: Outliers : 5.90 % Allowed : 21.09 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.19 (0.09), residues: 6489 helix: -2.65 (0.10), residues: 1825 sheet: -2.56 (0.14), residues: 1074 loop : -2.98 (0.09), residues: 3590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 8 127 HIS 0.017 0.002 HIS m 13 PHE 0.040 0.002 PHE Z 36 TYR 0.019 0.002 TYR H 167 ARG 0.020 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7062 (tttt) REVERT: 8 83 ARG cc_start: 0.5910 (ttm170) cc_final: 0.4780 (ttm110) REVERT: 8 101 ARG cc_start: 0.5775 (OUTLIER) cc_final: 0.5275 (mtm180) REVERT: 8 211 MET cc_start: 0.5304 (ptm) cc_final: 0.4920 (mmm) REVERT: 8 393 THR cc_start: 0.6747 (m) cc_final: 0.6441 (m) REVERT: 8 409 MET cc_start: 0.2113 (tmm) cc_final: 0.1812 (ppp) REVERT: 8 603 GLU cc_start: 0.5305 (tp30) cc_final: 0.4518 (tp30) REVERT: 8 617 MET cc_start: 0.7973 (mpp) cc_final: 0.7376 (mpp) REVERT: 8 635 LEU cc_start: 0.8735 (mp) cc_final: 0.8531 (mp) REVERT: b 153 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7882 (mp) REVERT: c 1 MET cc_start: 0.4455 (ppp) cc_final: 0.2985 (mmm) REVERT: d 166 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6080 (mmtt) REVERT: e 82 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5811 (m-10) REVERT: e 129 MET cc_start: 0.5552 (mtp) cc_final: 0.5323 (mtp) REVERT: e 153 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6578 (pt) REVERT: f 142 GLN cc_start: 0.8287 (mm110) cc_final: 0.7888 (mm110) REVERT: a 8 MET cc_start: 0.5125 (mtm) cc_final: 0.3742 (pmm) REVERT: j 25 LEU cc_start: 0.8667 (tp) cc_final: 0.8397 (tp) REVERT: j 96 ARG cc_start: 0.6944 (mtp85) cc_final: 0.6679 (mtp85) REVERT: j 129 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: k 3 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: k 4 GLU cc_start: 0.6908 (tt0) cc_final: 0.6519 (tt0) REVERT: m 31 PHE cc_start: 0.7096 (m-10) cc_final: 0.6779 (m-10) REVERT: o 15 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6765 (mmt90) REVERT: o 29 HIS cc_start: 0.7938 (t-170) cc_final: 0.7512 (t-170) REVERT: o 88 LYS cc_start: 0.7163 (tptp) cc_final: 0.6934 (tptt) REVERT: o 104 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8214 (tp40) REVERT: r 35 PHE cc_start: 0.7454 (m-80) cc_final: 0.6763 (m-80) REVERT: s 78 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: t 24 MET cc_start: 0.7311 (tmm) cc_final: 0.6971 (tmm) REVERT: u 28 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6556 (tt) REVERT: u 81 ARG cc_start: 0.8321 (mtm110) cc_final: 0.7624 (mtm110) REVERT: v 43 ASP cc_start: 0.7335 (t0) cc_final: 0.7118 (t0) REVERT: v 79 ARG cc_start: 0.6844 (mpt180) cc_final: 0.6602 (mpt180) REVERT: w 25 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7378 (mt-10) REVERT: x 31 ASN cc_start: 0.8030 (t0) cc_final: 0.7520 (t0) REVERT: y 7 ARG cc_start: 0.6221 (ppt170) cc_final: 0.5312 (ttm110) REVERT: y 8 GLU cc_start: 0.6692 (mt-10) cc_final: 0.5922 (mt-10) REVERT: y 12 GLU cc_start: 0.7071 (tt0) cc_final: 0.6287 (tm-30) REVERT: y 20 ASN cc_start: 0.7963 (m-40) cc_final: 0.7605 (m110) REVERT: y 26 PHE cc_start: 0.8485 (t80) cc_final: 0.8236 (t80) REVERT: y 30 MET cc_start: 0.6861 (tmm) cc_final: 0.6619 (mmt) REVERT: y 39 GLN cc_start: 0.7371 (mt0) cc_final: 0.7165 (mt0) REVERT: A 1 MET cc_start: 0.5273 (tmm) cc_final: 0.4713 (tmm) REVERT: B 47 TYR cc_start: 0.8040 (m-80) cc_final: 0.7731 (m-10) REVERT: C 38 PHE cc_start: 0.7252 (t80) cc_final: 0.6965 (t80) REVERT: E 44 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.6986 (ttp80) REVERT: F 24 ARG cc_start: 0.6907 (mtp85) cc_final: 0.6599 (mtt90) REVERT: G 92 ASN cc_start: 0.4950 (p0) cc_final: 0.4699 (p0) REVERT: G 131 LYS cc_start: 0.8713 (tttt) cc_final: 0.8361 (tttt) REVERT: G 142 LYS cc_start: 0.6839 (tttt) cc_final: 0.6166 (tptm) REVERT: G 147 LEU cc_start: 0.6957 (tp) cc_final: 0.6701 (tt) REVERT: G 212 TYR cc_start: 0.6364 (m-80) cc_final: 0.5957 (m-80) REVERT: H 131 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7623 (tpm170) REVERT: I 34 GLU cc_start: 0.6242 (pm20) cc_final: 0.5721 (pm20) REVERT: I 61 ARG cc_start: 0.6230 (mtp85) cc_final: 0.5928 (ttm110) REVERT: I 70 GLN cc_start: 0.7920 (mt0) cc_final: 0.7628 (tm-30) REVERT: I 71 PHE cc_start: 0.8204 (t80) cc_final: 0.7765 (t80) REVERT: I 74 TYR cc_start: 0.8321 (m-80) cc_final: 0.7715 (m-80) REVERT: I 82 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7264 (mttt) REVERT: I 169 TRP cc_start: 0.6339 (p90) cc_final: 0.6097 (p90) REVERT: I 205 LYS cc_start: 0.7364 (ptmt) cc_final: 0.6614 (tptp) REVERT: J 25 LYS cc_start: 0.6462 (ttpt) cc_final: 0.5876 (tttp) REVERT: J 72 ASN cc_start: 0.7932 (m-40) cc_final: 0.7445 (p0) REVERT: J 94 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5543 (p90) REVERT: J 96 GLN cc_start: 0.8341 (tt0) cc_final: 0.8092 (tp40) REVERT: J 127 TYR cc_start: 0.7680 (m-80) cc_final: 0.7191 (m-80) REVERT: L 100 MET cc_start: 0.4611 (mtm) cc_final: 0.2987 (mmp) REVERT: L 140 VAL cc_start: 0.5059 (m) cc_final: 0.4748 (t) REVERT: M 48 PHE cc_start: 0.6990 (p90) cc_final: 0.6590 (p90) REVERT: M 60 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5437 (pp) REVERT: M 113 ARG cc_start: 0.7445 (tpm170) cc_final: 0.6705 (ptm-80) REVERT: N 84 ARG cc_start: 0.4341 (mpt180) cc_final: 0.2467 (tpt-90) REVERT: N 87 MET cc_start: 0.6162 (tpt) cc_final: 0.5263 (tpt) REVERT: N 97 LEU cc_start: 0.3443 (OUTLIER) cc_final: 0.2672 (mt) REVERT: P 60 PHE cc_start: 0.6469 (m-80) cc_final: 0.6244 (m-80) REVERT: P 86 LYS cc_start: 0.7056 (ttpt) cc_final: 0.6586 (tttt) REVERT: S 39 ASP cc_start: 0.7438 (m-30) cc_final: 0.7041 (p0) REVERT: S 59 GLN cc_start: 0.3630 (OUTLIER) cc_final: 0.3430 (mp10) REVERT: T 13 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7458 (tm-30) REVERT: U 1 MET cc_start: 0.2984 (ttp) cc_final: 0.2521 (tpt) REVERT: U 31 ARG cc_start: 0.6648 (ttt90) cc_final: 0.6431 (tpt170) REVERT: U 59 HIS cc_start: 0.3716 (OUTLIER) cc_final: 0.2849 (t70) REVERT: U 63 GLN cc_start: 0.4201 (OUTLIER) cc_final: 0.3670 (mt0) REVERT: V 30 HIS cc_start: 0.7470 (t70) cc_final: 0.7220 (t70) REVERT: V 61 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7316 (mtp85) REVERT: W 42 ARG cc_start: 0.6879 (ttt-90) cc_final: 0.6661 (ttt-90) REVERT: W 52 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7168 (mtm-85) REVERT: X 35 ARG cc_start: 0.6830 (ptm160) cc_final: 0.6435 (ptm160) REVERT: Y 28 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7596 (mtt90) REVERT: Z 9 GLU cc_start: 0.6848 (mp0) cc_final: 0.6521 (mm-30) outliers start: 318 outliers final: 224 residues processed: 1452 average time/residue: 1.3857 time to fit residues: 3455.9540 Evaluate side-chains 1436 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1197 time to evaluate : 6.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 155 VAL Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 256 VAL Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 523 TYR Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 634 ASP Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain f residue 70 LEU Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 129 GLU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 126 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain o residue 15 ARG Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 67 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 50 VAL Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 46 MET Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain T residue 10 ILE Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 994 optimal weight: 0.8980 chunk 756 optimal weight: 9.9990 chunk 522 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 480 optimal weight: 3.9990 chunk 675 optimal weight: 0.3980 chunk 1009 optimal weight: 20.0000 chunk 1069 optimal weight: 9.9990 chunk 527 optimal weight: 20.0000 chunk 957 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 120 GLN ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 71 ASN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 5 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN W 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 165944 Z= 0.272 Angle : 0.709 14.580 247519 Z= 0.362 Chirality : 0.040 0.451 31530 Planarity : 0.005 0.082 13817 Dihedral : 23.599 178.192 81198 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.28 % Favored : 87.50 % Rotamer: Outliers : 5.86 % Allowed : 23.68 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.84 (0.09), residues: 6489 helix: -2.16 (0.11), residues: 1821 sheet: -2.38 (0.15), residues: 1100 loop : -2.88 (0.09), residues: 3568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 8 193 HIS 0.026 0.001 HIS m 13 PHE 0.037 0.002 PHE Z 36 TYR 0.019 0.002 TYR f 163 ARG 0.008 0.001 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1566 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1250 time to evaluate : 6.