Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 16:20:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t6r_8368/04_2023/5t6r_8368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t6r_8368/04_2023/5t6r_8368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t6r_8368/04_2023/5t6r_8368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t6r_8368/04_2023/5t6r_8368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t6r_8368/04_2023/5t6r_8368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t6r_8368/04_2023/5t6r_8368.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.004 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: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 3483 5.49 5 Mg 86 5.21 5 S 100 5.16 5 C 66161 2.51 5 N 23347 2.21 5 O 33436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "E TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 290": "OD1" <-> "OD2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 320": "OD1" <-> "OD2" Residue "E PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 285": "OD1" <-> "OD2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G ASP 29": "OD1" <-> "OD2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G ARG 140": "NH1" <-> "NH2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G GLU 189": "OE1" <-> "OE2" Residue "G ASP 191": "OD1" <-> "OD2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G ASP 213": "OD1" <-> "OD2" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G ASP 215": "OD1" <-> "OD2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "G PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 221": "OE1" <-> "OE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G ASP 250": "OD1" <-> "OD2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G GLU 268": "OE1" <-> "OE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J ASP 124": "OD1" <-> "OD2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ASP 156": "OD1" <-> "OD2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J GLU 228": "OE1" <-> "OE2" Residue "J ASP 247": "OD1" <-> "OD2" Residue "J ASP 254": "OD1" <-> "OD2" Residue "K TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "K PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K ASP 107": "OD1" <-> "OD2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 189": "OE1" <-> "OE2" Residue "K ASP 190": "OD1" <-> "OD2" Residue "L ARG 4": "NH1" <-> "NH2" Residue "L TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 142": "OD1" <-> "OD2" Residue "L ASP 146": "OD1" <-> "OD2" Residue "L GLU 150": "OE1" <-> "OE2" Residue "L TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 177": "OD1" <-> "OD2" Residue "L ARG 185": "NH1" <-> "NH2" Residue "L GLU 189": "OE1" <-> "OE2" Residue "L ASP 192": "OD1" <-> "OD2" Residue "L ASP 193": "OD1" <-> "OD2" Residue "L PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 207": "OE1" <-> "OE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "M GLU 15": "OE1" <-> "OE2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M ASP 28": "OD1" <-> "OD2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M GLU 77": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 117": "OD1" <-> "OD2" Residue "M ASP 126": "OD1" <-> "OD2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 157": "OE1" <-> "OE2" Residue "M TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 170": "OD1" <-> "OD2" Residue "M ASP 173": "OD1" <-> "OD2" Residue "N PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N GLU 164": "OE1" <-> "OE2" Residue "N PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 194": "OE1" <-> "OE2" Residue "O ASP 4": "OD1" <-> "OD2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ASP 40": "OD1" <-> "OD2" Residue "O ASP 47": "OD1" <-> "OD2" Residue "O GLU 92": "OE1" <-> "OE2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "O PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a ASP 46": "OD1" <-> "OD2" Residue "a PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 124": "OD1" <-> "OD2" Residue "a TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 136": "OD1" <-> "OD2" Residue "a ASP 153": "OD1" <-> "OD2" Residue "a PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 189": "OD1" <-> "OD2" Residue "b TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 40": "OE1" <-> "OE2" Residue "c ARG 56": "NH1" <-> "NH2" Residue "c PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c ARG 128": "NH1" <-> "NH2" Residue "c TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 154": "OE1" <-> "OE2" Residue "c GLU 155": "OE1" <-> "OE2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c ARG 181": "NH1" <-> "NH2" Residue "d TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 125": "OD1" <-> "OD2" Residue "d GLU 148": "OE1" <-> "OE2" Residue "d PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 176": "NH1" <-> "NH2" Residue "d ARG 178": "NH1" <-> "NH2" Residue "d PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 62": "NH1" <-> "NH2" Residue "e TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e ASP 116": "OD1" <-> "OD2" Residue "e TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 126": "OE1" <-> "OE2" Residue "e ASP 148": "OD1" <-> "OD2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e ARG 163": "NH1" <-> "NH2" Residue "e GLU 179": "OE1" <-> "OE2" Residue "f GLU 6": "OE1" <-> "OE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 104": "OE1" <-> "OE2" Residue "f ARG 117": "NH1" <-> "NH2" Residue "f GLU 128": "OE1" <-> "OE2" Residue "f TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "f TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 8": "NH1" <-> "NH2" Residue "g PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 104": "OE1" <-> "OE2" Residue "g PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 108": "NH1" <-> "NH2" Residue "g ARG 139": "NH1" <-> "NH2" Residue "g PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 29": "OD1" <-> "OD2" Residue "h ASP 39": "OD1" <-> "OD2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h ASP 59": "OD1" <-> "OD2" Residue "h PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 91": "OD1" <-> "OD2" Residue "h PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 27": "OD1" <-> "OD2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 97": "OD1" <-> "OD2" Residue "j ASP 6": "OD1" <-> "OD2" Residue "j PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "k GLU 101": "OE1" <-> "OE2" Residue "k GLU 104": "OE1" <-> "OE2" Residue "k ASP 106": "OD1" <-> "OD2" Residue "k ARG 125": "NH1" <-> "NH2" Residue "k ASP 129": "OD1" <-> "OD2" Residue "k ARG 138": "NH1" <-> "NH2" Residue "k TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 38": "OE1" <-> "OE2" Residue "l GLU 67": "OE1" <-> "OE2" Residue "l ARG 121": "NH1" <-> "NH2" Residue "m GLU 31": "OE1" <-> "OE2" Residue "m PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 84": "NH1" <-> "NH2" Residue "m TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 90": "OE1" <-> "OE2" Residue "m PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 135": "NH1" <-> "NH2" Residue "n TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 97": "OE1" <-> "OE2" Residue "n ASP 103": "OD1" <-> "OD2" Residue "n TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 135": "OE1" <-> "OE2" Residue "o TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 57": "OE1" <-> "OE2" Residue "p TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 97": "OD1" <-> "OD2" Residue "p ASP 99": "OD1" <-> "OD2" Residue "q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 54": "OE1" <-> "OE2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q GLU 83": "OE1" <-> "OE2" Residue "q GLU 94": "OE1" <-> "OE2" Residue "r PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 3": "OE1" <-> "OE2" Residue "s TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 87": "OE1" <-> "OE2" Residue "t GLU 96": "OE1" <-> "OE2" Residue "t GLU 97": "OE1" <-> "OE2" Residue "t GLU 107": "OE1" <-> "OE2" Residue "u GLU 15": "OE1" <-> "OE2" Residue "u GLU 30": "OE1" <-> "OE2" Residue "u GLU 60": "OE1" <-> "OE2" Residue "u TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 89": "OE1" <-> "OE2" Residue "w TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 63": "NH1" <-> "NH2" Residue "x PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 19": "OD1" <-> "OD2" Residue "x PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 79": "OE1" <-> "OE2" Residue "z TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "R ASP 38": "OD1" <-> "OD2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "V ARG 162": "NH1" <-> "NH2" Residue "V PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 186": "OD1" <-> "OD2" Residue "V GLU 192": "OE1" <-> "OE2" Residue "V ASP 198": "OD1" <-> "OD2" Residue "V PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 212": "OD1" <-> "OD2" Residue "V PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 226": "OE1" <-> "OE2" Residue "V GLU 227": "OE1" <-> "OE2" Residue "V TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 254": "OD1" <-> "OD2" Residue "V ASP 255": "OD1" <-> "OD2" Residue "V PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 303": "NH1" <-> "NH2" Residue "V PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 317": "OE1" <-> "OE2" Residue "V PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 322": "OD1" <-> "OD2" Residue "V ASP 324": "OD1" <-> "OD2" Residue "V ARG 330": "NH1" <-> "NH2" Residue "V ASP 337": "OD1" <-> "OD2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ASP 345": "OD1" <-> "OD2" Residue "V ASP 350": "OD1" <-> "OD2" Residue "V TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 356": "NH1" <-> "NH2" Residue "V TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 382": "OD1" <-> "OD2" Residue "V PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 385": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 126616 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 68535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3204, 68535 Classifications: {'RNA': 3204} Modifications used: {'rna2p_pur': 329, 'rna2p_pyr': 219, 'rna3p_pur': 1448, 'rna3p_pyr': 1208} Link IDs: {'rna2p': 548, 'rna3p': 2655} Chain breaks: 2 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "C" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 128} Chain: "D" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1914 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "H" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "I" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "J" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "L" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1705 