Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 02:33:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t62_8362/04_2023/5t62_8362_updated.pdb" } resolution = 3.3 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= 0.015 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 2 8.98 5 P 3486 5.49 5 Mg 160 5.21 5 S 118 5.16 5 C 69370 2.51 5 N 24245 2.21 5 O 34385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 209": "OD1" <-> "OD2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 130": "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 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 ASP 177": "OD1" <-> "OD2" 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 GLU 294": "OE1" <-> "OE2" 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 PHE 55": "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 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 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 ASP 142": "OD1" <-> "OD2" 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 GLU 131": "OE1" <-> "OE2" 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 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 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" 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 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 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 ASP 153": "OD1" <-> "OD2" 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 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 103": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 130": "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 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "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 PHE 95": "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 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 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 TYR 52": "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 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 94": "OE1" <-> "OE2" Residue "r PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 58": "OE1" <-> "OE2" Residue "s PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 103": "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 60": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 53": "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 "x PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 52": "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 "R TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "R ASP 38": "OD1" <-> "OD2" Residue "R PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "V PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V ARG 63": "NH1" <-> "NH2" Residue "V PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 75": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 106": "OE1" <-> "OE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ARG 111": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 133": "OE1" <-> "OE2" Residue "V GLU 135": "OE1" <-> "OE2" Residue "V ASP 145": "OD1" <-> "OD2" Residue "V ARG 148": "NH1" <-> "NH2" 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" Residue "W PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 183": "NH1" <-> "NH2" Residue "W ARG 197": "NH1" <-> "NH2" Residue "W ARG 208": "NH1" <-> "NH2" Residue "W ARG 214": "NH1" <-> "NH2" Residue "W ARG 220": "NH1" <-> "NH2" Residue "W GLU 224": "OE1" <-> "OE2" Residue "W ASP 226": "OD1" <-> "OD2" Residue "W ARG 246": "NH1" <-> "NH2" Residue "W PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 381": "OD1" <-> "OD2" Residue "W PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 402": "OE1" <-> "OE2" Residue "W ASP 412": "OD1" <-> "OD2" Residue "W ASP 416": "OD1" <-> "OD2" Residue "W GLU 426": "OE1" <-> "OE2" Residue "W ARG 427": "NH1" <-> "NH2" Residue "W GLU 434": "OE1" <-> "OE2" Residue "W ARG 466": "NH1" <-> "NH2" Residue "W ARG 468": "NH1" <-> "NH2" Residue "W GLU 480": "OE1" <-> "OE2" Residue "W ARG 482": "NH1" <-> "NH2" Residue "W ARG 485": "NH1" <-> "NH2" Residue "W TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 490": "OD1" <-> "OD2" Residue "W TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 131766 Number of models: 1 Model: "" Number of chains: 57 Chain: "X" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1633 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 68535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3204, 68535 Classifications: {'RNA': 3204} Modifications used: {'rna2p': 2, 'rna2p_pur': 331, 'rna2p_pyr': 221, 'rna3p': 2, 'rna3p_pur': 1446, 'rna3p_pyr': 1202} Link IDs: {'rna2p': 554, 'rna3p': 2649} 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: 2 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: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} 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: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2713 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "W" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2236 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain breaks: 6 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Unusual residues: {' K': 2, ' MG': 148} Classifications: {'undetermined': 150} Link IDs: {None: 149} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "W" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 48.85, per 1000 