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7066 (ttmt) REVERT: 8 83 ARG cc_start: 0.5884 (ttm170) cc_final: 0.4797 (ttm110) REVERT: 8 101 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.4935 (mtm180) REVERT: 8 124 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5452 (mt-10) REVERT: 8 211 MET cc_start: 0.5247 (ptm) cc_final: 0.4818 (mmp) REVERT: 8 461 MET cc_start: 0.2843 (mtm) cc_final: 0.2237 (mtt) REVERT: 8 603 GLU cc_start: 0.5332 (tp30) cc_final: 0.4569 (tp30) REVERT: 8 617 MET cc_start: 0.8002 (mpp) cc_final: 0.7373 (mpp) REVERT: b 86 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7059 (mtt90) REVERT: b 199 HIS cc_start: 0.8375 (t-90) cc_final: 0.7981 (t-170) REVERT: c 1 MET cc_start: 0.4233 (ppp) cc_final: 0.2939 (mmm) REVERT: c 74 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6721 (pp20) REVERT: e 82 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5739 (m-10) REVERT: e 129 MET cc_start: 0.5516 (mtp) cc_final: 0.5179 (mmm) REVERT: e 153 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6554 (pt) REVERT: f 142 GLN cc_start: 0.8257 (mm110) cc_final: 0.7856 (mm110) REVERT: f 163 TYR cc_start: 0.6591 (m-80) cc_final: 0.6314 (m-80) REVERT: a 8 MET cc_start: 0.5282 (mtm) cc_final: 0.3791 (pmm) REVERT: a 184 LYS cc_start: 0.4865 (OUTLIER) cc_final: 0.4559 (ptpp) REVERT: a 214 ILE cc_start: 0.1998 (OUTLIER) cc_final: 0.1638 (tt) REVERT: j 7 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7222 (mtmm) REVERT: j 25 LEU cc_start: 0.8635 (tp) cc_final: 0.8383 (tp) REVERT: j 131 ASN cc_start: 0.7145 (p0) cc_final: 0.6860 (p0) REVERT: k 3 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: l 4 ASN cc_start: 0.7874 (p0) cc_final: 0.7562 (p0) REVERT: m 31 PHE cc_start: 0.7141 (m-80) cc_final: 0.6910 (m-10) REVERT: m 73 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6840 (mm) REVERT: o 29 HIS cc_start: 0.7837 (t-170) cc_final: 0.7394 (t-170) REVERT: r 35 PHE cc_start: 0.7438 (m-80) cc_final: 0.6801 (m-80) REVERT: u 28 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6573 (tt) REVERT: u 81 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7662 (mtm110) REVERT: w 75 PHE cc_start: 0.8091 (m-80) cc_final: 0.7882 (m-80) REVERT: x 31 ASN cc_start: 0.7912 (t0) cc_final: 0.7424 (t0) REVERT: y 7 ARG cc_start: 0.6114 (ppt170) cc_final: 0.5286 (ttm110) REVERT: y 8 GLU cc_start: 0.6638 (mt-10) cc_final: 0.5922 (mt-10) REVERT: y 12 GLU cc_start: 0.7138 (tt0) cc_final: 0.6423 (tm-30) REVERT: y 20 ASN cc_start: 0.7928 (m-40) cc_final: 0.7577 (m110) REVERT: y 26 PHE cc_start: 0.8287 (t80) cc_final: 0.8038 (t80) REVERT: y 30 MET cc_start: 0.6783 (tmm) cc_final: 0.6534 (mmt) REVERT: C 8 ILE cc_start: 0.7593 (tp) cc_final: 0.7294 (pt) REVERT: C 38 PHE cc_start: 0.7191 (t80) cc_final: 0.6962 (t80) REVERT: C 39 ASP cc_start: 0.6913 (t0) cc_final: 0.6681 (t0) REVERT: E 44 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.6985 (ttp80) REVERT: F 24 ARG cc_start: 0.6884 (mtp85) cc_final: 0.6559 (mtt90) REVERT: G 51 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5895 (tm-30) REVERT: G 92 ASN cc_start: 0.5047 (p0) cc_final: 0.4817 (p0) REVERT: G 131 LYS cc_start: 0.8699 (tttt) cc_final: 0.8367 (tttt) REVERT: G 142 LYS cc_start: 0.6671 (tttt) cc_final: 0.6061 (tptp) REVERT: G 212 TYR cc_start: 0.6389 (m-80) cc_final: 0.5896 (m-80) REVERT: G 224 ARG cc_start: 0.6668 (mmm160) cc_final: 0.6448 (tpp-160) REVERT: H 131 ARG cc_start: 0.7989 (ttt90) cc_final: 0.7524 (tpp-160) REVERT: I 34 GLU cc_start: 0.6318 (pm20) cc_final: 0.5769 (pm20) REVERT: I 61 ARG cc_start: 0.6129 (mtp85) cc_final: 0.5626 (ttm110) REVERT: I 70 GLN cc_start: 0.7818 (mt0) cc_final: 0.7485 (tm-30) REVERT: I 71 PHE cc_start: 0.8190 (t80) cc_final: 0.7671 (t80) REVERT: I 82 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7246 (mttt) REVERT: I 205 LYS cc_start: 0.7276 (ptmt) cc_final: 0.6402 (tptp) REVERT: J 25 LYS cc_start: 0.6397 (ttpt) cc_final: 0.5776 (tttp) REVERT: J 63 MET cc_start: 0.6971 (mmm) cc_final: 0.6736 (mmm) REVERT: J 94 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5657 (p90) REVERT: J 96 GLN cc_start: 0.8331 (tt0) cc_final: 0.8056 (tp40) REVERT: J 127 TYR cc_start: 0.7644 (m-80) cc_final: 0.7235 (m-80) REVERT: L 100 MET cc_start: 0.4422 (mtm) cc_final: 0.2825 (mmp) REVERT: M 48 PHE cc_start: 0.7213 (p90) cc_final: 0.6963 (p90) REVERT: M 60 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5580 (pp) REVERT: M 113 ARG cc_start: 0.7482 (tpm170) cc_final: 0.6670 (ptm-80) REVERT: N 84 ARG cc_start: 0.4262 (mpt180) cc_final: 0.2561 (tpt-90) REVERT: N 97 LEU cc_start: 0.3435 (OUTLIER) cc_final: 0.2681 (mt) REVERT: O 6 ILE cc_start: 0.3598 (OUTLIER) cc_final: 0.2808 (mm) REVERT: O 88 MET cc_start: 0.5071 (OUTLIER) cc_final: 0.4316 (ppp) REVERT: P 22 ILE cc_start: 0.7475 (mm) cc_final: 0.7197 (mp) REVERT: P 86 LYS cc_start: 0.6987 (ttpt) cc_final: 0.6518 (tttt) REVERT: Q 95 HIS cc_start: 0.6466 (m90) cc_final: 0.5259 (t-90) REVERT: R 86 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7472 (mtm-85) REVERT: S 39 ASP cc_start: 0.7533 (m-30) cc_final: 0.7161 (p0) REVERT: S 59 GLN cc_start: 0.3397 (OUTLIER) cc_final: 0.3172 (mp10) REVERT: U 59 HIS cc_start: 0.3733 (OUTLIER) cc_final: 0.2941 (t70) REVERT: V 30 HIS cc_start: 0.7526 (t70) cc_final: 0.7220 (t70) REVERT: W 52 ARG cc_start: 0.7488 (mtp85) cc_final: 0.7195 (mtm-85) REVERT: X 35 ARG cc_start: 0.6732 (ptm160) cc_final: 0.6334 (ptm160) REVERT: Y 75 LYS cc_start: 0.7824 (tppt) cc_final: 0.7337 (mtmm) REVERT: Z 9 GLU cc_start: 0.6843 (mp0) cc_final: 0.6519 (mm-30) REVERT: Z 38 GLU cc_start: 0.6974 (tp30) cc_final: 0.6680 (tp30) outliers start: 316 outliers final: 221 residues processed: 1430 average time/residue: 1.4394 time to fit residues: 3487.5379 Evaluate side-chains 1434 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1195 time to evaluate : 7.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 124 GLU Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 658 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 184 LYS Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 890 optimal weight: 10.0000 chunk 606 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 795 optimal weight: 4.9990 chunk 441 optimal weight: 10.0000 chunk 912 optimal weight: 0.9980 chunk 738 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 545 optimal weight: 5.9990 chunk 959 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 120 GLN ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 GLN ** i 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 71 ASN s 61 ASN t 72 GLN ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 5 GLN Q 72 ASN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 165944 Z= 0.248 Angle : 0.686 15.361 247519 Z= 0.350 Chirality : 0.039 0.449 31530 Planarity : 0.005 0.077 13817 Dihedral : 23.605 179.274 81198 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.45 % Favored : 87.33 % Rotamer: Outliers : 6.47 % Allowed : 24.94 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.58 (0.09), residues: 6489 helix: -1.85 (0.11), residues: 1818 sheet: -2.33 (0.15), residues: 1055 loop : -2.74 (0.09), residues: 3616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 8 193 HIS 0.018 0.001 HIS m 13 PHE 0.036 0.002 PHE Z 36 TYR 0.022 0.002 TYR f 163 ARG 0.007 0.001 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 1236 time to evaluate : 6.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7071 (ttmt) REVERT: 8 83 ARG cc_start: 0.5951 (ttm170) cc_final: 0.4864 (ttm110) REVERT: 8 101 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.4854 (mtm180) REVERT: 8 211 MET cc_start: 0.5265 (ptm) cc_final: 0.4919 (mmp) REVERT: 8 431 MET cc_start: 0.4896 (tpp) cc_final: 0.4560 (tpp) REVERT: 8 603 GLU cc_start: 0.5377 (tp30) cc_final: 0.4628 (tp30) REVERT: b 153 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7882 (mp) REVERT: b 199 HIS cc_start: 0.8394 (t-90) cc_final: 0.8029 (t-170) REVERT: c 1 MET cc_start: 0.4162 (ppp) cc_final: 0.2889 (mmm) REVERT: c 74 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6751 (pp20) REVERT: d 96 VAL cc_start: 0.8135 (t) cc_final: 0.7933 (p) REVERT: e 82 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5735 (m-10) REVERT: e 95 MET cc_start: 0.7627 (tmm) cc_final: 0.6721 (tmm) REVERT: e 129 MET cc_start: 0.5569 (mtp) cc_final: 0.5229 (mmm) REVERT: e 153 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.6568 (pt) REVERT: f 142 GLN cc_start: 0.8252 (mm110) cc_final: 0.7840 (mm110) REVERT: f 163 TYR cc_start: 0.6623 (m-80) cc_final: 0.6409 (m-80) REVERT: a 8 MET cc_start: 0.5333 (mtm) cc_final: 0.3820 (pmm) REVERT: a 184 LYS cc_start: 0.4868 (OUTLIER) cc_final: 0.4559 (ptpp) REVERT: a 214 ILE cc_start: 0.2003 (OUTLIER) cc_final: 0.1643 (tt) REVERT: j 7 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7176 (mtmm) REVERT: j 25 LEU cc_start: 0.8631 (tp) cc_final: 0.8377 (tp) REVERT: j 61 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7483 (mmtp) REVERT: j 131 ASN cc_start: 0.7254 (p0) cc_final: 0.6997 (p0) REVERT: l 4 ASN cc_start: 0.7938 (p0) cc_final: 0.7737 (p0) REVERT: m 1 MET cc_start: 0.6208 (mtm) cc_final: 0.5883 (mtt) REVERT: m 31 PHE cc_start: 0.7241 (m-80) cc_final: 