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 3} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "N" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "O" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "a" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "b" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "c" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "e" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain: "f" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "g" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "h" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "i" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "j" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 699 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "k" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "m" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "n" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "o" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "p" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "s" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 406 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "t" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "u" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "v" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "w" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "x" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "Q" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 847 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "R" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "S" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "V" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1975 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Unusual residues: {' K': 3, ' MG': 84} Classifications: {'undetermined': 87} Link IDs: {None: 86} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 45.80, per 1000 atoms: 0.36 Number of scatterers: 126616 At special positions: 0 Unit cell: (264.6, 219.24, 260.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 100 16.00 P 3483 15.00 Mg 86 11.99 O 33436 8.00 N 23347 7.00 C 66161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.58 Conformation dependent library (CDL) restraints added in 7.0 seconds 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12440 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 69 sheets defined 37.9% alpha, 15.1% beta 1023 base pairs and 1654 stacking pairs defined. Time for finding SS restraints: 37.76 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 173 through 177 removed outlier: 3.684A pdb=" N ASP D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 177' Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.690A pdb=" N ALA D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'E' and resid 13 through 17 removed outlier: 3.713A pdb=" N PHE E 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.598A pdb=" N ALA E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 139 removed outlier: 3.961A pdb=" N GLN E 139 " --> pdb=" O LYS E 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 141 through 154 removed outlier: 3.905A pdb=" N GLU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 199 removed outlier: 3.632A pdb=" N VAL E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 removed outlier: 4.179A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 234 Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'F' and resid 31 through 43 removed outlier: 3.560A pdb=" N SER F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 129 removed outlier: 3.515A pdb=" N THR F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.671A pdb=" N VAL F 135 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 138 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 157 removed outlier: 3.574A pdb=" N LEU F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 173 Processing helix chain 'F' and resid 174 through 184 removed outlier: 4.269A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 251 through 263 removed outlier: 4.530A pdb=" N ASP F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLN F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.503A pdb=" N ASN F 291 " --> pdb=" O THR F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.566A pdb=" N SER F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 327 removed outlier: 3.770A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 337 Processing helix chain 'F' and resid 352 through 360 removed outlier: 3.592A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 16 Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.984A pdb=" N ARG G 35 " --> pdb=" O TYR G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 81 through 86 Proline residue: G 84 - end of helix No H-bonds generated for 'chain 'G' and resid 81 through 86' Processing helix chain 'G' and resid 94 through 113 removed outlier: 3.557A pdb=" N LYS G 112 " --> pdb=" O ARG G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 removed outlier: 3.903A pdb=" N ALA G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 200 removed outlier: 3.506A pdb=" N LEU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.732A pdb=" N TYR G 207 " --> pdb=" O HIS G 203 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.534A pdb=" N PHE G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU G 221 " --> pdb=" O GLU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 removed outlier: 3.511A pdb=" N LEU G 227 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 250 removed outlier: 3.620A pdb=" N ILE G 239 " --> pdb=" O SER G 235 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 270 removed outlier: 3.563A pdb=" N TYR G 265 " --> pdb=" O THR G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 293 removed outlier: 3.701A pdb=" N ALA G 283 " --> pdb=" O LYS G 279 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 73 Processing helix chain 'H' and resid 131 through 150 removed outlier: 4.004A pdb=" N VAL H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 139 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS H 143 " --> pdb=" O LYS H 139 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA H 144 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 161 removed outlier: 3.512A pdb=" N LEU H 159 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 73 removed outlier: 3.620A pdb=" N GLU I 56 " --> pdb=" O GLN I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 106 removed outlier: 3.598A pdb=" N VAL I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 130 removed outlier: 3.588A pdb=" N GLU I 125 " --> pdb=" O LYS I 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 130 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 151 Processing helix chain 'I' and resid 165 through 174 removed outlier: 4.047A pdb=" N ILE I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN I 172 " --> pdb=" O ILE I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 180 through 191 Processing helix chain 'I' and resid 194 through 202 removed outlier: 3.510A pdb=" N LEU I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 235 through 244 removed outlier: 3.699A pdb=" N LEU I 239 " --> pdb=" O PHE I 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.915A pdb=" N VAL J 50 " --> pdb=" O SER J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 69 removed outlier: 3.509A pdb=" N GLN J 59 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 97 removed outlier: 3.730A pdb=" N ALA J 88 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.605A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 145 removed outlier: 3.502A pdb=" N ASN J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'J' and resid 182 through 189 removed outlier: 3.744A pdb=" N LEU J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 222 removed outlier: 3.978A pdb=" N LEU J 211 " --> pdb=" O ASP J 207 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR J 217 " --> pdb=" O LYS J 213 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 230 Processing helix chain 'J' and resid 239 through 253 removed outlier: 3.611A pdb=" N ALA J 244 " --> pdb=" O ASN J 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 84 removed outlier: 3.685A pdb=" N VAL K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA K 67 " --> pdb=" O LYS K 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 165 removed outlier: 3.500A pdb=" N GLN K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 81 removed outlier: 3.512A pdb=" N THR L 78 " --> pdb=" O LYS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 159 removed outlier: 3.918A pdb=" N ARG L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA L 155 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR L 157 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS L 158 " --> pdb=" O ARG L 154 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 187 removed outlier: 3.806A pdb=" N LEU L 182 " --> pdb=" O ARG L 178 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 212 removed outlier: 3.810A pdb=" N GLU L 212 " --> pdb=" O ASN L 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 42 removed outlier: 3.849A pdb=" N LYS M 35 " --> pdb=" O THR M 31 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 87 removed outlier: 3.954A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS M 85 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 removed outlier: 3.548A pdb=" N LEU M 112 " --> pdb=" O HIS M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.889A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 166 removed outlier: 3.627A pdb=" N THR M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 21 removed outlier: 3.697A pdb=" N GLU N 20 " --> pdb=" O HIS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 47 Processing helix chain 'N' and resid 61 through 66 removed outlier: 3.943A pdb=" N TYR N 65 " --> pdb=" O PRO N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 3.519A pdb=" N LYS N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 93 removed outlier: 3.679A pdb=" N ARG N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE N 93 " --> pdb=" O TYR N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 122 removed outlier: 3.666A pdb=" N PHE N 109 " --> pdb=" O ASN N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.763A pdb=" N THR N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 