atoms: 0.37 Number of scatterers: 131766 At special positions: 0 Unit cell: (265.96, 221.27, 264.87, 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 2 19.00 S 118 16.00 P 3486 15.00 Mg 160 11.99 O 34385 8.00 N 24245 7.00 C 69370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS w 19 " - pdb=" SG CYS w 22 " distance=2.79 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 34 " distance=2.97 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 37 " distance=1.83 Simple disulfide: pdb=" SG CYS w 34 " - pdb=" SG CYS w 37 " distance=2.76 Simple disulfide: pdb=" SG CYS V 58 " - pdb=" SG CYS V 61 " distance=2.12 Simple disulfide: pdb=" SG CYS V 58 " - pdb=" SG CYS V 143 " distance=2.15 Simple disulfide: pdb=" SG CYS V 61 " - pdb=" SG CYS V 143 " distance=1.94 Simple disulfide: pdb=" SG CYS V 143 " - pdb=" SG CYS V 146 " distance=2.15 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 47.57 Conformation dependent library (CDL) restraints added in 6.4 seconds 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13728 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 241 helices and 70 sheets defined 40.0% alpha, 14.0% beta 993 base pairs and 1610 stacking pairs defined. Time for finding SS restraints: 54.65 Creating SS restraints... Processing helix chain 'X' and resid 12 through 17 removed outlier: 4.006A pdb=" N PHE X 16 " --> pdb=" O GLU X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 43 removed outlier: 3.852A pdb=" N TYR X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA X 37 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU X 42 " --> pdb=" O PHE X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 77 through 88 removed outlier: 3.565A pdb=" N LEU X 84 " --> pdb=" O GLU X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 108 removed outlier: 3.860A pdb=" N VAL X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.734A pdb=" N GLU X 127 " --> pdb=" O ARG X 123 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU X 128 " --> pdb=" O GLU X 124 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU X 133 " --> pdb=" O ILE X 129 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 152 removed outlier: 4.031A pdb=" N TYR X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 178 removed outlier: 3.764A pdb=" N GLN X 170 " --> pdb=" O SER X 166 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER X 175 " --> pdb=" O GLU X 171 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU X 176 " --> pdb=" O GLU X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 197 removed outlier: 3.718A pdb=" N GLY X 196 " --> pdb=" O VAL X 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET X 197 " --> pdb=" O VAL X 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 192 through 197' Processing helix chain 'X' and resid 211 through 223 removed outlier: 4.018A pdb=" N VAL X 217 " --> pdb=" O PRO X 213 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE X 218 " --> pdb=" O GLU X 214 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU X 219 " --> pdb=" O LEU X 215 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE X 221 " --> pdb=" O VAL X 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG X 223 " --> pdb=" O GLU X 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 removed outlier: 3.564A pdb=" N LYS D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.696A pdb=" N HIS D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.628A pdb=" N VAL D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Proline residue: D 108 - end of helix No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.750A pdb=" N ALA D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.967A pdb=" N MET D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 200 through 205' Processing helix chain 'E' and resid 111 through 120 removed outlier: 4.346A pdb=" N ARG E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.952A pdb=" N ALA E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR E 137 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 154 removed outlier: 3.706A pdb=" N GLU E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 removed outlier: 4.740A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Proline residue: E 170 - end of helix No H-bonds generated for 'chain 'E' and resid 165 through 170' Processing helix chain 'E' and resid 187 through 199 removed outlier: 3.546A pdb=" N GLU E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 removed outlier: 4.454A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 347 through 352 removed outlier: 7.954A pdb=" N LEU E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 347 through 352' Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'F' and resid 31 through 46 removed outlier: 3.919A pdb=" N SER F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN F 45 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 131 removed outlier: 3.627A pdb=" N ALA F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL F 131 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 139 removed outlier: 3.523A pdb=" N LEU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 138 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY F 139 " --> pdb=" O VAL F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 4.144A pdb=" N SER F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 159' Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.613A pdb=" N