0.6986 (m-10) REVERT: m 73 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6864 (mm) REVERT: o 29 HIS cc_start: 0.7830 (t-170) cc_final: 0.7421 (t-170) REVERT: q 31 TYR cc_start: 0.8056 (t80) cc_final: 0.7651 (t80) REVERT: r 35 PHE cc_start: 0.7483 (m-80) cc_final: 0.6872 (m-80) REVERT: u 28 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6578 (tt) REVERT: u 81 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7653 (mtm110) REVERT: w 75 PHE cc_start: 0.8108 (m-80) cc_final: 0.7885 (m-80) REVERT: x 31 ASN cc_start: 0.7893 (t0) cc_final: 0.7407 (t0) REVERT: y 6 LEU cc_start: 0.7531 (tp) cc_final: 0.7323 (tt) REVERT: y 7 ARG cc_start: 0.6158 (ppt170) cc_final: 0.5465 (ttm110) REVERT: y 8 GLU cc_start: 0.6641 (mt-10) cc_final: 0.5370 (mt-10) REVERT: y 12 GLU cc_start: 0.7120 (tt0) cc_final: 0.6076 (tm-30) REVERT: y 20 ASN cc_start: 0.7919 (m-40) cc_final: 0.7585 (m110) REVERT: z 8 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: A 1 MET cc_start: 0.6032 (tmm) cc_final: 0.4876 (tmm) REVERT: C 38 PHE cc_start: 0.7198 (t80) cc_final: 0.6988 (t80) REVERT: C 39 ASP cc_start: 0.6875 (t0) cc_final: 0.6567 (t0) REVERT: E 2 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6858 (ptpp) REVERT: E 44 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.6976 (ttp80) REVERT: F 24 ARG cc_start: 0.6879 (mtp85) cc_final: 0.6468 (mtt90) REVERT: G 51 GLU cc_start: 0.6289 (tm-30) cc_final: 0.6030 (tm-30) REVERT: G 131 LYS cc_start: 0.8706 (tttt) cc_final: 0.8383 (tttt) REVERT: G 142 LYS cc_start: 0.6649 (tttt) cc_final: 0.6008 (tptp) REVERT: G 212 TYR cc_start: 0.6398 (m-80) cc_final: 0.5878 (m-80) REVERT: H 131 ARG cc_start: 0.7895 (ttt90) cc_final: 0.7521 (tpm170) REVERT: I 61 ARG cc_start: 0.6061 (mtp85) cc_final: 0.5695 (ttm110) REVERT: I 70 GLN cc_start: 0.7771 (mt0) cc_final: 0.7443 (tm-30) REVERT: I 71 PHE cc_start: 0.8180 (t80) cc_final: 0.7632 (t80) REVERT: I 82 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7334 (mttt) REVERT: I 205 LYS cc_start: 0.7259 (ptmt) cc_final: 0.6394 (tptp) REVERT: J 25 LYS cc_start: 0.6413 (ttpt) cc_final: 0.5833 (tttp) REVERT: J 94 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.5569 (p90) REVERT: J 111 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7520 (ttm-80) REVERT: J 127 TYR cc_start: 0.7610 (m-80) cc_final: 0.7202 (m-80) REVERT: L 100 MET cc_start: 0.4392 (mtm) cc_final: 0.2838 (mmp) REVERT: M 48 PHE cc_start: 0.7485 (p90) cc_final: 0.7180 (p90) REVERT: M 60 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5582 (pp) REVERT: M 113 ARG cc_start: 0.7447 (tpm170) cc_final: 0.6704 (ptm-80) REVERT: N 84 ARG cc_start: 0.4207 (mpt180) cc_final: 0.2573 (tpt-90) REVERT: N 97 LEU cc_start: 0.3334 (OUTLIER) cc_final: 0.2586 (mt) REVERT: O 6 ILE cc_start: 0.3756 (OUTLIER) cc_final: 0.2999 (mm) REVERT: O 88 MET cc_start: 0.5095 (ppp) cc_final: 0.4353 (ppp) REVERT: P 22 ILE cc_start: 0.7531 (mm) cc_final: 0.7275 (mp) REVERT: P 86 LYS cc_start: 0.6991 (ttpt) cc_final: 0.6551 (tttt) REVERT: Q 95 HIS cc_start: 0.6507 (m90) cc_final: 0.5324 (t-90) REVERT: R 91 ARG cc_start: 0.5908 (ttp80) cc_final: 0.5139 (ttp80) REVERT: S 39 ASP cc_start: 0.7518 (m-30) cc_final: 0.7138 (p0) REVERT: S 59 GLN cc_start: 0.3420 (OUTLIER) cc_final: 0.3190 (mp10) REVERT: T 87 ARG cc_start: 0.6147 (ttp80) cc_final: 0.5920 (tpt-90) REVERT: U 59 HIS cc_start: 0.3936 (OUTLIER) cc_final: 0.3156 (t70) REVERT: U 63 GLN cc_start: 0.4077 (OUTLIER) cc_final: 0.3602 (mt0) REVERT: V 30 HIS cc_start: 0.7516 (t70) cc_final: 0.7197 (t70) REVERT: W 52 ARG cc_start: 0.7521 (mtp85) cc_final: 0.7233 (mtm-85) REVERT: X 35 ARG cc_start: 0.6725 (ptm160) cc_final: 0.6411 (ptm-80) REVERT: Y 2 ASN cc_start: 0.6757 (m110) cc_final: 0.6288 (m-40) REVERT: Y 75 LYS cc_start: 0.7670 (tppt) cc_final: 0.7168 (mtmt) REVERT: Z 9 GLU cc_start: 0.6867 (mp0) cc_final: 0.6465 (mm-30) REVERT: Z 55 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5018 (m-70) outliers start: 349 outliers final: 248 residues processed: 1450 average time/residue: 1.3691 time to fit residues: 3408.4245 Evaluate side-chains 1452 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1185 time to evaluate : 6.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 249 LYS Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 658 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 144 GLU Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 124 CYS Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 184 LYS Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 138 GLN Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 67 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 46 ASN Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain z residue 8 GLN Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 359 optimal weight: 10.0000 chunk 962 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 627 optimal weight: 0.0980 chunk 263 optimal weight: 20.0000 chunk 1070 optimal weight: 0.7980 chunk 888 optimal weight: 0.7980 chunk 495 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 353 optimal weight: 7.9990 chunk 561 optimal weight: 5.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 92 HIS ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN c 148 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN q 71 ASN ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 165944 Z= 0.208 Angle : 0.646 15.345 247519 Z= 0.331 Chirality : 0.037 0.563 31530 Planarity : 0.005 0.076 13817 Dihedral : 23.578 179.772 81198 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.53 % Favored : 88.27 % Rotamer: Outliers : 6.16 % Allowed : 26.24 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.38 (0.10), residues: 6489 helix: -1.56 (0.11), residues: 1820 sheet: -2.26 (0.15), residues: 1105 loop : -2.67 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP 8 193 HIS 0.022 0.001 HIS m 13 PHE 0.039 0.002 PHE 8 322 TYR 0.016 0.002 TYR g 25 ARG 0.009 0.000 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1241 time to evaluate : 8.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7138 (pttp) REVERT: 8 101 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.4740 (mtm180) REVERT: 8 120 GLN cc_start: 0.5425 (OUTLIER) cc_final: 0.4975 (tm-30) REVERT: 8 211 MET cc_start: 0.5293 (ptm) cc_final: 0.5053 (mmm) REVERT: 8 258 ASN cc_start: 0.6716 (m-40) cc_final: 0.6467 (p0) REVERT: 8 351 ASN cc_start: 0.5892 (t0) cc_final: 0.5471 (t0) REVERT: 8 603 GLU cc_start: 0.5357 (tp30) cc_final: 0.4660 (tp30) REVERT: 8 617 MET cc_start: 0.7920 (mpp) cc_final: 0.6862 (mpp) REVERT: 8 657 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.4861 (mp0) REVERT: 8 660 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.4774 (tt) REVERT: b 85 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7332 (p0) REVERT: b 86 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6858 (mtt90) REVERT: b 153 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7895 (mp) REVERT: b 199 HIS cc_start: 0.8368 (t-90) cc_final: 0.8052 (t-170) REVERT: c 1 MET cc_start: 0.4109 (ppp) cc_final: 0.2886 (mmm) REVERT: c 74 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6791 (pp20) REVERT: d 88 ARG cc_start: 0.7396 (ptt180) cc_final: 0.7081 (ptt180) REVERT: e 82 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.5752 (m-10) REVERT: e 95 MET cc_start: 0.7544 (tmm) cc_final: 0.6725 (tmm) REVERT: e 153 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.6535 (pt) REVERT: f 142 GLN cc_start: 0.8259 (mm110) cc_final: 0.7841 (mm110) REVERT: f 163 TYR cc_start: 0.6615 (m-80) cc_final: 0.6414 (m-80) REVERT: a 8 MET cc_start: 0.5345 (mtm) cc_final: 0.3847 (pmm) REVERT: a 184 LYS cc_start: 0.4625 (OUTLIER) cc_final: 0.4393 (ptpp) REVERT: a 214 ILE cc_start: 0.2017 (OUTLIER) cc_final: 0.1679 (tt) REVERT: j 7 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7133 (mtmm) REVERT: j 25 LEU cc_start: 0.8628 (tp) cc_final: 0.8398 (tp) REVERT: l 4 ASN cc_start: 0.7901 (p0) cc_final: 0.7652 (p0) REVERT: m 1 MET cc_start: 0.6273 (mtm) cc_final: 0.5964 (mtt) REVERT: m 31 PHE cc_start: 0.7187 (m-80) cc_final: 0.6932 (m-10) REVERT: m 73 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6763 (mm) REVERT: o 29 HIS cc_start: 0.7784 (t-170) cc_final: 0.7348 (t-170) REVERT: o 104 GLN cc_start: 0.8568 (tp40) cc_final: 0.8341 (tp40) REVERT: p 5 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8145 (mtpt) REVERT: q 31 TYR cc_start: 0.8024 (t80) cc_final: 0.7666 (t80) REVERT: q 46 TYR cc_start: 0.8307 (t80) cc_final: 0.7944 (t80) REVERT: r 35 PHE cc_start: 0.7490 (m-80) cc_final: 0.6912 (m-80) REVERT: r 82 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7949 (t70) REVERT: s 78 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: t 77 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7909 (ttm110) REVERT: u 28 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6548 (tt) REVERT: u 81 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7633 (mtm110) REVERT: v 48 MET cc_start: 0.7780 (tpt) cc_final: 0.7541 (tpt) REVERT: x 31 ASN cc_start: 