179 Processing helix chain 'N' and resid 180 through 193 Processing helix chain 'O' and resid 77 through 88 removed outlier: 3.531A pdb=" N LYS O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 97 removed outlier: 3.554A pdb=" N LYS O 93 " --> pdb=" O ALA O 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER O 97 " --> pdb=" O LYS O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 111 removed outlier: 3.524A pdb=" N ARG O 106 " --> pdb=" O LYS O 102 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU O 107 " --> pdb=" O ILE O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 138 removed outlier: 3.590A pdb=" N TYR O 129 " --> pdb=" O LYS O 125 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA O 134 " --> pdb=" O THR O 130 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA O 136 " --> pdb=" O LYS O 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 12 removed outlier: 3.796A pdb=" N ARG a 12 " --> pdb=" O GLU a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 32 removed outlier: 3.526A pdb=" N LEU a 22 " --> pdb=" O VAL a 18 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG a 24 " --> pdb=" O ARG a 20 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 51 Processing helix chain 'a' and resid 75 through 79 removed outlier: 3.625A pdb=" N GLY a 78 " --> pdb=" O VAL a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 110 Processing helix chain 'a' and resid 139 through 145 Processing helix chain 'a' and resid 148 through 157 Proline residue: a 154 - end of helix Processing helix chain 'a' and resid 158 through 163 removed outlier: 4.019A pdb=" N ARG a 162 " --> pdb=" O HIS a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 173 Processing helix chain 'a' and resid 186 through 194 Processing helix chain 'b' and resid 15 through 29 removed outlier: 3.540A pdb=" N LYS b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 40 Processing helix chain 'b' and resid 46 through 59 Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 92 through 101 removed outlier: 3.618A pdb=" N ARG b 101 " --> pdb=" O ALA b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 123 removed outlier: 3.576A pdb=" N ALA b 123 " --> pdb=" O VAL b 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 120 through 123' Processing helix chain 'b' and resid 124 through 129 Processing helix chain 'b' and resid 138 through 145 Processing helix chain 'b' and resid 149 through 186 removed outlier: 3.606A pdb=" N VAL b 153 " --> pdb=" O TYR b 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS b 159 " --> pdb=" O LYS b 155 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL b 162 " --> pdb=" O ALA b 158 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS b 176 " --> pdb=" O ARG b 172 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 197 removed outlier: 3.677A pdb=" N LEU b 194 " --> pdb=" O VAL b 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 36 removed outlier: 3.535A pdb=" N ILE c 36 " --> pdb=" O THR c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 53 removed outlier: 3.749A pdb=" N LEU c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP c 53 " --> pdb=" O GLU c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 76 removed outlier: 3.770A pdb=" N GLY c 73 " --> pdb=" O THR c 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU c 75 " --> pdb=" O GLN c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 106 removed outlier: 3.563A pdb=" N LEU c 94 " --> pdb=" O PHE c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 110 No H-bonds generated for 'chain 'c' and resid 108 through 110' Processing helix chain 'c' and resid 169 through 183 removed outlier: 3.555A pdb=" N GLY c 174 " --> pdb=" O SER c 170 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG c 175 " --> pdb=" O ARG c 171 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE c 176 " --> pdb=" O GLN c 172 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS c 180 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG c 181 " --> pdb=" O ALA c 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 40 removed outlier: 3.619A pdb=" N LEU d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE d 35 " --> pdb=" O LYS d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 3.863A pdb=" N PHE d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 72 removed outlier: 3.557A pdb=" N LYS d 72 " --> pdb=" O ALA d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 117 Processing helix chain 'd' and resid 123 through 131 Processing helix chain 'd' and resid 148 through 152 Processing helix chain 'e' and resid 4 through 16 removed outlier: 3.618A pdb=" N ARG e 9 " --> pdb=" O ARG e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 22 removed outlier: 3.608A pdb=" N VAL e 22 " --> pdb=" O LYS e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 35 removed outlier: 3.669A pdb=" N GLN e 34 " --> pdb=" O SER e 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA e 35 " --> pdb=" O GLU e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.574A pdb=" N LEU e 44 " --> pdb=" O ALA e 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS e 46 " --> pdb=" O ARG e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 73 Processing helix chain 'e' and resid 77 through 81 removed outlier: 3.574A pdb=" N ARG e 81 " --> pdb=" O TYR e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 Processing helix chain 'e' and resid 90 through 112 removed outlier: 3.583A pdb=" N LYS e 108 " --> pdb=" O ARG e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 130 removed outlier: 3.901A pdb=" N VAL e 122 " --> pdb=" O HIS e 118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS e 125 " --> pdb=" O HIS e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 177 removed outlier: 3.508A pdb=" N ARG e 167 " --> pdb=" O ARG e 163 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL e 177 " --> pdb=" O ARG e 173 " (cutoff:3.500A) Processing helix chain 'e' and resid 178 through 189 removed outlier: 3.733A pdb=" N LEU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP e 188 " --> pdb=" O LEU e 184 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA e 189 " --> pdb=" O LEU e 185 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 49 removed outlier: 3.501A pdb=" N SER f 39 " --> pdb=" O VAL f 35 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS f 47 " --> pdb=" O TYR f 43 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU f 48 " --> pdb=" O PHE f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 115 Processing helix chain 'f' and resid 117 through 119 No H-bonds generated for 'chain 'f' and resid 117 through 119' Processing helix chain 'f' and resid 137 through 142 Processing helix chain 'f' and resid 143 through 145 No H-bonds generated for 'chain 'f' and resid 143 through 145' Processing helix chain 'g' and resid 27 through 32 Processing helix chain 'g' and resid 54 through 58 Processing helix chain 'g' and resid 99 through 123 removed outlier: 3.604A pdb=" N GLN g 103 " --> pdb=" O SER g 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU g 107 " --> pdb=" O GLN g 103 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG g 108 " --> pdb=" O GLU g 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 25 removed outlier: 3.999A pdb=" N ASN h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 3.670A pdb=" N TYR h 33 " --> pdb=" O ASP h 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU h 37 " --> pdb=" O TYR h 33 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE h 41 " --> pdb=" O LEU h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 87 removed outlier: 3.507A pdb=" N LEU h 76 " --> pdb=" O SER h 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS h 82 " --> pdb=" O TYR h 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN h 87 " --> pdb=" O TYR h 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 119 through 126 removed outlier: 3.659A pdb=" N LEU i 125 " --> pdb=" O GLU i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 133 removed outlier: 3.527A pdb=" N ALA i 130 " --> pdb=" O TRP i 126 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN i 132 " --> pdb=" O ARG i 128 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 42 removed outlier: 3.501A pdb=" N ALA j 37 " --> pdb=" O ASN j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 45 through 49 removed outlier: 3.558A pdb=" N ILE j 49 " --> pdb=" O PRO j 46 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 59 removed outlier: 3.649A pdb=" N ARG j 56 " --> pdb=" O THR j 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS j 58 " --> pdb=" O LEU j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 68 removed outlier: 3.767A pdb=" N ALA j 68 " --> pdb=" O THR j 64 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 94 removed outlier: 4.064A pdb=" N GLU j 92 " --> pdb=" O ASP j 88 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 69 through 78 removed outlier: 3.698A pdb=" N LYS k 75 " --> pdb=" O THR k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 Processing helix chain 'k' and resid 131 through 139 removed outlier: 3.640A pdb=" N ILE k 135 " --> pdb=" O ASP k 131 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 21 removed outlier: 3.671A pdb=" N LYS l 17 " --> pdb=" O ARG l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 31 removed outlier: 4.149A pdb=" N VAL l 29 " --> pdb=" O SER l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 43 Processing helix chain 'l' and resid 100 through 102 No H-bonds generated for 'chain 'l' and resid 100 through 102' Processing helix chain 'l' and resid 112 through 123 removed outlier: 3.630A pdb=" N LYS l 116 " --> pdb=" O ASP l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 66 removed outlier: 3.623A pdb=" N ARG m 65 " --> pdb=" O LYS m 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR m 66 " --> pdb=" O VAL m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 123 removed outlier: 3.812A pdb=" N ALA m 110 " --> pdb=" O GLN m 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL m 113 " --> pdb=" O GLU m 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 6 removed outlier: 3.688A pdb=" N PHE n 5 " --> pdb=" O PRO n 2 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 46 Processing helix chain 'n' and resid 78 through 82 removed outlier: 3.541A pdb=" N ILE n 82 " --> pdb=" O TRP n 79 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 92 removed outlier: 4.170A pdb=" N ASP n 88 " --> pdb=" O GLU n 84 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN n 89 " --> pdb=" O ASP n 85 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR n 90 " --> pdb=" O LYS n 86 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS n 92 " --> pdb=" O ASP n 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 104 through 108 Processing helix chain 'n' and resid 131 through 142 removed outlier: 3.588A pdb=" N GLU n 136 " --> pdb=" O LYS n 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS n 137 " --> pdb=" O LEU n 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 17 Processing helix chain 'o' and resid 36 through 58 removed outlier: 3.681A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 21 removed outlier: 4.007A pdb=" N LEU p 16 " --> pdb=" O GLN p 12 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL p 17 " --> pdb=" O LYS p 13 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE p 18 " --> pdb=" O LEU p 14 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS p 19 " --> pdb=" O ALA p 15 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER p 20 " --> pdb=" O LEU p 16 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 37 Processing helix chain 'p' and resid 49 through 64 removed outlier: 3.517A pdb=" N LEU p 62 " --> pdb=" O TYR p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 82 removed outlier: 3.657A pdb=" N THR p 79 " --> pdb=" O ASN p 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 20 Processing helix chain 'q' and resid 24 through 26 No H-bonds generated for 'chain 'q' and resid 24 through 26' Processing helix chain 'q' and resid 27 through 45 Processing helix chain 'q' and resid 52 through 61 Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 54 through 58 Processing helix chain 'r' and resid 78 through 83 Processing helix chain 'r' and resid 84 through 86 No H-bonds generated for 'chain 'r' and resid 84 through 86' Processing helix chain 'r' and resid 101 through 116 removed outlier: 3.527A pdb=" N VAL r 106 " --> pdb=" O ALA r 102 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL r 107 " --> pdb=" O LYS r 103 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 42 Processing helix chain 's' and resid 43 through 45 No H-bonds generated for 'chain 's' and resid 43 through 45' Processing helix chain 't' and resid 66 through 71 removed outlier: 4.054A pdb=" N LYS t 70 " --> pdb=" O SER t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 81 through 112 removed outlier: 3.661A pdb=" N ILE t 100 " --> pdb=" O GLU t 96 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU t 107 " --> pdb=" O LYS t 103 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN t 108 " --> pdb=" O VAL t 104 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU t 110 " --> pdb=" O LYS t 106 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 10 removed outlier: 3.531A pdb=" N ARG u 10 " --> pdb=" O ALA u 6 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 36 removed outlier: 3.785A pdb=" N SER u 19 " --> pdb=" O GLU u 15 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL u 22 " --> pdb=" O ALA u 18 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU u 36 " --> pdb=" O LYS u 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 42 through 70 removed outlier: 4.299A pdb=" N THR u 46 " --> pdb=" O PRO u 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA u 52 " --> pdb=" O ARG u 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA u 65 " --> pdb=" O GLN u 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU u 69 " --> pdb=" O ALA u 65 " (cutoff:3.500A) Processing helix chain 'u' and resid 85 through 91 Processing helix chain 'u' and resid 93 through 99 Processing helix chain 'u' and resid 101 through 111 removed outlier: 3.754A pdb=" N LYS u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS u 107 " --> pdb=" O LYS u 103 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 30 removed outlier: 3.622A pdb=" N LYS v 30 " --> pdb=" O SER v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 49 removed outlier: 3.508A pdb=" N ARG v 45 " --> pdb=" O ARG v 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU v 46 " --> pdb=" O SER v 42 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE v 47 " --> pdb=" O LEU v 43 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 64 removed outlier: 3.633A pdb=" N ILE v 58 " --> pdb=" O GLU v 54 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP v 59 " --> pdb=" O ARG v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 64 through 77 removed outlier: 4.320A pdb=" N ARG v 68 " --> pdb=" O SER v 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA v 69 " --> pdb=" O GLY v 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS v 71 " --> pdb=" O LYS v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 97 removed outlier: 3.614A pdb=" N ALA v 83 " --> pdb=" O SER v 79 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA v 85 " --> pdb=" O THR v 81 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 9 removed outlier: 3.677A pdb=" N GLY w 9 " --> pdb=" O THR w 5 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 56 removed outlier: 3.625A pdb=" N LYS w 54 " --> pdb=" O GLY w 50 " (cutoff:3.500A) Processing helix chain 'w' and resid 66 through 68 No H-bonds generated for 'chain 'w' and resid 66 through 68' Processing helix chain 'w' and resid 69 through 77 Processing helix chain 'x' and resid 7 through 15 removed outlier: 3.635A pdb=" N PHE x 11 " --> pdb=" O ASP x 7 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU x 12 " --> pdb=" O ILE x 8 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU x 13 " --> pdb=" O LYS x 9 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU x 14 " --> pdb=" O GLN x 10 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR x 15 " --> pdb=" O PHE x 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 7 through 15' Processing helix chain 'x' and resid 58 through 68 removed outlier: 3.505A pdb=" N ALA x 62 " --> pdb=" O ASP x 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS x 63 " --> pdb=" O ALA x 59 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS x 64 " --> pdb=" O GLY x 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 20 removed outlier: 3.595A pdb=" N LYS y 12 " --> pdb=" O ARG y 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS y 18 " --> pdb=" O ALA y 14 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 28 Processing helix chain 'z' and resid 79 through 91 removed outlier: 3.595A pdb=" N ALA z 84 " --> pdb=" O PRO z 80 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR z 89 " --> pdb=" O LEU z 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 48 Processing helix chain 'R' and resid 8 through 15 removed outlier: 3.515A pdb=" N THR R 11 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS R 13 " --> pdb=" O ILE R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 35 removed outlier: 3.850A pdb=" N GLN R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 91 removed outlier: 3.532A pdb=" N SER R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 removed outlier: 4.198A pdb=" N UNK S 11 " --> pdb=" O UNK S 7 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N UNK S 12 " --> pdb=" O UNK S 8 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N UNK S 13 " --> pdb=" O UNK S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 71 removed outlier: 3.529A pdb=" N UNK S 69 " --> pdb=" O UNK S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 86 Processing helix chain 'S' and resid 90 through 99 removed outlier: 3.785A pdb=" N UNK S 99 " --> pdb=" O UNK S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 116 Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 138 through 147 removed outlier: 3.617A pdb=" N UNK S 142 " --> pdb=" O UNK S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 185 removed outlier: 3.505A pdb=" N UNK S 173 " --> pdb=" O UNK S 169 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N UNK S 174 " --> pdb=" O UNK S 170 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N UNK S 182 " --> pdb=" O UNK S 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 182 removed outlier: 3.943A pdb=" N LEU V 172 " --> pdb=" O LYS V 168 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS V 180 " --> pdb=" O GLN V 176 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS V 181 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 218 removed outlier: 3.902A pdb=" N ALA V 207 " --> pdb=" O GLN V 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS V 209 " --> pdb=" O ASN V 205 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET V 210 " --> pdb=" O HIS V 206 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL V 217 " --> pdb=" O PHE V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 267 Processing helix chain 'V' and resid 297 through 303 removed outlier: 3.690A pdb=" N ARG V 303 " --> pdb=" O SER V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 315 Processing helix chain 'V' and resid 343 through 348 removed outlier: 4.299A pdb=" N GLY V 347 " --> pdb=" O THR V 343 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL V 348 " --> pdb=" O SER V 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 343 through 348' Processing helix chain 'V' and resid 375 through 377 No H-bonds generated for 'chain 'V' and resid 375 through 377' Processing helix chain 'V' and resid 381 through 386 Processing sheet with id=AA1, first strand: chain 'D' and resid 71 through 77 removed outlier: 6.634A pdb=" N LEU D 58 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE D 48 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS D 60 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG D 64 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG D 42 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 41 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 101 through 103 removed outlier: 3.689A pdb=" N LEU D 102 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG D 147 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N HIS D 139 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS D 145 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'E' and resid 356 through 359 removed outlier: 6.704A pdb=" N VAL E 57 " --> pdb=" O LYS E 357 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE E 359 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR E 55 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE E 335 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL E 220 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 215 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE E 282 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS E 325 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG E 70 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP E 59 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 72 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL E 57 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 74 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR E 55 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 76 " --> pdb=" O MET E 53 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET E 53 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL E 78 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 98 through 106 removed outlier: 5.228A pdb=" N LEU E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR E 95 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER E 101 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 93 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR E 103 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 161 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL E 89 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG E 159 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY E 91 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL E 157 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 98 through 106 removed outlier: 5.228A pdb=" N LEU E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR E 95 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER E 101 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 93 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR E 103 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 225 through 227 removed outlier: 3.691A pdb=" N GLY E 225 " --> pdb=" O ARG E 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AB1, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.490A pdb=" N LEU F 206 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 73 through 79 removed outlier: 5.422A pdb=" N VAL G 74 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER G 66 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA G 76 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 59 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 53 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.670A pdb=" N ARG H 77 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER H 66 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR H 54 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL H 39 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 75 through 77 Processing sheet with id=AB5, first strand: chain 'I' and resid 205 through 206 removed outlier: 4.138A pdb=" N SER I 113 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY I 137 " --> pdb=" O PHE I 85 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL I 134 " --> pdb=" O GLY I 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AB7, first strand: chain 'J' and resid 133 through 134 removed outlier: 6.441A pdb=" N VAL J 151 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL J 180 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE J 153 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 3 through 10 removed outlier: 6.924A pdb=" N ILE K 4 " --> pdb=" O ASN K 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 17 through 21 removed outlier: 3.635A pdb=" N LYS K 21 " --> pdb=" O ILE K 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 133 through 136 removed outlier: 7.073A pdb=" N LYS K 87 " --> pdb=" O LYS K 184 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS K 184 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS K 89 " --> pdb=" O SER K 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 100 through 104 Processing sheet with id=AC3, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.284A pdb=" N ILE L 134 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER L 54 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE L 136 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 95 through 99 removed outlier: 6.787A pdb=" N HIS L 95 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU L 125 " --> pdb=" O HIS L 95 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU L 97 " --> pdb=" O HIS L 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 190 through 192 Processing sheet with id=AC6, first strand: chain 'M' and resid 46 through 48 removed outlier: 3.638A pdb=" N VAL M 67 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE M 14 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN M 132 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS M 16 " --> pdb=" O VAL M 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 23 through 24 removed outlier: 6.353A pdb=" N LYS N 23 " --> pdb=" O LEU a 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N' and resid 57 through 59 Processing sheet with id=AC9, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AD1, first strand: chain 'N' and resid 156 through 157 removed outlier: 6.550A pdb=" N VAL n 125 " --> pdb=" O GLU n 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 14 through 15 removed outlier: 3.674A pdb=" N PHE f 150 " --> pdb=" O VAL O 15 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 53 through 59 removed outlier: 4.846A pdb=" N GLY O 48 " --> pdb=" O PRO O 54 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LYS O 43 " --> pdb=" O ILE O 38 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE O 38 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a' and resid 36 through 39 removed outlier: 4.667A pdb=" N ILE a 61 " --> pdb=" O ALA a 39 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU a 131 " --> pdb=" O TRP a 120 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TRP a 120 " --> pdb=" O GLU a 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE a 133 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER a 118 " --> pdb=" O ILE a 133 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL a 135 " --> pdb=" O LEU a 116 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU a 116 " --> pdb=" O VAL a 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 6 through 10 Processing sheet with id=AD6, first strand: chain 'b' and resid 42 through 44 Processing sheet with id=AD7, first strand: chain 'c' and resid 14 through 22 removed outlier: 3.633A pdb=" N TYR c 21 " --> pdb=" O SER c 144 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER c 144 " --> pdb=" O TYR c 21 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS c 116 " --> pdb=" O VAL c 149 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR c 151 " --> pdb=" O VAL c 114 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL c 114 " --> pdb=" O THR c 151 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'd' and resid 62 through 63 removed outlier: 6.564A pdb=" N VAL d 81 " --> pdb=" O ALA d 102 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU d 104 " --> pdb=" O VAL d 81 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N VAL d 83 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE d 106 " --> pdb=" O VAL d 83 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N GLY d 85 " --> pdb=" O PHE d 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL d 101 " --> pdb=" O ILE d 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 62 through 63 removed outlier: 3.502A pdb=" N LEU d 138 " --> pdb=" O THR d 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 23 through 24 removed outlier: 3.543A pdb=" N VAL e 51 " --> pdb=" O TRP e 23 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 58 through 63 removed outlier: 6.691A pdb=" N ILE f 10 " --> pdb=" O VAL f 59 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE f 61 " --> pdb=" O GLN f 8 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN f 8 " --> pdb=" O ILE f 61 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN f 63 " --> pdb=" O GLU f 6 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU f 6 " --> pdb=" O GLN f 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 87 through 96 removed outlier: 3.645A pdb=" N LYS f 125 " --> pdb=" O TRP f 78 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG f 80 " --> pdb=" O ILE f 123 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE f 123 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP f 82 " --> pdb=" O ILE f 121 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE f 121 " --> pdb=" O ASP f 82 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'g' and resid 83 through 92 removed outlier: 3.530A pdb=" N ARG g 83 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN g 66 " --> pdb=" O GLY g 73 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE g 75 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL g 64 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ASN g 77 " --> pdb=" O GLY g 62 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N GLY g 62 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'h' and resid 55 through 58 removed outlier: 3.583A pdb=" N THR h 55 " --> pdb=" O VAL h 66 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL h 66 " --> pdb=" O THR h 55 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR h 103 " --> pdb=" O THR h 14 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR h 16 " --> pdb=" O TYR h 103 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU h 105 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASP h 18 " --> pdb=" O LEU h 105 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'i' and resid 108 through 109 removed outlier: 3.751A pdb=" N GLU i 108 " --> pdb=" O ASN i 104 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA i 99 " --> pdb=" O VAL i 79 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET i 57 " --> pdb=" O VAL i 39 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL i 39 " --> pdb=" O MET i 57 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET i 59 " --> pdb=" O ILE i 37 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN i 33 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY i 65 " --> pdb=" O ALA i 31 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA i 31 " --> pdb=" O GLY i 65 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG i 32 " --> pdb=" O CYS i 25 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY i 100 " --> pdb=" O ILE i 22 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN i 24 " --> pdb=" O GLY i 100 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE i 102 " --> pdb=" O ASN i 24 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'i' and resid 85 through 86 removed