ALA F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 185 removed outlier: 3.596A pdb=" N LEU F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 181 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.090A pdb=" N ARG F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.545A pdb=" N ARG F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 Proline residue: F 240 - end of helix Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.557A pdb=" N LYS F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 292 removed outlier: 4.335A pdb=" N ILE F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.752A pdb=" N ALA F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 328 removed outlier: 3.914A pdb=" N LEU F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 338 removed outlier: 4.381A pdb=" N VAL F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 336 " --> pdb=" O LYS F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 361 removed outlier: 3.858A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 357 " --> pdb=" O ALA F 353 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 16 removed outlier: 3.568A pdb=" N SER G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG G 15 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE G 16 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 26 Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.997A pdb=" N ARG G 35 " --> pdb=" O TYR G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 removed outlier: 4.231A pdb=" N LEU G 83 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Proline residue: G 84 - end of helix Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.570A pdb=" N TYR G 99 " --> pdb=" O TRP G 95 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 112 " --> pdb=" O ARG G 108 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 170 removed outlier: 3.943A pdb=" N GLY G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.514A pdb=" N ARG G 196 " --> pdb=" O PRO G 192 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE G 199 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 removed outlier: 4.252A pdb=" N ASP G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 removed outlier: 4.013A pdb=" N PHE G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU G 221 " --> pdb=" O GLU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 233 through 250 removed outlier: 4.551A pdb=" N GLU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE G 239 " --> pdb=" O SER G 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG G 248 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 274 removed outlier: 3.693A pdb=" N TYR G 265 " --> pdb=" O THR G 261 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR G 272 " --> pdb=" O GLU G 268 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN G 274 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 293 removed outlier: 3.856A pdb=" N ALA G 283 " --> pdb=" O LYS G 279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 removed outlier: 4.085A pdb=" N VAL H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 80 through 85' Processing helix chain 'H' and resid 102 through 107 removed outlier: 4.263A pdb=" N PHE H 106 " --> pdb=" O ASN H 102 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA H 107 " --> pdb=" O VAL H 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 102 through 107' Processing helix chain 'H' and resid 131 through 150 removed outlier: 4.119A pdb=" N VAL H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS H 139 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA H 144 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 162 removed outlier: 3.623A pdb=" N SER H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N SER H 162 " --> pdb=" O TYR H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 73 removed outlier: 4.073A pdb=" N ALA I 32 " --> pdb=" O ALA I 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG I 41 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA I 42 " --> pdb=" O LYS I 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE I 43 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU I 56 " --> pdb=" O GLN I 52 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS I 66 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 107 removed outlier: 3.546A pdb=" N LYS I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 removed outlier: 4.057A pdb=" N LEU I 124 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 151 removed outlier: 3.781A pdb=" N ILE I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 173 removed outlier: 4.215A pdb=" N ILE I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN I 172 " --> pdb=" O ILE I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 191 removed outlier: 3.570A pdb=" N LEU I 184 " --> pdb=" O SER I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 203 removed outlier: 3.679A pdb=" N LEU I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP I 203 " --> pdb=" O ASN I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 244 removed outlier: 3.533A pdb=" N LEU I 239 " --> pdb=" O PHE I 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER I 242 " --> pdb=" O LYS I 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 69 removed outlier: 3.659A pdb=" N GLN J 59 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 81 removed outlier: 4.471A pdb=" N ALA J 76 " --> pdb=" O PRO