0.7884 (t0) cc_final: 0.7390 (t0) REVERT: y 7 ARG cc_start: 0.6176 (ppt170) cc_final: 0.5472 (ttm110) REVERT: y 8 GLU cc_start: 0.6641 (mt-10) cc_final: 0.5384 (mt-10) REVERT: y 12 GLU cc_start: 0.7047 (tt0) cc_final: 0.5991 (tm-30) REVERT: y 20 ASN cc_start: 0.7953 (m-40) cc_final: 0.7634 (m110) REVERT: y 26 PHE cc_start: 0.8539 (t80) cc_final: 0.8187 (t80) REVERT: z 8 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6705 (tm-30) REVERT: z 30 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6480 (mtm110) REVERT: A 1 MET cc_start: 0.6081 (tmm) cc_final: 0.4788 (tmm) REVERT: C 8 ILE cc_start: 0.7575 (tp) cc_final: 0.7285 (pt) REVERT: C 20 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5649 (m-10) REVERT: C 38 PHE cc_start: 0.7184 (t80) cc_final: 0.5765 (t80) REVERT: C 39 ASP cc_start: 0.6888 (t0) cc_final: 0.6599 (t0) REVERT: E 2 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6791 (ptpp) REVERT: E 44 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7068 (ttp80) REVERT: F 24 ARG cc_start: 0.6875 (mtp85) cc_final: 0.6554 (mtt90) REVERT: G 131 LYS cc_start: 0.8673 (tttt) cc_final: 0.8356 (tttt) REVERT: G 142 LYS cc_start: 0.6722 (tttt) cc_final: 0.6094 (tptp) REVERT: G 212 TYR cc_start: 0.6339 (m-80) cc_final: 0.5954 (m-80) REVERT: H 131 ARG cc_start: 0.7913 (ttt90) cc_final: 0.7537 (tpm170) REVERT: I 61 ARG cc_start: 0.5999 (mtp85) cc_final: 0.5576 (ttm110) REVERT: I 70 GLN cc_start: 0.7694 (mt0) cc_final: 0.7395 (tm-30) REVERT: I 71 PHE cc_start: 0.8149 (t80) cc_final: 0.7666 (t80) REVERT: I 82 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7174 (mttt) REVERT: I 205 LYS cc_start: 0.7219 (ptmt) cc_final: 0.6345 (tptp) REVERT: J 25 LYS cc_start: 0.6377 (ttpt) cc_final: 0.5787 (tttp) REVERT: J 63 MET cc_start: 0.6883 (mmm) cc_final: 0.6619 (mmm) REVERT: J 111 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7489 (ttm-80) REVERT: L 100 MET cc_start: 0.4392 (mtm) cc_final: 0.2774 (mmp) REVERT: M 29 SER cc_start: 0.7841 (p) cc_final: 0.7639 (t) REVERT: M 60 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5540 (pp) REVERT: M 113 ARG cc_start: 0.7433 (tpm170) cc_final: 0.6677 (ptm-80) REVERT: N 84 ARG cc_start: 0.4175 (mpt180) cc_final: 0.2602 (tpt-90) REVERT: N 97 LEU cc_start: 0.3370 (OUTLIER) cc_final: 0.2600 (mt) REVERT: O 6 ILE cc_start: 0.3816 (OUTLIER) cc_final: 0.3115 (mm) REVERT: O 88 MET cc_start: 0.5113 (ppp) cc_final: 0.4374 (ppp) REVERT: P 22 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7257 (mp) REVERT: P 75 GLU cc_start: 0.7281 (pm20) cc_final: 0.6887 (pm20) REVERT: P 86 LYS cc_start: 0.6967 (ttpt) cc_final: 0.6524 (tttt) REVERT: Q 95 HIS cc_start: 0.6395 (m90) cc_final: 0.6116 (m-70) REVERT: R 88 LEU cc_start: 0.6270 (mm) cc_final: 0.5993 (mm) REVERT: S 39 ASP cc_start: 0.7493 (m-30) cc_final: 0.7138 (p0) REVERT: S 59 GLN cc_start: 0.3360 (OUTLIER) cc_final: 0.3159 (mp10) REVERT: U 59 HIS cc_start: 0.3947 (OUTLIER) cc_final: 0.3184 (t70) REVERT: U 63 GLN cc_start: 0.4003 (OUTLIER) cc_final: 0.3545 (mt0) REVERT: V 30 HIS cc_start: 0.7512 (t70) cc_final: 0.7169 (t70) REVERT: W 42 ARG cc_start: 0.6823 (ttt-90) cc_final: 0.6490 (ttt-90) REVERT: W 52 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7250 (mtm-85) REVERT: X 35 ARG cc_start: 0.6627 (ptm160) cc_final: 0.6311 (ptm-80) REVERT: Y 2 ASN cc_start: 0.6736 (m110) cc_final: 0.6277 (m-40) REVERT: Y 75 LYS cc_start: 0.7626 (tppt) cc_final: 0.7196 (mttt) REVERT: Z 9 GLU cc_start: 0.6911 (mp0) cc_final: 0.6493 (mm-30) REVERT: Z 55 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5051 (m-70) outliers start: 332 outliers final: 234 residues processed: 1445 average time/residue: 1.4158 time to fit residues: 3524.8320 Evaluate side-chains 1443 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1181 time to evaluate : 6.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 120 GLN Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 249 LYS Chi-restraints excluded: chain 8 residue 391 VAL Chi-restraints excluded: chain 8 residue 418 ILE Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 526 GLU Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain 8 residue 658 VAL Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 144 GLU Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 184 LYS Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 8 GLN Chi-restraints excluded: chain z residue 30 ARG Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 1031 optimal weight: 2.9990 chunk 120 optimal weight: 30.0000 chunk 609 optimal weight: 8.9990 chunk 781 optimal weight: 5.9990 chunk 605 optimal weight: 20.0000 chunk 900 optimal weight: 7.9990 chunk 597 optimal weight: 0.3980 chunk 1066 optimal weight: 8.9990 chunk 667 optimal weight: 0.9990 chunk 649 optimal weight: 9.9990 chunk 492 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 92 HIS 8 129 GLN ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 31 GLN z 8 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS J 96 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 165944 Z= 0.233 Angle : 0.666 16.878 247519 Z= 0.338 Chirality : 0.038 0.510 31530 Planarity : 0.005 0.073 13817 Dihedral : 23.588 179.958 81197 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.10 % Favored : 87.73 % Rotamer: Outliers : 6.51 % Allowed : 26.80 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.28 (0.10), residues: 6489 helix: -1.43 (0.12), residues: 1827 sheet: -2.19 (0.15), residues: 1085 loop : -2.64 (0.10), residues: 3577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 8 193 HIS 0.026 0.001 HIS m 13 PHE 0.038 0.002 PHE j 119 TYR 0.020 0.002 TYR g 25 ARG 0.007 0.000 ARG l 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1206 time to evaluate : 7.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7126 (pttp) REVERT: 8 101 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.4718 (mtm180) REVERT: 8 120 GLN cc_start: 0.5251 (OUTLIER) cc_final: 0.4790 (tm-30) REVERT: 8 211 MET cc_start: 0.5297 (ptm) cc_final: 0.4964 (mmp) REVERT: 8 258 ASN cc_start: 0.6670 (m-40) cc_final: 0.6418 (p0) REVERT: 8 322 PHE cc_start: 0.5929 (p90) cc_final: 0.5644 (p90) REVERT: 8 351 ASN cc_start: 0.5849 (t0) cc_final: 0.5270 (t0) REVERT: 8 451 GLU cc_start: 0.5663 (mt-10) cc_final: 0.4588 (pm20) REVERT: 8 521 ASP cc_start: 0.7168 (m-30) cc_final: 0.6917 (m-30) REVERT: 8 603 GLU cc_start: 0.5467 (tp30) cc_final: 0.4763 (tp30) REVERT: 8 660 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5047 (mt) REVERT: 8 682 MET cc_start: 0.6157 (ptt) cc_final: 0.5771 (ptp) REVERT: b 85 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7286 (p0) REVERT: b 86 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6860 (mtt90) REVERT: b 153 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7855 (mp) REVERT: b 199 HIS cc_start: 0.8363 (t-90) cc_final: 0.8062 (t-170) REVERT: c 1 MET cc_start: 0.4014 (ppp) cc_final: 0.2836 (mmm) REVERT: c 74 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6811 (pp20) REVERT: d 88 ARG cc_start: 0.7439 (ptt180) cc_final: 0.7127 (ptt180) REVERT: e 82 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5770 (m-10) REVERT: e 95 MET cc_start: 0.7619 (tmm) cc_final: 0.6675 (tmm) REVERT: e 129 MET cc_start: 0.5549 (mtp) cc_final: 0.5243 (mtp) REVERT: e 151 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7218 (pt) REVERT: e 153 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6670 (pt) REVERT: f 142 GLN cc_start: 0.8260 (mm110) cc_final: 0.7860 (mm110) REVERT: a 8 MET cc_start: 0.5316 (mtm) cc_final: 0.3849 (pmm) REVERT: a 184 LYS cc_start: 0.4747 (OUTLIER) cc_final: 0.4443 (ptpp) REVERT: a 214 ILE cc_start: 0.2037 (OUTLIER) cc_final: 0.1724 (tt) REVERT: j 7 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7107 (mtmm) REVERT: j 25 LEU cc_start: 0.8676 (tp) cc_final: 0.8433 (tp) REVERT: k 92 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: l 4 ASN cc_start: 0.7927 (p0) cc_final: 0.7715 (p0) REVERT: l 106 GLU cc_start: 0.7449 (mp0) cc_final: 0.7171 (mp0) REVERT: m 31 PHE cc_start: 0.7188 (m-80) cc_final: 0.6964 (m-10) REVERT: m 73 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.6840 (mm) REVERT: o 29 HIS cc_start: 0.7803 (t-170) cc_final: 0.7384 (t-170) REVERT: o 104 GLN cc_start: 0.8598 (tp40) cc_final: 0.8322 (tp40) REVERT: p 5 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7983 (ptpt) REVERT: q 31 TYR cc_start: 0.8050 (t80) cc_final: 0.7691 (t80) REVERT: r 35 PHE cc_start: 0.7499 (m-80) cc_final: 0.6933 (m-80) REVERT: r 82 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7926 (t70) REVERT: s 78 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: s 97 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6992 (mm) REVERT: u 28 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6526 (tt) REVERT: u 81 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7636 (mtm110) REVERT: v 48 MET cc_start: 0.7754 (tpt) cc_final: 0.7542 (tpt) REVERT: x 31 ASN cc_start: 0.7889 (t0) cc_final: 0.7403 (t0) REVERT: y 7 ARG cc_start: 0.6187 (ppt170) cc_final: 0.5483 (ttm110) REVERT: y 8 GLU cc_start: 0.6644 (mt-10) cc_final: 0.5411 (mt-10) REVERT: y 12 GLU cc_start: 0.7029 (tt0) cc_final: 0.6007 (tm-30) REVERT: y 20 ASN cc_start: 0.7916 (m-40) cc_final: 0.7582 (m110) REVERT: z 30 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6792 (mtm110) REVERT: C 8 ILE cc_start: 0.7686 (tp) cc_final: 0.7302 (pt) REVERT: C 20 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5574 (m-10) REVERT: C 38 PHE cc_start: 0.7252 (t80) cc_final: 0.5869 (t80) REVERT: C 39 ASP cc_start: 0.6894 (t0) cc_final: 0.6573 (t0) REVERT: D 16 HIS cc_start: 0.8624 (m-70) cc_final: 0.8360 (m170) REVERT: E 2 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6876 (ptpp) REVERT: E 44 ARG cc_start: 0.7621 (ttp-110) cc_final: 0.7004 (ttp80) REVERT: G 131 LYS cc_start: 0.8657 (tttt) cc_final: 0.8356 (tttt) REVERT: G 142 LYS cc_start: 0.6760 (tttt) cc_final: 0.6133 (tptp) REVERT: G 212 TYR cc_start: 0.6319 (m-80) cc_final: 0.5926 (m-80) REVERT: H 131 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7529 (tpm170) REVERT: I 57 LYS cc_start: 0.7737 (mttm) cc_final: 0.7069 (mttp) REVERT: I 61 ARG cc_start: 0.5676 (mtp85) cc_final: 0.5058 (ttm110) REVERT: I 70 GLN cc_start: 0.7800 (mt0) cc_final: 0.7389 (tm-30) REVERT: I 71 PHE cc_start: 0.8216 (t80) cc_final: 0.7723 (t80) REVERT: I 82 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7305 (mttt) REVERT: I 205 LYS cc_start: 0.7327 (ptmt) cc_final: 0.6449 (tptp) REVERT: J 25 LYS cc_start: 0.6409 (ttpt) cc_final: 0.5819 (tttp) REVERT: J 63 MET cc_start: 0.6883 (mmm) cc_final: 0.6596 (mmm) REVERT: L 100 MET cc_start: 0.4388 (mtm) cc_final: 0.2764 (mmp) REVERT: M 29 SER cc_start: 0.7733 (p) cc_final: 0.7485 (t) REVERT: M 60 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5512 (pp) REVERT: M 113 ARG cc_start: 0.7471 (tpm170) cc_final: 0.6475 (mtp-110) REVERT: N 84 ARG cc_start: 0.4127 (mpt180) cc_final: 0.2632 (tpt-90) REVERT: N 87 MET cc_start: 0.5945 (tpt) cc_final: 0.5041 (mmm) REVERT: N 97 LEU cc_start: 0.3464 (OUTLIER) cc_final: 0.2709 (mt) REVERT: O 6 ILE cc_start: 0.3784 (OUTLIER) cc_final: 0.3123 (mm) REVERT: O 88 MET cc_start: 0.5133 (ppp) cc_final: 0.4381 (ppp) REVERT: P 22 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7293 (mp) REVERT: P 75 GLU cc_start: 0.7396 (pm20) cc_final: 0.6992 (pm20) REVERT: P 86 LYS cc_start: 0.6968 (ttpt) cc_final: 0.6518 (tttt) REVERT: Q 95 HIS cc_start: 0.6392 (m90) cc_final: 0.6184 (m-70) REVERT: S 39 ASP cc_start: 0.7514 (m-30) cc_final: 0.7138 (p0) REVERT: U 59 HIS cc_start: 0.3931 (OUTLIER) cc_final: 0.3144 (t70) REVERT: U 63 GLN cc_start: 0.3886 (OUTLIER) cc_final: 0.3402 (mt0) REVERT: V 30 HIS cc_start: 0.7540 (t70) cc_final: 0.7184 (t70) REVERT: W 52 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7306 (mtm-85) REVERT: W 53 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8813 (mm-40) REVERT: X 35 ARG cc_start: 0.6644 (ptm160) cc_final: 0.6338 (ptm-80) REVERT: X 65 MET cc_start: 0.7583 (ptp) cc_final: 0.7357 (mtm) REVERT: Y 2 ASN cc_start: 0.6827 (m110) cc_final: 0.6424 (m-40) REVERT: Y 50 PHE cc_start: 0.7572 (t80) cc_final: 0.7290 (t80) REVERT: Y 68 LYS cc_start: 0.6939 (mmtm) cc_final: 0.6718 (tptt) REVERT: Y 75 LYS cc_start: 0.7600 (tppt) cc_final: 0.7198 (mttt) REVERT: Z 9 GLU cc_start: 0.6902 (mp0) cc_final: 0.6485 (mm-30) REVERT: Z 55 HIS cc_start: 0.6209 (OUTLIER) cc_final: 0.5098 (m-70) outliers start: 351 outliers final: 271 residues processed: 1424 average time/residue: 1.3515 time to fit residues: 3317.6388 Evaluate side-chains 1471 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1172 time to evaluate : 6.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 120 GLN Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 249 LYS Chi-restraints excluded: chain 8 residue 391 VAL Chi-restraints excluded: chain 8 residue 418 ILE Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 526 GLU Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 660 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 85 ASN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 144 GLU Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 184 LYS Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 4 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 74 GLN Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 65 ASP Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 25 LYS Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 8 GLN Chi-restraints excluded: chain z residue 30 ARG Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain Y residue 19 HIS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 659 optimal weight: 8.9990 chunk 425 optimal weight: 10.0000 chunk 636 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 677 optimal weight: 9.9990 chunk 726 optimal weight: 7.9990 chunk 527 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 837 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 HIS ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN r 12 HIS ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN F 33 HIS ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN J 121 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 165944 Z= 0.407 Angle : 0.860 16.528 247519 Z= 0.428 Chirality : 0.046 0.422 31530 Planarity : 0.007 0.086 13817 Dihedral : 23.860 177.850 81196 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.16 % Favored : 85.64 % Rotamer: Outliers : 7.08 % Allowed : 27.34 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.59 (0.09), residues: 6489 helix: -1.80 (0.11), residues: 1818 sheet: -2.23 (0.15), residues: 1068 loop : -2.82 (0.09), residues: 3603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 8 193 HIS 0.030 0.002 HIS m 13 PHE 0.042 0.003 PHE j 119 TYR 0.028 0.003 TYR v 57 ARG 0.011 0.001 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1201 time to evaluate : 7.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7592 (ttmt) cc_final: 0.6867 (ttmm) REVERT: 8 120 GLN cc_start: 0.5068 (OUTLIER) cc_final: 0.4568 (tm-30) REVERT: 8 124 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5351 (mt-10) REVERT: 8 211 MET cc_start: 0.5329 (ptm) cc_final: 0.5069 (mmp) REVERT: 8 351 ASN cc_start: 0.5911 (t0) cc_final: 0.5294 (t0) REVERT: 8 451 GLU cc_start: 0.5734 (mt-10) cc_final: 0.4575 (pm20) REVERT: 8 603 GLU cc_start: 0.5523 (tp30) cc_final: 0.4765 (tp30) REVERT: 8 657 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5029 (mp0) REVERT: 8 663 MET cc_start: 0.2268 (ptt) cc_final: 0.1517 (mmm) REVERT: b 153 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7840 (mp) REVERT: c 1 MET cc_start: 0.4286 (ppp) cc_final: 0.3098 (mmm) REVERT: c 183 GLU cc_start: 0.6811 (mp0) cc_final: 0.6319 (mp0) REVERT: e 35 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7701 (mt) REVERT: e 82 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5717 (m-10) REVERT: e 95 MET cc_start: 0.7812 (tmm) cc_final: 0.6672 (tmm) REVERT: e 129 MET cc_start: 0.5681 (mtp) cc_final: 0.5071 (mtp) REVERT: e 151 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7166 (pt) REVERT: e 153 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.6645 (pt) REVERT: f 142 GLN cc_start: 0.8327 (mm110) cc_final: 0.7906 (mm110) REVERT: a 184 LYS cc_start: 0.4880 (OUTLIER) cc_final: 0.4563 (ptpp) REVERT: a 214 ILE cc_start: 0.1948 (OUTLIER) cc_final: 0.1697 (tt) REVERT: j 7 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7389 (mtmm) REVERT: l 4 ASN cc_start: 0.8049 (p0) cc_final: 0.7765 (p0) REVERT: m 73 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7059 (mm) REVERT: o 16 ARG cc_start: 0.8003 (mmp80) cc_final: 0.7680 (mmp80) REVERT: o 29 HIS cc_start: 0.7897 (t-170) cc_final: 0.7511 (t-170) REVERT: p 5 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8127 (mtmt) REVERT: r 35 PHE cc_start: 0.7517 (m-80) cc_final: 0.6946 (m-80) REVERT: r 82 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8088 (t70) REVERT: s 78 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: s 97 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7224 (mm) REVERT: u 6 ARG cc_start: 0.7614 (ttt180) cc_final: 0.6857 (ttm170) REVERT: u 28 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6569 (tt) REVERT: u 81 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7584 (mtm110) REVERT: x 31 ASN cc_start: 0.8097 (t0) cc_final: 0.7694 (t0) REVERT: x 71 ARG cc_start: 0.7904 (mmp80) cc_final: 0.7696 (mtm-85) REVERT: y 7 ARG cc_start: 0.6106 (ppt170) cc_final: 0.5366 (ttm110) REVERT: y 8 GLU cc_start: 0.6764 (mt-10) cc_final: 0.5535 (mt-10) REVERT: y 12 GLU cc_start: 0.7090 (tt0) cc_final: 0.6078 (tm-30) REVERT: y 20 ASN cc_start: 0.7924 (m-40) cc_final: 0.7563 (m110) REVERT: z 30 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6909 (mtm110) REVERT: B 21 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7668 (mm) REVERT: C 20 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5627 (m-10) REVERT: C 38 PHE cc_start: 0.7461 (t80) cc_final: 0.6372 (t80) REVERT: C 39 ASP cc_start: 0.7012 (t0) cc_final: 0.6730 (t0) REVERT: E 2 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7157 (ptpp) REVERT: E 44 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7110 (ttp80) REVERT: G 131 LYS cc_start: 0.8617 (tttt) cc_final: 0.8294 (tttt) REVERT: G 142 LYS cc_start: 0.6712 (tttt) cc_final: 0.6086 (tptp) REVERT: G 153 MET cc_start: 0.4977 (mtp) cc_final: 0.4711 (mtp) REVERT: G 212 TYR cc_start: 0.6368 (m-80) cc_final: 0.5675 (m-80) REVERT: H 131 ARG cc_start: 0.8035 (ttt90) cc_final: 0.7591 (tpm170) REVERT: I 61 ARG cc_start: 0.5777 (mtp85) cc_final: 0.5143 (ttm110) REVERT: I 70 GLN cc_start: 0.7822 (mt0) cc_final: 0.7364 (tm-30) REVERT: I 71 PHE cc_start: 0.8279 (t80) cc_final: 0.8034 (t80) REVERT: I 82 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7395 (mttt) REVERT: I 205 LYS cc_start: 0.7527 (ptmt) cc_final: 0.6674 (tptp) REVERT: J 25 LYS cc_start: 0.6466 (ttpt) cc_final: 0.5816 (tttt) REVERT: J 51 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6552 (ptpp) REVERT: J 70 MET cc_start: 0.5844 (mmt) cc_final: 0.5595 (mmt) REVERT: J 94 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.5364 (p90) REVERT: J 127 TYR cc_start: 0.7750 (m-80) cc_final: 0.7244 (m-80) REVERT: L 52 ARG cc_start: 0.6008 (mmt90) cc_final: 0.5759 (mmt90) REVERT: L 100 MET cc_start: 0.4278 (mtm) cc_final: 0.2828 (mmp) REVERT: M 29 SER cc_start: 0.7778 (p) cc_final: 0.7332 (t) REVERT: M 60 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5592 (pp) REVERT: M 113 ARG cc_start: 0.7583 (tpm170) cc_final: 0.6790 (ptm-80) REVERT: N 54 VAL cc_start: 0.3769 (OUTLIER) cc_final: 0.3565 (p) REVERT: N 84 ARG cc_start: 0.4113 (mpt180) cc_final: 0.2561 (tpt-90) REVERT: O 6 ILE cc_start: 0.3982 (OUTLIER) cc_final: 0.3342 (mm) REVERT: O 88 MET cc_start: 0.5221 (ppp) cc_final: 0.4382 (ppp) REVERT: P 22 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7333 (mp) REVERT: P 86 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6562 (tttt) REVERT: Q 95 HIS cc_start: 0.6455 (m90) cc_final: 0.6235 (m-70) REVERT: R 86 ARG cc_start: 0.7836 (mtm180) cc_final: 0.7504 (mtm-85) REVERT: S 39 ASP cc_start: 0.7615 (m-30) cc_final: 0.7090 (p0) REVERT: U 59 HIS cc_start: 0.3735 (OUTLIER) cc_final: 0.2833 (t70) REVERT: U 63 GLN cc_start: 0.3812 (OUTLIER) cc_final: 0.3243 (mt0) REVERT: V 30 HIS cc_start: 0.7642 (t70) cc_final: 0.7312 (t70) REVERT: W 42 ARG cc_start: 0.6922 (ttt-90) cc_final: 0.6648 (ttt-90) REVERT: W 53 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8881 (mm-40) REVERT: X 35 ARG cc_start: 0.6798 (ptm160) cc_final: 0.6497 (ptm-80) REVERT: Y 2 ASN cc_start: 0.6882 (m110) cc_final: 0.6571 (m-40) REVERT: Y 75 LYS cc_start: 0.7705 (tppt) cc_final: 0.7124 (mttt) REVERT: Z 55 HIS cc_start: 0.6189 (OUTLIER) cc_final: 0.5142 (m-70) outliers start: 382 outliers final: 295 residues processed: 1446 average time/residue: 1.3440 time to fit residues: 3361.2391 Evaluate side-chains 1493 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1169 time to evaluate : 6.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 120 GLN Chi-restraints excluded: chain 8 residue 124 GLU Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 249 LYS Chi-restraints excluded: chain 8 residue 391 VAL Chi-restraints excluded: chain 8 residue 418 ILE Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 526 GLU Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain 8 residue 657 GLU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 115 ILE Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 171 VAL Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 144 GLU Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 184 ASP Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 135 ILE Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 184 LYS Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 96 ARG Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 27 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 119 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 43 ASN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 31 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 81 SER Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 37 ASP Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 25 LYS Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 30 ARG Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain Y residue 69 ASN Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 969 optimal weight: 8.9990 chunk 1021 optimal weight: 10.0000 chunk 931 optimal weight: 30.0000 chunk 993 optimal weight: 6.9990 chunk 1020 optimal weight: 20.0000 chunk 597 optimal weight: 5.9990 chunk 432 optimal weight: 20.0000 chunk 780 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 897 optimal weight: 3.9990 chunk 939 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 71 ASN ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** T 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 165944 Z= 0.275 Angle : 0.721 18.900 247519 Z= 0.364 Chirality : 0.040 0.442 31530 Planarity : 0.005 0.076 13817 Dihedral : 23.782 179.554 81196 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.30 % Favored : 87.50 % Rotamer: Outliers : 6.29 % Allowed : 28.52 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.42 (0.10), residues: 6489 helix: -1.58 (0.11), residues: 1824 sheet: -2.20 (0.15), residues: 1086 loop : -2.73 (0.10), residues: 3579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 8 193 HIS 0.020 0.001 HIS m 13 PHE 0.037 0.002 PHE Z 36 TYR 0.019 0.002 TYR W 69 ARG 0.013 0.001 ARG H 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1192 time to evaluate : 7.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7638 (ttmt) cc_final: 0.6924 (ttmm) REVERT: 8 120 GLN cc_start: 0.5097 (OUTLIER) cc_final: 0.4577 (tm-30) REVERT: 8 124 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5111 (mt-10) REVERT: 8 278 MET cc_start: 0.6037 (ptp) cc_final: 0.5825 (pmm) REVERT: 8 351 ASN cc_start: 0.5931 (t0) cc_final: 0.5290 (t0) REVERT: 8 451 GLU cc_start: 0.5637 (mt-10) cc_final: 0.4613 (pm20) REVERT: 8 574 MET cc_start: 0.7009 (pmm) cc_final: 0.6781 (pmm) REVERT: 8 603 GLU cc_start: 0.5528 (tp30) cc_final: 0.4786 (tp30) REVERT: 8 663 MET cc_start: 0.2010 (ptt) cc_final: 0.1644 (mmt) REVERT: b 86 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6960 (mtt90) REVERT: b 153 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7849 (mp) REVERT: c 1 MET cc_start: 0.4256 (ppp) cc_final: 0.3018 (mmm) REVERT: c 74 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6806 (pp20) REVERT: e 35 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7692 (mt) REVERT: e 82 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5631 (m-10) REVERT: e 95 MET cc_start: 0.7629 (tmm) cc_final: 0.6698 (tmm) REVERT: e 129 MET cc_start: 0.5453 (mtp) cc_final: 0.4888 (mtp) REVERT: e 151 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7132 (pt) REVERT: e 153 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.6700 (pt) REVERT: f 142 GLN cc_start: 0.8276 (mm110) cc_final: 0.7890 (mm110) REVERT: a 214 ILE cc_start: 0.1871 (OUTLIER) cc_final: 0.1580 (tt) REVERT: j 7 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7164 (mtmm) REVERT: l 4 ASN cc_start: 0.7975 (p0) cc_final: 0.7728 (p0) REVERT: l 105 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7372 (mt) REVERT: l 106 GLU cc_start: 0.7469 (mp0) cc_final: 0.7151 (mp0) REVERT: m 73 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.6908 (mm) REVERT: o 29 HIS cc_start: 0.7824 (t-170) cc_final: 0.7398 (t-170) REVERT: p 5 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8151 (mtpt) REVERT: q 31 TYR cc_start: 0.7987 (t80) cc_final: 0.7598 (t80) REVERT: r 35 PHE cc_start: 0.7513 (m-80) cc_final: 0.6945 (m-80) REVERT: r 82 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.8003 (t70) REVERT: s 78 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: s 97 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7033 (mm) REVERT: t 69 ARG cc_start: 0.7596 (ttt90) cc_final: 0.7356 (ttt90) REVERT: u 28 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6552 (tt) REVERT: u 81 ARG cc_start: 0.8281 (mtm110) cc_final: 0.7620 (mtm110) REVERT: x 31 ASN cc_start: 0.8008 (t0) cc_final: 0.7565 (t0) REVERT: y 7 ARG cc_start: 0.6099 (ppt170) cc_final: 0.5479 (ttm110) REVERT: y 8 GLU cc_start: 0.6716 (mt-10) cc_final: 0.5473 (mt-10) REVERT: y 12 GLU cc_start: 0.7058 (tt0) cc_final: 0.6017 (tm-30) REVERT: y 20 ASN cc_start: 0.7878 (m-40) cc_final: 0.7515 (m110) REVERT: z 30 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6924 (mtm110) REVERT: B 21 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7590 (mm) REVERT: C 8 ILE cc_start: 0.7711 (tp) cc_final: 0.7483 (pt) REVERT: C 20 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5659 (m-10) REVERT: C 38 PHE cc_start: 0.7329 (t80) cc_final: 0.6201 (t80) REVERT: C 39 ASP cc_start: 0.6968 (t0) cc_final: 0.6585 (t0) REVERT: E 2 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7047 (ptpp) REVERT: E 44 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7077 (ttp80) REVERT: G 131 LYS cc_start: 