outlier: 6.560A pdb=" N PHE i 92 " --> pdb=" O LEU j 20 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL j 22 " --> pdb=" O PHE i 92 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR i 94 " --> pdb=" O VAL j 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 4 through 5 removed outlier: 3.821A pdb=" N GLU j 4 " --> pdb=" O ILE j 13 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'k' and resid 63 through 66 removed outlier: 3.552A pdb=" N GLN k 65 " --> pdb=" O GLN k 85 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS k 120 " --> pdb=" O VAL k 86 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS k 109 " --> pdb=" O ARG k 125 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'l' and resid 32 through 34 Processing sheet with id=AF3, first strand: chain 'l' and resid 96 through 99 removed outlier: 5.203A pdb=" N ILE l 97 " --> pdb=" O VAL l 82 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL l 82 " --> pdb=" O ILE l 97 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA l 79 " --> pdb=" O VAL l 73 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL l 73 " --> pdb=" O ALA l 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN l 81 " --> pdb=" O SER l 71 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS l 69 " --> pdb=" O ASP l 83 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL l 85 " --> pdb=" O GLU l 67 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N GLU l 67 " --> pdb=" O VAL l 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU l 55 " --> pdb=" O THR l 107 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'm' and resid 73 through 76 removed outlier: 3.759A pdb=" N LYS m 27 " --> pdb=" O LEU m 42 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS m 9 " --> pdb=" O ILE m 25 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL m 10 " --> pdb=" O THR m 83 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 46 through 48 removed outlier: 6.863A pdb=" N LYS m 69 " --> pdb=" O GLU m 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'n' and resid 72 through 74 removed outlier: 5.871A pdb=" N LEU n 73 " --> pdb=" O LEU n 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'p' and resid 24 through 25 removed outlier: 3.691A pdb=" N LEU p 41 " --> pdb=" O ILE p 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE p 42 " --> pdb=" O LYS p 66 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'q' and resid 13 through 15 removed outlier: 3.635A pdb=" N LEU q 71 " --> pdb=" O ILE q 14 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'q' and resid 13 through 15 removed outlier: 3.635A pdb=" N LEU q 71 " --> pdb=" O ILE q 14 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'r' and resid 72 through 73 removed outlier: 6.065A pdb=" N LYS r 72 " --> pdb=" O ALA r 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 's' and resid 11 through 18 removed outlier: 8.671A pdb=" N GLY s 11 " --> pdb=" O ILE s 30 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE s 30 " --> pdb=" O GLY s 11 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N HIS s 13 " --> pdb=" O SER s 28 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N SER s 28 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 11.557A pdb=" N SER s 15 " --> pdb=" O ASN s 26 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ASN s 26 " --> pdb=" O SER s 15 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN s 17 " --> pdb=" O ASN s 24 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 't' and resid 19 through 24 removed outlier: 4.711A pdb=" N LYS t 19 " --> pdb=" O VAL t 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL t 35 " --> pdb=" O LYS t 19 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'w' and resid 16 through 17 Processing sheet with id=AG5, first strand: chain 'x' and resid 51 through 56 removed outlier: 5.209A pdb=" N THR x 22 " --> pdb=" O ARG x 46 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'z' and resid 102 through 103 Processing sheet with id=AG7, first strand: chain 'Q' and resid 3 through 4 Processing sheet with id=AG8, first strand: chain 'Q' and resid 7 through 12 Processing sheet with id=AG9, first strand: chain 'Q' and resid 26 through 27 removed outlier: 4.045A pdb=" N VAL Q 68 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 47 through 49 Processing sheet with id=AH2, first strand: chain 'S' and resid 199 through 200 removed outlier: 4.023A pdb=" N UNK S 200 " --> pdb=" O UNK S 208 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N UNK S 208 " --> pdb=" O UNK S 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'V' and resid 187 through 193 removed outlier: 3.811A pdb=" N SER V 189 " --> pdb=" O PHE V 200 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR V 158 " --> pdb=" O TYR V 244 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL V 246 " --> pdb=" O THR V 158 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN V 160 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE V 248 " --> pdb=" O GLN V 160 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG V 162 " --> pdb=" O ILE V 248 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 187 through 193 removed outlier: 3.811A pdb=" N SER V 189 " --> pdb=" O PHE V 200 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR V 158 " --> pdb=" O TYR V 244 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL V 246 " --> pdb=" O THR V 158 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN V 160 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE V 248 " --> pdb=" O GLN V 160 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG V 162 " --> pdb=" O ILE V 248 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 256 through 258 Processing sheet with id=AH6, first strand: chain 'V' and resid 353 through 357 removed outlier: 6.197A pdb=" N ASP V 337 " --> pdb=" O VAL V 323 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL V 323 " --> pdb=" O ASP V 337 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR V 339 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET V 370 " --> pdb=" O VAL V 398 " (cutoff:3.500A) 1765 hydrogen bonds defined for protein. 4980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2490 hydrogen bonds 4092 hydrogen bond angles 0 basepair planarities 1023 basepair parallelities 1654 stacking parallelities Total time for adding SS restraints: 194.51 Time building geometry restraints manager: 47.09 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: 16153 1.33 - 1.45: 55289 1.45 - 1.57: 57746 1.57 - 1.69: 6963 1.69 - 1.81: 157 Bond restraints: 136308 Sorted by residual: bond pdb=" CA VAL O 53 " pdb=" CB VAL O 53 " ideal model delta sigma weight residual 1.540 1.572 -0.032 7.70e-03 1.69e+04 1.74e+01 bond pdb=" N TYR a 94 " pdb=" CA TYR a 94 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.21e+01 bond pdb=" CA PRO b 109 " pdb=" C PRO b 109 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.16e+01 bond pdb=" N ALA V 157 " pdb=" CA ALA V 157 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.13e-02 7.83e+03 1.14e+01 bond pdb=" CA VAL M 130 " pdb=" CB VAL M 130 " ideal model delta sigma weight residual 1.539 1.577 -0.038 1.18e-02 7.18e+03 1.03e+01 ... (remaining 136303 not shown) Histogram of bond angle deviations from ideal: 98.46 - 110.31: 59216 110.31 - 122.16: 108896 122.16 - 134.00: 32995 134.00 - 145.85: 6 145.85 - 157.70: 1 Bond angle restraints: 201114 Sorted by residual: angle pdb=" C GLY V 386 " pdb=" N LEU V 387 " pdb=" CA LEU V 387 " ideal model delta sigma weight residual 122.16 157.70 -35.54 1.32e+00 5.74e-01 7.25e+02 angle pdb=" O GLY V 386 " pdb=" C GLY V 386 " pdb=" N LEU V 387 " ideal model delta sigma weight residual 122.70 101.68 21.02 1.30e+00 5.92e-01 2.62e+02 angle pdb=" C ARG j 80 " pdb=" N PRO j 81 " pdb=" CA PRO j 81 " ideal model delta sigma weight residual 119.84 133.20 -13.36 1.25e+00 6.40e-01 1.14e+02 angle pdb=" CA GLY V 386 " pdb=" C GLY V 386 " pdb=" N LEU V 387 " ideal model delta sigma weight residual 116.69 138.20 -21.51 2.04e+00 2.40e-01 1.11e+02 angle pdb=" O3' G A1307 " pdb=" C3' G A1307 " pdb=" C2' G A1307 " ideal model delta sigma weight residual 109.50 125.15 -15.65 1.50e+00 4.44e-01 1.09e+02 ... (remaining 201109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 70946 35.93 - 71.86: 3157 71.86 - 107.79: 213 107.79 - 143.73: 27 143.73 - 179.66: 60 Dihedral angle restraints: 74403 sinusoidal: 55138 harmonic: 19265 Sorted by residual: dihedral pdb=" C5' G A3353 " pdb=" C4' G A3353 " pdb=" C3' G A3353 " pdb=" O3' G A3353 " ideal model delta sinusoidal sigma weight residual 147.00 82.17 64.83 1 8.00e+00 1.56e-02 8.62e+01 dihedral pdb=" O4' U A2846 " pdb=" C1' U A2846 " pdb=" N1 U A2846 " pdb=" C2 U A2846 " ideal model delta sinusoidal sigma weight residual 200.00 23.80 176.20 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A3214 " pdb=" C1' U A3214 " pdb=" N1 U A3214 " pdb=" C2 U A3214 " ideal model delta sinusoidal sigma weight residual -160.00 12.67 -172.67 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 74400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 21214 0.145 - 0.290: 4059 0.290 - 0.435: 18 0.435 - 0.581: 14 0.581 - 0.726: 10 Chirality restraints: 25315 Sorted by residual: chirality pdb=" C3' U A1329 " pdb=" C4' U A1329 " pdb=" O3' U A1329 " pdb=" C2' U A1329 " both_signs ideal model delta sigma weight residual False -2.74 -2.02 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C3' G A1097 " pdb=" C4' G A1097 " pdb=" O3' G A1097 " pdb=" C2' G A1097 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C3' G A1307 " pdb=" C4' G A1307 " pdb=" O3' G A1307 " pdb=" C2' G A1307 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 25312 not shown) Planarity restraints: 12557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A2434 " 0.028 2.00e-02 2.50e+03 2.51e-02 1.41e+01 pdb=" N1 U A2434 " -0.025 2.00e-02 2.50e+03 pdb=" C2 U A2434 " -0.014 2.00e-02 2.50e+03 pdb=" O2 U A2434 " -0.017 2.00e-02 2.50e+03 pdb=" N3 U A2434 " 0.051 2.00e-02 2.50e+03 pdb=" C4 U A2434 " -0.033 2.00e-02 2.50e+03 pdb=" O4 U A2434 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U A2434 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U A2434 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A2558 " 0.042 2.00e-02 2.50e+03 2.41e-02 1.31e+01 pdb=" N1 U A2558 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U A2558 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U A2558 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U A2558 " 0.011 2.00e-02 2.50e+03 pdb=" C4 U A2558 " -0.029 2.00e-02 2.50e+03 pdb=" O4 U A2558 " 0.037 2.00e-02 2.50e+03 pdb=" C5 U A2558 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U A2558 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 30 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO J 31 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO J 31 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 31 " 0.041 5.00e-02 4.00e+02 ... (remaining 12554 not shown) Histogram of nonbonded interaction distances: 1.23 - 2.01: 49 2.01 - 2.79: 20362 2.79 - 3.58: 196945 3.58 - 4.36: 437992 4.36 - 5.14: 624017 Nonbonded interactions: 1279365 Sorted by model distance: nonbonded pdb=" CE MET L 102 " pdb=" CB THR V 152 " model vdw 1.229 3.890 nonbonded pdb=" N6 A A2462 " pdb=" N3 A A2494 " model vdw 1.317 2.600 nonbonded pdb=" CD2 LEU V 291 " pdb=" CG2 VAL V 334 " model vdw 1.518 3.880 nonbonded pdb=" CE MET L 102 " pdb=" CG2 THR V 152 " model vdw 1.573 3.880 nonbonded pdb=" O4 U A2434 " pdb=" N1 A A2595 " model vdw 1.603 2.496 ... (remaining 1279360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 15.140 Check model and map are aligned: 1.340 Set scattering table: 0.810 Process input model: 412.280 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 436.