J 72 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN J 77 " --> pdb=" O PRO J 73 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE J 78 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLN J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR J 81 " --> pdb=" O GLN J 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 72 through 81' Processing helix chain 'J' and resid 84 through 98 removed outlier: 3.985A pdb=" N ALA J 88 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG J 98 " --> pdb=" O PHE J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 115 removed outlier: 3.704A pdb=" N LYS J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU J 107 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 146 removed outlier: 3.655A pdb=" N ASN J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 removed outlier: 3.551A pdb=" N LYS J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 191 removed outlier: 3.529A pdb=" N LEU J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 222 removed outlier: 3.916A pdb=" N GLU J 208 " --> pdb=" O ARG J 204 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA J 209 " --> pdb=" O ALA J 205 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA J 210 " --> pdb=" O GLU J 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU J 214 " --> pdb=" O ALA J 210 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL J 215 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER J 216 " --> pdb=" O ALA J 212 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR J 217 " --> pdb=" O LYS J 213 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 233 removed outlier: 3.633A pdb=" N LYS J 231 " --> pdb=" O ASP J 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TRP J 233 " --> pdb=" O VAL J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 253 removed outlier: 3.929A pdb=" N ASN J 252 " --> pdb=" O LYS J 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 84 removed outlier: 3.509A pdb=" N LEU K 68 " --> pdb=" O HIS K 64 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 166 removed outlier: 3.778A pdb=" N VAL K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU K 161 " --> pdb=" O ASN K 157 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG K 166 " --> pdb=" O GLN K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 176 removed outlier: 4.004A pdb=" N LEU K 176 " --> pdb=" O ILE K 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 10 removed outlier: 4.251A pdb=" N TYR L 9 " --> pdb=" O PRO L 5 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 5 through 10' Processing helix chain 'L' and resid 42 through 47 removed outlier: 4.173A pdb=" N PHE L 46 " --> pdb=" O THR L 42 " (cutoff:3.500A) Proline residue: L 47 - end of helix No H-bonds generated for 'chain 'L' and resid 42 through 47' Processing helix chain 'L' and resid 61 through 80 removed outlier: 3.533A pdb=" N CYS L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.547A pdb=" N VAL L 148 " --> pdb=" O ASN L 144 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA L 155 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR L 157 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS L 158 " --> pdb=" O ARG L 154 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Proline residue: L 160 - end of helix Processing helix chain 'L' and resid 177 through 188 removed outlier: 3.618A pdb=" N LEU L 182 " --> pdb=" O ARG L 178 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 214 removed outlier: 3.620A pdb=" N ILE L 210 " --> pdb=" O LEU L 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG L 211 " --> pdb=" O GLU L 207 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 212 " --> pdb=" O ASN L 208 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE L 213 " --> pdb=" O ASN L 209 " (cutoff:3.500A) Proline residue: L 214 - end of helix Processing helix chain 'M' and resid 27 through 42 removed outlier: 3.636A pdb=" N ALA M 33 " --> pdb=" O ARG M 29 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS M 35 " --> pdb=" O THR M 31 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 88 removed outlier: 4.198A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS M 85 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 113 removed outlier: 4.990A pdb=" N LEU M 112 " --> pdb=" O GLU M 108 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY M 113 " --> pdb=" O HIS M 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 108 through 113' Processing helix chain 'M' and resid 135 through 141 removed outlier: 4.735A pdb=" N THR M 139 " --> pdb=" O GLY M 135 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 167 removed outlier: 4.782A pdb=" N TYR M 167 " --> pdb=" O PHE M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 removed outlier: 4.285A pdb=" N ARG N 21 " --> pdb=" O HIS N 17 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL N 22 " --> pdb=" O TRP N 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 17 through 22' Processing helix chain 'N' and resid 27 through 47 removed outlier: 3.722A pdb=" N VAL N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG N 39 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS N 45 " --> pdb=" O THR N 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE N 46 " --> pdb=" O ARG N 42 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 3.533A pdb=" N LYS N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA N 83 " --> pdb=" O GLU N 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 94 removed outlier: 3.916A pdb=" N ARG N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE N 93 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 123 removed outlier: 3.785A pdb=" N PHE N 109 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE N 123 " --> pdb=" O TYR N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 146 removed outlier: 3.536A pdb=" N THR N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 165 through 180 removed outlier: 5.528A pdb=" N THR N 169 " --> pdb=" O SER N 165 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE N 179 " --> pdb=" O SER N 175 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG N 180 " --> pdb=" O GLU N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 194 removed outlier: 4.971A pdb=" N GLU N 194 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 64 removed outlier: 4.206A pdb=" N VAL O 63 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 59 through 64' Processing helix chain 'O' and resid 77 through 89 Processing helix chain 'O' and resid 90 through 98 removed outlier: 3.567A pdb=" N SER O 97 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER O 98 " --> pdb=" O TRP O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 112 removed outlier: 4.202A pdb=" N LEU O 112 " --> pdb=" O ARG O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 138 removed outlier: 3.580A pdb=" N GLN O 126 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA O 134 " --> pdb=" O THR O 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 14 removed outlier: 4.263A pdb=" N TYR a 6 " --> pdb=" O GLY a 2 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG a 12 " --> pdb=" O GLU a 8 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS a 13 " --> pdb=" O GLU a 9 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS a 14 " --> pdb=" O LEU a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 34 removed outlier: 3.627A pdb=" N LEU a 22 " --> pdb=" O VAL a 18 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG a 24 " --> pdb=" O ARG a 20 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS a 33 " --> pdb=" O GLU a 29 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 52 removed outlier: 3.569A pdb=" N ARG a 49 " --> pdb=" O PRO a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 88 removed outlier: 3.714A pdb=" N GLN a 87 " --> pdb=" O LYS a 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLY a 88 " --> pdb=" O PRO a 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 83 through 88' Processing helix chain 'a' and resid 97 through 111 removed outlier: 3.691A pdb=" N ARG a 109 " --> pdb=" O ARG a 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA a 111 " --> pdb=" O GLY a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 145 removed outlier: 4.101A pdb=" N ASP a 145 " --> pdb=" O ALA a 141 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 163 removed outlier: 3.898A 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 196 removed outlier: 3.746A pdb=" N THR a 196 " --> pdb=" O LYS a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 153 removed outlier: 4.999A pdb=" N TRP a 150 " --> pdb=" O ARG a 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE a 151 " --> pdb=" O TYR a 148 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 30 removed outlier: 3.762A pdb=" N VAL b 22 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 61 removed outlier: 3.656A pdb=" N TYR b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA b 61 " --> pdb=" O PHE b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 70 removed outlier: 3.807A pdb=" N GLY b 69 " --> pdb=" O ASN b 65 " (cutoff:3.500A) Proline residue: b 70 - end of helix No H-bonds generated for 'chain 'b' and resid 65 through 70' Processing helix chain 'b' and resid 75 through 89 removed outlier: 3.576A pdb=" N ALA b 83 " --> pdb=" O ILE b 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL b 88 " --> pdb=" O LEU b 84 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 103 removed outlier: 4.252A pdb=" N LEU b 102 " --> pdb=" O ALA b 98 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LYS b 103 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 116 removed outlier: 4.532A pdb=" N LYS b 114 " --> pdb=" O PRO b 110 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS b 115 " --> pdb=" O PRO b 111 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS b 116 " --> pdb=" O TYR b 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 110 through 116' Processing helix chain 'b' and resid 124 through 129 Processing helix chain 'b' and resid 137 through 146 removed outlier: 3.510A pdb=" N SER b 142 " --> pdb=" O LEU b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 187 removed outlier: 3.523A pdb=" N LYS b 155 " --> pdb=" O ASP b 151 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA b 158 " --> pdb=" O ALA b 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL b 162 " --> pdb=" O ALA b 158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER b 163 " --> pdb=" O LYS b 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS b 170 " --> pdb=" O GLU b 166 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU b 187 " --> pdb=" O ALA b 183 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 198 removed outlier: 3.882A pdb=" N LEU b 194 " --> pdb=" O VAL b 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.205A