0.8582 (tttt) cc_final: 0.8256 (tttt) REVERT: G 142 LYS cc_start: 0.6784 (tttt) cc_final: 0.6131 (tptp) REVERT: G 212 TYR cc_start: 0.6359 (m-80) cc_final: 0.5674 (m-80) REVERT: H 131 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7540 (tpm170) REVERT: I 70 GLN cc_start: 0.7768 (mt0) cc_final: 0.7345 (tm-30) REVERT: I 71 PHE cc_start: 0.8223 (t80) cc_final: 0.7976 (t80) REVERT: I 82 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7322 (mttt) REVERT: I 205 LYS cc_start: 0.7362 (ptmt) cc_final: 0.6442 (tptp) REVERT: J 25 LYS cc_start: 0.6469 (ttpt) cc_final: 0.5837 (tttp) REVERT: J 51 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6359 (ptpp) REVERT: J 127 TYR cc_start: 0.7683 (m-80) cc_final: 0.7247 (m-80) REVERT: K 4 TYR cc_start: 0.7006 (m-10) cc_final: 0.6633 (m-10) REVERT: K 93 LYS cc_start: 0.3252 (ptpp) cc_final: 0.2942 (pttp) REVERT: L 100 MET cc_start: 0.4203 (mtm) cc_final: 0.2779 (mmp) REVERT: M 29 SER cc_start: 0.7754 (p) cc_final: 0.7402 (t) REVERT: M 60 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5615 (pp) REVERT: M 113 ARG cc_start: 0.7533 (tpm170) cc_final: 0.6782 (ptm-80) REVERT: N 20 ILE cc_start: 0.3790 (OUTLIER) cc_final: 0.3589 (tt) REVERT: N 54 VAL cc_start: 0.3798 (OUTLIER) cc_final: 0.3365 (p) REVERT: N 56 MET cc_start: 0.4410 (mmt) cc_final: 0.3824 (mtm) REVERT: N 84 ARG cc_start: 0.4385 (mpt180) cc_final: 0.2779 (tpt-90) REVERT: N 87 MET cc_start: 0.6031 (tpt) cc_final: 0.5091 (tpt) REVERT: O 6 ILE cc_start: 0.3945 (OUTLIER) cc_final: 0.3357 (mm) REVERT: O 88 MET cc_start: 0.5330 (ppp) cc_final: 0.4419 (ppp) REVERT: P 22 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7333 (mp) REVERT: P 75 GLU cc_start: 0.7495 (pm20) cc_final: 0.6963 (pm20) REVERT: P 86 LYS cc_start: 0.7014 (ttpt) cc_final: 0.6551 (tttt) REVERT: Q 94 TYR cc_start: 0.7699 (m-80) cc_final: 0.7351 (m-80) REVERT: S 39 ASP cc_start: 0.7572 (m-30) cc_final: 0.7100 (p0) REVERT: U 59 HIS cc_start: 0.3651 (OUTLIER) cc_final: 0.2783 (t70) REVERT: U 63 GLN cc_start: 0.3743 (OUTLIER) cc_final: 0.3172 (mt0) REVERT: V 30 HIS cc_start: 0.7547 (t70) cc_final: 0.7186 (t70) REVERT: W 42 ARG cc_start: 0.6970 (ttt-90) cc_final: 0.6669 (ttt-90) REVERT: W 52 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7231 (mtm-85) REVERT: X 35 ARG cc_start: 0.6646 (ptm160) cc_final: 0.6298 (ptm-80) REVERT: Y 2 ASN cc_start: 0.6754 (m110) cc_final: 0.6550 (m-40) REVERT: Y 75 LYS cc_start: 0.7548 (tppt) cc_final: 0.7020 (mttt) REVERT: Z 55 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5130 (m-70) outliers start: 339 outliers final: 277 residues processed: 1412 average time/residue: 1.3670 time to fit residues: 3326.2634 Evaluate side-chains 1464 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1158 time to evaluate : 6.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 101 ARG Chi-restraints excluded: chain 8 residue 120 GLN Chi-restraints excluded: chain 8 residue 124 GLU Chi-restraints excluded: chain 8 residue 186 VAL Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 214 LEU Chi-restraints excluded: chain 8 residue 234 MET Chi-restraints excluded: chain 8 residue 249 LYS Chi-restraints excluded: chain 8 residue 391 VAL Chi-restraints excluded: chain 8 residue 418 ILE Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 526 GLU Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 605 PHE Chi-restraints excluded: chain 8 residue 621 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 166 ARG Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 202 ARG Chi-restraints excluded: chain b residue 203 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 266 ILE Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 108 ASP Chi-restraints excluded: chain c residue 110 THR Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 170 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 144 GLU Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 175 ILE Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 131 VAL Chi-restraints excluded: chain e residue 136 ILE Chi-restraints excluded: chain e residue 151 LEU Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 120 ILE Chi-restraints excluded: chain g residue 2 GLN Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 47 ASN Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain a residue 222 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 7 LYS Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 90 GLU Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 4 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 24 VAL Chi-restraints excluded: chain k residue 49 ARG Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 VAL Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain k residue 92 GLU Chi-restraints excluded: chain l residue 27 LEU Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 25 ASP Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain n residue 107 ASN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 18 SER Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 94 THR Chi-restraints excluded: chain r residue 95 ASP Chi-restraints excluded: chain s residue 3 THR Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 72 THR Chi-restraints excluded: chain s residue 78 GLU Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain t residue 63 VAL Chi-restraints excluded: chain u residue 10 VAL Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 39 ASN Chi-restraints excluded: chain u residue 51 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 8 VAL Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 25 LYS Chi-restraints excluded: chain v residue 60 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain v residue 89 ILE Chi-restraints excluded: chain v residue 90 ASP Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain y residue 16 THR Chi-restraints excluded: chain y residue 57 LEU Chi-restraints excluded: chain z residue 30 ARG Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 47 ILE Chi-restraints excluded: chain z residue 55 LYS Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 CYS Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 27 GLN Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 59 HIS Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 ASP Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 38 ILE Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 989 optimal weight: 0.3980 chunk 652 optimal weight: 8.9990 chunk 1050 optimal weight: 0.7980 chunk 641 optimal weight: 40.0000 chunk 498 optimal weight: 10.0000 chunk 730 optimal weight: 1.9990 chunk 1101 optimal weight: 7.9990 chunk 1014 optimal weight: 0.0980 chunk 877 optimal weight: 0.0370 chunk 91 optimal weight: 10.0000 chunk 677 optimal weight: 5.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 92 HIS 8 129 GLN 8 627 ASN ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 ASN ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 11 GLN j 136 GLN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN q 19 GLN s 40 ASN ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN H 189 HIS J 121 ASN M 3 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN Q 28 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN T 27 GLN T 36 ASN T 50 HIS V 8 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 165944 Z= 0.138 Angle : 0.602 20.951 247519 Z= 0.307 Chirality : 0.034 0.485 31530 Planarity : 0.005 0.071 13817 Dihedral : 23.585 177.458 81196 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.66 % Favored : 90.18 % Rotamer: Outliers : 3.52 % Allowed : 31.82 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.03 (0.10), residues: 6489 helix: -1.13 (0.12), residues: 1852 sheet: -2.06 (0.15), residues: 1112 loop : -2.54 (0.10), residues: 3525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 8 193 HIS 0.028 0.001 HIS G 93 PHE 0.031 0.002 PHE m 31 TYR 0.020 0.001 TYR j 75 ARG 0.009 0.001 ARG l 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12978 Ramachandran restraints generated. 6489 Oldfield, 0 Emsley, 6489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1466 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1276 time to evaluate : 6.