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 0.049 136308 Z= 0.406 Angle : 1.050 35.538 201114 Z= 0.699 Chirality : 0.094 0.726 25315 Planarity : 0.005 0.086 12557 Dihedral : 16.986 179.658 61963 Min Nonbonded Distance : 1.229 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.54 % Favored : 90.57 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.08), residues: 6355 helix: -2.25 (0.08), residues: 1962 sheet: -2.46 (0.16), residues: 748 loop : -2.48 (0.08), residues: 3645 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2976 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 2680 time to evaluate : 6.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 296 outliers final: 35 residues processed: 2813 average time/residue: 1.2193 time to fit residues: 5638.0196 Evaluate side-chains 1513 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1478 time to evaluate : 7.350 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.9876 time to fit residues: 69.6108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 838 optimal weight: 6.9990 chunk 752 optimal weight: 0.0040 chunk 417 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 507 optimal weight: 8.9990 chunk 402 optimal weight: 20.0000 chunk 778 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 473 optimal weight: 2.9990 chunk 579 optimal weight: 20.0000 chunk 901 optimal weight: 3.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS D 86 GLN D 215 ASN D 250 GLN E 165 GLN E 173 GLN E 243 HIS E 273 HIS ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN F 296 GLN F 307 GLN F 311 HIS ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 ASN G 63 GLN G 81 HIS G 274 GLN I 37 ASN I 52 GLN I 80 GLN I 146 GLN I 209 ASN I 225 GLN J 77 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 ASN K 5 GLN K 157 ASN ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 GLN L 12 GLN L 14 ASN M 62 ASN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN N 137 GLN O 119 GLN ** a 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 HIS a 90 ASN a 182 ASN a 195 ASN b 50 ASN c 37 ASN c 55 GLN c 72 GLN d 5 HIS d 73 GLN e 118 HIS ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS i 4 ASN i 28 ASN i 81 GLN i 98 ASN l 98 ASN l 110 HIS m 36 HIS m 78 ASN ** m 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN o 10 HIS q 87 ASN ** t 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 34 HIS t 52 GLN u 61 GLN w 30 GLN x 28 ASN Q 22 GLN Q 27 GLN Q 38 GLN Q 47 GLN Q 82 GLN R 33 GLN V 160 GLN ** V 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 234 HIS ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.164 136308 Z= 0.272 Angle : 0.709 14.500 201114 Z= 0.371 Chirality : 0.042 0.347 25315 Planarity : 0.006 0.091 12557 Dihedral : 15.762 179.411 49167 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.11 % Favored : 93.03 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.09), residues: 6355 helix: -0.61 (0.10), residues: 2068 sheet: -1.81 (0.15), residues: 855 loop : -2.26 (0.09), residues: 3432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1733 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1718 time to evaluate : 6.165 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 outliers start: 15 outliers final: 4 residues processed: 1726 average time/residue: 1.1627 time to fit residues: 3436.6107 Evaluate side-chains 1254 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1250 time to evaluate : 6.127 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8729 time to fit residues: 13.8180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 501 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 750 optimal weight: 0.0770 chunk 614 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 903 optimal weight: 8.9990 chunk 975 optimal weight: 7.9990 chunk 804 optimal weight: 0.0050 chunk 895 optimal weight: 0.8980 chunk 307 optimal weight: 30.0000 chunk 724 optimal weight: 10.0000 overall best weight: 1.9956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN E 11 HIS E 173 GLN E 319 ASN F 311 HIS ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN J 28 HIS J 95 ASN J 138 HIS J 240 ASN ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN N 102 GLN a 90 ASN b 31 GLN c 50 GLN c 72 GLN ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 154 HIS f 157 GLN g 77 ASN g 98 HIS j 59 HIS ** l 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 110 HIS ** n 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 HIS q 57 GLN r 52 GLN r 104 ASN t 3 GLN t 18 ASN ** t 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN V 181 HIS V 332 ASN ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 136308 Z= 0.171 Angle : 0.586 12.597 201114 Z= 0.310 Chirality : 0.036 0.352 25315 Planarity : 0.005 0.124 12557 Dihedral : 15.329 179.960 49167 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.96 % Favored : 93.30 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.10), residues: 6355 helix: 0.12 (0.11), residues: 2048 sheet: -1.14 (0.17), residues: 832 loop : -1.98 (0.09), residues: 3475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1675 time to evaluate : 6.195 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 outliers start: 2 outliers final: 0 residues processed: 1677 average time/residue: 1.1168 time to fit residues: 3202.5742 Evaluate side-chains 1221 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1221 time to evaluate : 6.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 892 optimal weight: 2.9990 chunk 679 optimal weight: 10.0000 chunk 468 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 431 optimal weight: 4.9990 chunk 606 optimal weight: 8.9990 chunk 906 optimal weight: 0.9980 chunk 959 optimal weight: 20.0000 chunk 473 optimal weight: 0.3980 chunk 859 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN D 215 ASN E 182 GLN F 45 ASN F 307 GLN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 90 HIS H 172 HIS I 37 ASN I 104 GLN J 28 HIS J 240 ASN K 5 GLN K 8 GLN K 64 HIS K 157 ASN ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS a 87 GLN a 195 ASN b 55 HIS c 54 HIS c 72 GLN ** c 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN e 118 HIS f 46 GLN f 49 HIS ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 ASN g 26 HIS g 98 HIS j 59 HIS ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 HIS p 47 ASN t 3 GLN ** t 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 GLN ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 136308 Z= 0.205 Angle : 0.602 12.893 201114 Z= 0.315 Chirality : 0.036 0.317 25315 Planarity : 0.005 0.086 12557 Dihedral : 15.269 179.901 49167 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.09 % Favored : 93.20 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.10), residues: 6355 helix: 0.40 (0.11), residues: 2044 sheet: -0.96 (0.17), residues: 853 loop : -1.88 (0.09), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1558 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1556 time to evaluate : 6.203 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 outliers start: 2 outliers final: 0 residues processed: 1557 average time/residue: 1.1190 time to fit residues: 2999.6024 Evaluate side-chains 1177 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1177 time to evaluate : 5.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 799 optimal weight: 7.9990 chunk 544 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 714 optimal weight: 40.0000 chunk 396 optimal weight: 9.9990 chunk 819 optimal weight: 10.0000 chunk 663 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 490 optimal weight: 6.9990 chunk 861 optimal weight: 0.0270 chunk 242 optimal weight: 10.0000 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN F 114 ASN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN I 112 ASN J 38 GLN J 77 GLN K 64 HIS ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 GLN ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 195 ASN b 55 HIS b 90 HIS c 72 GLN d 45 ASN ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 ASN f 122 HIS f 142 GLN g 98 HIS h 101 ASN j 59 HIS n 25 HIS ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 HIS s 17 GLN t 18 ASN v 100 HIS y 20 ASN y 33 ASN Q 27 GLN ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 231 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 136308 Z= 0.341 Angle : 0.742 13.647 201114 Z= 0.381 Chirality : 0.042 0.342 25315 Planarity : 0.006 0.098 12557 Dihedral : 15.744 179.778 49167 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.54 % Favored : 91.72 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.10), residues: 6355 helix: 0.09 (0.11), residues: 2076 sheet: -0.83 (0.17), residues: 847 loop : -1.98 (0.10), residues: 3432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1427 time to evaluate : 6.319 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 outliers start: 2 outliers final: 0 residues processed: 1427 average time/residue: 1.1720 time to fit residues: 2895.6531 Evaluate side-chains 1110 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1110 time to evaluate : 5.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 322 optimal weight: 10.0000 chunk 864 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 563 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 960 optimal weight: 40.0000 chunk 797 optimal weight: 0.0060 chunk 444 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 504 optimal weight: 3.