pdb=" N SER c 14 " --> pdb=" O ASN c 10 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 10 through 15' Processing helix chain 'c' and resid 25 through 37 removed outlier: 3.680A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE c 36 " --> pdb=" O THR c 32 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN c 37 " --> pdb=" O ALA c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 54 removed outlier: 3.737A pdb=" N LYS c 46 " --> pdb=" O THR c 42 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP c 53 " --> pdb=" O GLU c 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS c 54 " --> pdb=" O GLN c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 77 removed outlier: 4.837A pdb=" N LYS c 74 " --> pdb=" O THR c 70 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU c 75 " --> pdb=" O ALA c 71 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE c 76 " --> pdb=" O GLN c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 106 removed outlier: 3.541A pdb=" N VAL c 88 " --> pdb=" O PRO c 84 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN c 96 " --> pdb=" O GLN c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 183 removed outlier: 3.952A pdb=" N ARG c 175 " --> pdb=" O ARG c 171 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE c 176 " --> pdb=" O GLN c 172 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG c 181 " --> pdb=" O ALA c 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 40 removed outlier: 3.537A pdb=" N LEU d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE d 35 " --> pdb=" O LYS d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 54 removed outlier: 3.750A pdb=" N PHE d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU d 54 " --> pdb=" O LYS d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 60 Proline residue: d 60 - end of helix Processing helix chain 'd' and resid 63 through 73 removed outlier: 3.503A pdb=" N ALA d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 118 removed outlier: 3.573A pdb=" N ALA d 117 " --> pdb=" O LYS d 113 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY d 118 " --> pdb=" O ILE d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 131 Processing helix chain 'd' and resid 147 through 154 removed outlier: 4.152A pdb=" N ARG d 151 " --> pdb=" O ARG d 147 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS d 152 " --> pdb=" O GLU d 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE d 153 " --> pdb=" O ALA d 149 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY d 154 " --> pdb=" O VAL d 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 147 through 154' Processing helix chain 'd' and resid 169 through 174 removed outlier: 5.257A pdb=" N GLU d 173 " --> pdb=" O GLY d 169 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG d 174 " --> pdb=" O ARG d 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 169 through 174' Processing helix chain 'e' and resid 4 through 16 Processing helix chain 'e' and resid 28 through 36 removed outlier: 3.806A pdb=" N GLN e 34 " --> pdb=" O SER e 30 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA e 35 " --> pdb=" O GLU e 31 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 48 removed outlier: 3.663A pdb=" N LEU e 44 " --> pdb=" O ALA e 40 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS e 46 " --> pdb=" O ARG e 42 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN e 47 " --> pdb=" O LYS e 43 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 73 removed outlier: 3.698A pdb=" N ARG e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU e 72 " --> pdb=" O GLN e 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY e 73 " --> pdb=" O SER e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 82 removed outlier: 3.939A pdb=" N ARG e 81 " --> pdb=" O GLY e 77 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS e 82 " --> pdb=" O TYR e 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 77 through 82' Processing helix chain 'e' and resid 84 through 113 Proline residue: e 90 - end of helix removed outlier: 6.838A pdb=" N VAL e 93 " --> pdb=" O LEU e 89 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL e 94 " --> pdb=" O PRO e 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 130 removed outlier: 3.755A pdb=" N VAL e 122 " --> pdb=" O HIS e 118 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS e 125 " --> pdb=" O HIS e 121 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN e 130 " --> pdb=" O GLU e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 187 removed outlier: 3.502A pdb=" N HIS e 141 " --> pdb=" O ALA e 137 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG e 167 " --> pdb=" O ARG e 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA e 168 " --> pdb=" O LEU e 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG e 172 " --> pdb=" O ALA e 168 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL e 177 " --> pdb=" O ARG e 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS e 180 " --> pdb=" O ARG e 176 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG e 181 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 49 removed outlier: 3.811A pdb=" N LEU f 48 " --> pdb=" O PHE f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 114 removed outlier: 3.751A pdb=" N GLN f 108 " --> pdb=" O GLU f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 122 removed outlier: 