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 23 LYS cc_start: 0.7573 (ttmt) cc_final: 0.7021 (tttt) REVERT: 8 120 GLN cc_start: 0.5034 (OUTLIER) cc_final: 0.4568 (tm-30) REVERT: 8 188 MET cc_start: 0.5051 (mmm) cc_final: 0.4319 (mmm) REVERT: 8 374 ILE cc_start: 0.8147 (tp) cc_final: 0.7801 (mm) REVERT: 8 451 GLU cc_start: 0.5325 (mt-10) cc_final: 0.4640 (pm20) REVERT: 8 574 MET cc_start: 0.7019 (pmm) cc_final: 0.6784 (pmm) REVERT: 8 603 GLU cc_start: 0.5412 (tp30) cc_final: 0.4310 (tp30) REVERT: 8 663 MET cc_start: 0.1761 (ptt) cc_final: 0.1538 (mmm) REVERT: 8 682 MET cc_start: 0.6239 (ptt) cc_final: 0.5829 (ptp) REVERT: b 86 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7136 (mtt90) REVERT: b 199 HIS cc_start: 0.8226 (t-90) cc_final: 0.7701 (t-90) REVERT: c 1 MET cc_start: 0.3603 (ppp) cc_final: 0.2520 (mmm) REVERT: c 38 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7400 (mmmt) REVERT: c 139 SER cc_start: 0.8589 (m) cc_final: 0.8014 (t) REVERT: d 21 ARG cc_start: 0.6202 (mtp85) cc_final: 0.5600 (mtp180) REVERT: d 88 ARG cc_start: 0.7391 (ptt180) cc_final: 0.7183 (ptt180) REVERT: d 166 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6415 (mmtt) REVERT: e 82 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5616 (m-10) REVERT: e 129 MET cc_start: 0.5002 (mtp) cc_final: 0.4624 (mtp) REVERT: e 153 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6673 (pt) REVERT: f 138 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8391 (tm-30) REVERT: f 142 GLN cc_start: 0.8178 (mm110) cc_final: 0.7972 (mm-40) REVERT: a 214 ILE cc_start: 0.2044 (OUTLIER) cc_final: 0.1760 (tt) REVERT: i 116 MET cc_start: 0.0053 (tpt) cc_final: -0.0174 (tpt) REVERT: l 4 ASN cc_start: 0.7919 (p0) cc_final: 0.7704 (p0) REVERT: l 105 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (mt) REVERT: l 106 GLU cc_start: 0.7419 (mp0) cc_final: 0.7080 (mp0) REVERT: o 29 HIS cc_start: 0.7771 (t-170) cc_final: 0.7501 (t-170) REVERT: q 31 TYR cc_start: 0.7754 (t80) cc_final: 0.7429 (t80) REVERT: r 35 PHE cc_start: 0.7469 (m-80) cc_final: 0.6878 (m-80) REVERT: r 82 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7653 (t70) REVERT: s 97 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6679 (mm) REVERT: u 81 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7685 (mtm110) REVERT: u 94 PHE cc_start: 0.7208 (p90) cc_final: 0.6802 (p90) REVERT: x 31 ASN cc_start: 0.7816 (t0) cc_final: 0.7428 (t0) REVERT: y 5 GLU cc_start: 0.7630 (pp20) cc_final: 0.7289 (pp20) REVERT: y 7 ARG cc_start: 0.6176 (ppt170) cc_final: 0.5596 (ttm110) REVERT: y 8 GLU cc_start: 0.6578 (mt-10) cc_final: 0.5342 (mt-10) REVERT: y 12 GLU cc_start: 0.6967 (tt0) cc_final: 0.5896 (tm-30) REVERT: y 20 ASN cc_start: 0.7854 (m-40) cc_final: 0.7529 (m110) REVERT: y 28 LEU cc_start: 0.7517 (mm) cc_final: 0.7152 (mm) REVERT: z 46 MET cc_start: 0.8498 (ttm) cc_final: 0.8260 (ttm) REVERT: C 8 ILE cc_start: 0.7643 (tp) cc_final: 0.7430 (pt) REVERT: C 20 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5637 (m-10) REVERT: C 38 PHE cc_start: 0.6900 (t80) cc_final: 0.5937 (t80) REVERT: C 39 ASP cc_start: 0.6837 (t0) cc_final: 0.6494 (t0) REVERT: E 44 ARG cc_start: 0.7422 (ttp-110) cc_final: 0.6942 (ttp80) REVERT: G 131 LYS cc_start: 0.8582 (tttt) cc_final: 0.8273 (tttt) REVERT: G 142 LYS cc_start: 0.6808 (tttt) cc_final: 0.6190 (tptp) REVERT: G 212 TYR cc_start: 0.6145 (m-80) cc_final: 0.5851 (m-80) REVERT: H 131 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7431 (tpm170) REVERT: I 70 GLN cc_start: 0.7469 (mt0) cc_final: 0.7195 (tm-30) REVERT: I 71 PHE cc_start: 0.8138 (t80) cc_final: 0.7520 (t80) REVERT: I 74 TYR cc_start: 0.8265 (m-80) cc_final: 0.7776 (m-80) REVERT: I 75 TYR cc_start: 0.7284 (t80) cc_final: 0.6984 (t80) REVERT: I 82 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7283 (mttt) REVERT: I 205 LYS cc_start: 0.7104 (ptmt) cc_final: 0.5954 (tptp) REVERT: J 25 LYS cc_start: 0.6367 (ttpt) cc_final: 0.5745 (tttp) REVERT: J 51 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6187 (ptpp) REVERT: K 1 MET cc_start: 0.5200 (mtm) cc_final: 0.4840 (ptm) REVERT: K 4 TYR cc_start: 0.6317 (m-10) cc_final: 0.6060 (m-10) REVERT: K 93 LYS cc_start: 0.3734 (ptpp) cc_final: 0.3378 (pttp) REVERT: L 100 MET cc_start: 0.4240 (mtm) cc_final: 0.2654 (mmp) REVERT: M 29 SER cc_start: 0.7719 (p) cc_final: 0.7423 (t) REVERT: M 48 PHE cc_start: 0.6276 (p90) cc_final: 0.5956 (p90) REVERT: M 60 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5563 (pp) REVERT: M 91 LEU cc_start: 0.6113 (mt) cc_final: 0.5712 (mt) REVERT: M 113 ARG cc_start: 0.7419 (tpm170) cc_final: 0.6700 (ptm-80) REVERT: M 120 LEU cc_start: 0.4803 (OUTLIER) cc_final: 0.4506 (mt) REVERT: N 54 VAL cc_start: 0.3780 (OUTLIER) cc_final: 0.3437 (p) REVERT: N 56 MET cc_start: 0.4319 (mmt) cc_final: 0.3916 (mtm) REVERT: N 84 ARG cc_start: 0.4286 (mpt180) cc_final: 0.2977 (tpt-90) REVERT: N 87 MET cc_start: 0.5924 (tpt) cc_final: 0.4954 (mmm) REVERT: O 6 ILE cc_start: 0.3966 (OUTLIER) cc_final: 0.3431 (mm) REVERT: O 88 MET cc_start: 0.5275 (ppp) cc_final: 0.4540 (ppp) REVERT: P 75 GLU cc_start: 0.7438 (pm20) cc_final: 0.6742 (pm20) REVERT: P 76 TYR cc_start: 0.6927 (m-10) cc_final: 0.6456 (m-10) REVERT: P 86 LYS cc_start: 0.6997 (ttpt) cc_final: 0.6561 (tttt) REVERT: S 5 MET cc_start: 0.5812 (mmt) cc_final: 0.5044 (mmt) REVERT: S 39 ASP cc_start: 0.7314 (m-30) cc_final: 0.6978 (p0) REVERT: U 63 GLN cc_start: 0.3566 (OUTLIER) cc_final: 0.3010 (mp10) REVERT: V 80 LYS cc_start: 0.6220 (mmtm) cc_final: 0.5289 (tmtt) REVERT: W 42 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.6903 (ttt-90) REVERT: X 35 ARG cc_start: 0.6375 (ptm160) cc_final: 0.6091 (ptm-80) REVERT: Y 39 GLU cc_start: 0.5510 (tp30) cc_final: 0.5091 (tp30) REVERT: Z 9 GLU cc_start: 0.6746 (mp0) cc_final: 0.6304 (mm-30) outliers start: 190 outliers final: 119 residues processed: 1404 average time/residue: 1.3934 time to fit residues: 3336.7333 Evaluate side-chains 1313 residues out of total 5392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1179 time to evaluate : 6.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 68 THR Chi-restraints excluded: chain 8 residue 69 THR Chi-restraints excluded: chain 8 residue 96 THR Chi-restraints excluded: chain 8 residue 120 GLN Chi-restraints excluded: chain 8 residue 197 ASP Chi-restraints excluded: chain 8 residue 249 LYS Chi-restraints excluded: chain 8 residue 391 VAL Chi-restraints excluded: chain 8 residue 435 LEU Chi-restraints excluded: chain 8 residue 518 VAL Chi-restraints excluded: chain 8 residue 526 GLU Chi-restraints excluded: chain 8 residue 537 ILE Chi-restraints excluded: chain 8 residue 591 LEU Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 134 HIS Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 180 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 164 LEU Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain a residue 208 TYR Chi-restraints excluded: chain a residue 214 ILE Chi-restraints excluded: chain i residue 97 VAL Chi-restraints excluded: chain k residue 4 GLU Chi-restraints excluded: chain k residue 49 ARG Chi-restraints excluded: chain l residue 73 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 105 ILE Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 26 VAL Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 41 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain p residue 74 GLN Chi-restraints excluded: chain q residue 93 ILE Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain r residue 53 PHE Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 82 MET Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 7 LEU Chi-restraints excluded: chain t residue 53 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain v residue 25 LYS Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 31 SER Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 143 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain U residue 63 GLN Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 16 MET Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 65 MET Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 82 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 538 optimal weight: 8.9990 chunk 696 optimal weight: 0.0670 chunk 934 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 809 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 243 optimal weight: 10.0000 chunk 878 optimal weight: 0.6980 chunk 367 optimal weight: 30.0000 chunk 902 optimal weight: 0.6980 chunk 111 optimal weight: 20.0000 overall best weight: 2.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** m 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 19 GLN q 71 ASN q 80 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 22 ASN ** y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN Q 28 GLN ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN Y 19 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.182716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152518 restraints weight = 309618.841| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.49 r_work: 0.3840 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 165944 Z= 0.193 Angle : 0.627 20.056 247519 Z= 0.318 Chirality : 0.036 0.552 31530 Planarity : 0.005 0.071 13817 Dihedral : 23.534 179.151 81194 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.85 % Favored : 89.03 % Rotamer: Outliers : 3.28 % Allowed : 31.71 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.95 (0.10), residues: 6489 helix: -1.06 (0.12), residues: 1852 sheet: -1.92 (0.15), residues: 1116 loop : -2.53 (0.10), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 72 HIS 0.015 0.001 HIS m 13 PHE 0.036 0.002 PHE Z 36 TYR 0.032 0.002 TYR Q 94 ARG 0.011 0.001 ARG W 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48750.76 seconds wall clock time: 849 minutes 4.17 seconds (50944.17 seconds total)