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN E 273 HIS F 316 ASN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN I 104 GLN J 77 GLN K 8 GLN K 64 HIS ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 GLN ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN M 68 HIS ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 GLN a 195 ASN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN d 73 GLN ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 49 HIS f 89 ASN f 122 HIS g 98 HIS i 4 ASN ** m 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN r 13 HIS t 52 GLN ** x 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN R 32 GLN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 136308 Z= 0.283 Angle : 0.685 13.512 201114 Z= 0.354 Chirality : 0.040 0.302 25315 Planarity : 0.005 0.082 12557 Dihedral : 15.789 179.994 49167 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.32 % Favored : 91.99 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.10), residues: 6355 helix: 0.09 (0.11), residues: 2077 sheet: -0.78 (0.17), residues: 842 loop : -1.98 (0.10), residues: 3436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1434 time to evaluate : 6.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1436 average time/residue: 1.1219 time to fit residues: 2787.9153 Evaluate side-chains 1113 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1113 time to evaluate : 6.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 926 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 547 optimal weight: 0.3980 chunk 701 optimal weight: 0.1980 chunk 543 optimal weight: 6.9990 chunk 808 optimal weight: 7.9990 chunk 536 optimal weight: 3.9990 chunk 957 optimal weight: 30.0000 chunk 598 optimal weight: 0.8980 chunk 583 optimal weight: 8.9990 chunk 441 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 GLN D 215 ASN E 139 GLN E 273 HIS ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 GLN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN J 77 GLN K 8 GLN K 162 GLN K 163 GLN L 51 HIS ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN O 105 GLN a 87 GLN ** a 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 ASN a 194 GLN ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN f 46 GLN ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 ASN g 26 HIS g 54 HIS g 127 GLN ** l 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN o 12 GLN q 17 HIS t 34 HIS y 20 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN ** V 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 136308 Z= 0.143 Angle : 0.572 12.603 201114 Z= 0.299 Chirality : 0.034 0.284 25315 Planarity : 0.004 0.076 12557 Dihedral : 15.407 179.741 49167 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.12 % Favored : 93.23 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.10), residues: 6355 helix: 0.45 (0.11), residues: 2069 sheet: -0.64 (0.18), residues: 833 loop : -1.77 (0.10), residues: 3453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1492 time to evaluate : 6.236 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 outliers start: 1 outliers final: 0 residues processed: 1492 average time/residue: 1.1239 time to fit residues: 2897.4486 Evaluate side-chains 1143 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1143 time to evaluate : 6.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 592 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 571 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 608 optimal weight: 10.0000 chunk 652 optimal weight: 9.9990 chunk 473 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 752 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN E 173 GLN E 177 HIS E 273 HIS ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN I 172 ASN J 77 GLN K 5 GLN K 162 GLN ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 195 ASN b 55 HIS ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 ASN ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS ** l 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 127 ASN ** m 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 136308 Z= 0.253 Angle : 0.652 13.316 201114 Z= 0.336 Chirality : 0.038 0.297 25315 Planarity : 0.005 0.087 12557 Dihedral : 15.582 179.963 49167 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.65 % Favored : 91.71 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 6355 helix: 0.32 (0.11), residues: 2088 sheet: -0.67 (0.17), residues: 851 loop : -1.85 (0.10), residues: 3416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1351 time to evaluate : 6.161 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 outliers start: 1 outliers final: 0 residues processed: 1351 average time/residue: 1.1300 time to fit residues: 2665.8000 Evaluate side-chains 1100 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1100 time to evaluate : 6.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 870 optimal weight: 0.0870 chunk 916 optimal weight: 9.9990 chunk 836 optimal weight: 6.9990 chunk 891 optimal weight: 0.7980 chunk 536 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 700 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 805 optimal weight: 5.9990 chunk 843 optimal weight: 7.9990 chunk 888 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN I 104 GLN J 77 GLN K 8 GLN ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 ASN a 194 GLN b 55 HIS ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 ASN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 154 HIS g 98 HIS i 24 ASN ** j 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 98 ASN m 36 HIS m 127 ASN ** m 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 HIS ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN y 20 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 GLN R 32 GLN V 181 HIS ** V 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 136308 Z= 0.191 Angle : 0.598 13.193 201114 Z= 0.311 Chirality : 0.036 0.291 25315 Planarity : 0.005 0.076 12557 Dihedral : 15.502 179.985 49167 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.92 % Favored : 92.42 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.32 (0.10), residues: 6355 helix: 0.41 (0.11), residues: 2084 sheet: -0.60 (0.17), residues: 845 loop : -1.82 (0.10), residues: 3426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1364 time to evaluate : 6.194 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 outliers start: 1 outliers final: 0 residues processed: 1364 average time/residue: 1.1181 time to fit residues: 2657.7027 Evaluate side-chains 1116 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1116 time to evaluate : 6.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 585 optimal weight: 0.0270 chunk 943 optimal weight: 5.9990 chunk 575 optimal weight: 0.4980 chunk 447 optimal weight: 5.9990 chunk 655 optimal weight: 0.0030 chunk 989 optimal weight: 0.0670 chunk 910 optimal weight: 8.9990 chunk 787 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 608 optimal weight: 3.9990 chunk 483 optimal weight: 0.0010 overall best weight: 0.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 215 ASN E 139 GLN F 110 ASN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS J 77 GLN K 8 GLN K 51 GLN K 96 HIS K 162 GLN N 102 GLN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 ASN a 182 ASN d 5 HIS ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 HIS f 89 ASN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN j 32 GLN k 80 ASN l 98 ASN m 128 GLN n 25 HIS o 10 HIS o 12 GLN q 17 HIS u 59 ASN w 48 ASN y 20 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 117 HIS R 32 GLN ** V 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.148 136308 Z= 0.136 Angle : 0.548 12.215 201114 Z= 0.283 Chirality : 0.032 0.261 25315 Planarity : 0.004 0.082 12557 Dihedral : 15.181 179.942 49167 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.59 % Favored : 93.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.13 (0.10), residues: 6355 helix: 0.56 (0.11), residues: 2063 sheet: -0.51 (0.17), residues: 825 loop : -1.68 (0.10), residues: 3467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12710 Ramachandran restraints generated. 6355 Oldfield, 0 Emsley, 6355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1427 time to evaluate : 6.161 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 outliers start: 0 outliers final: 0 residues processed: 1427 average time/residue: 1.1414 time to fit residues: 2851.2992 Evaluate side-chains 1123 residues out of total 5387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1123 time to evaluate : 6.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 993 random chunks: chunk 625 optimal weight: 0.8980 chunk 839 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 726 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 789 optimal weight: 0.9980 chunk 330 optimal weight: 10.0000 chunk 810 optimal weight: 0.0040 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN H 172 HIS I 104 GLN I 172 ASN J 77 GLN ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 162 GLN N 102 GLN N 103 ASN O 41 GLN a 87 GLN ** a 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 ASN a 195 ASN ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 HIS i 24 ASN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 127 ASN n 25 HIS ** n 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN t 3 GLN y 11 GLN y 20 ASN ** z 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Q 47 GLN R 32 GLN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099741 restraints weight = 357075.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102034 restraints weight = 166843.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102998 restraints weight = 100283.867| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 136308 Z= 0.151 Angle : 0.548 13.682 201114 Z= 0.284 Chirality : 0.033 0.264 25315 Planarity : 0.004 0.066 12557 Dihedral : 15.159 179.847 49167 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.45 % Favored : 93.01 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.09 (0.10), residues: 6355 helix: 0.61 (0.12), residues: 2065 sheet: -0.51 (0.17), residues: 855 loop : -1.66 (0.10), residues: 3435 =============================================================================== Job complete usr+sys time: 38788.64 seconds wall clock time: 675 minutes 17.50 seconds (40517.50 seconds total)