3.841A pdb=" N ILE f 121 " --> pdb=" O ARG f 117 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS f 122 " --> pdb=" O PHE f 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 117 through 122' Processing helix chain 'f' and resid 137 through 145 removed outlier: 4.158A pdb=" N LYS f 141 " --> pdb=" O ARG f 137 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N PHE f 143 " --> pdb=" O TYR f 139 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU f 144 " --> pdb=" O VAL f 140 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR f 145 " --> pdb=" O LYS f 141 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 16 removed outlier: 3.987A pdb=" N PHE g 15 " --> pdb=" O THR g 11 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN g 16 " --> pdb=" O ARG g 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 11 through 16' Processing helix chain 'g' and resid 26 through 32 removed outlier: 4.408A pdb=" N TYR g 30 " --> pdb=" O HIS g 26 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS g 32 " --> pdb=" O SER g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 97 removed outlier: 4.464A pdb=" N ILE g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 92 through 97' Processing helix chain 'g' and resid 99 through 123 removed outlier: 3.592A pdb=" N GLN g 103 " --> pdb=" O SER g 99 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU g 107 " --> pdb=" O GLN g 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS g 110 " --> pdb=" O LEU g 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA g 121 " --> pdb=" O ALA g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 26 removed outlier: 4.535A pdb=" N THR h 23 " --> pdb=" O VAL h 19 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY h 26 " --> pdb=" O PRO h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 40 removed outlier: 3.693A pdb=" N TYR h 33 " --> pdb=" O ASP h 29 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR h 36 " --> pdb=" O SER h 32 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU h 37 " --> pdb=" O TYR h 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS h 40 " --> pdb=" O TYR h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 88 removed outlier: 3.552A pdb=" N LEU h 76 " --> pdb=" O SER h 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS h 77 " --> pdb=" O GLY h 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 71 removed outlier: 3.634A pdb=" N ARG i 70 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS i 71 " --> pdb=" O PRO i 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 66 through 71' Processing helix chain 'i' and resid 119 through 127 removed outlier: 4.159A pdb=" N LEU i 125 " --> pdb=" O GLU i 121 " (cutoff:3.500A) Proline residue: i 127 - end of helix Processing helix chain 'i' and resid 128 through 133 Processing helix chain 'j' and resid 33 through 43 Processing helix chain 'j' and resid 45 through 50 removed outlier: 3.942A pdb=" N ILE j 49 " --> pdb=" O ASN j 45 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA j 50 " --> pdb=" O PRO j 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 45 through 50' Processing helix chain 'j' and resid 52 through 60 removed outlier: 3.669A pdb=" N HIS j 58 " --> pdb=" O LEU j 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS j 60 " --> pdb=" O ARG j 56 " (cutoff:3.500A) Processing helix chain 'j' and resid 63 through 68 removed outlier: 3.554A pdb=" N ALA j 68 " --> pdb=" O THR j 64 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 94 removed outlier: 4.339A pdb=" N LYS j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU j 92 " --> pdb=" O ASP j 88 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 64 removed outlier: 3.653A pdb=" N ILE k 63 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU k 64 " --> pdb=" O TYR k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 79 Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.548A pdb=" N LYS k 97 " --> pdb=" O TYR k 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 131 through 140 removed outlier: 3.704A pdb=" N ILE k 135 " --> pdb=" O ASP k 131 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 22 removed outlier: 3.662A pdb=" N TYR l 19 " --> pdb=" O ALA l 15 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA l 22 " --> pdb=" O ALA l 18 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 32 removed outlier: 4.339A pdb=" N VAL l 29 " --> pdb=" O SER l 25 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER l 32 " --> pdb=" O ARG l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 44 Processing helix chain 'l' and resid 100 through 105 removed outlier: 3.913A pdb=" N LEU l 104 " --> pdb=" O HIS l 100 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL l 105 " --> pdb=" O PRO l 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 100 through 105' Processing helix chain 'l' and resid 112 through 123 Processing helix chain 'm' and resid 59 through 67 removed outlier: 3.837A pdb=" N ALA m 63 " --> pdb=" O ALA m 59 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS m 67 " --> pdb=" O ALA m 63 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 81 removed outlier: 3.926A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU m 81 " --> pdb=" O TYR m 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 76 through 81' Processing helix chain 'm' and resid 92 through 97 removed outlier: 4.297A pdb=" N VAL m 96 " --> pdb=" O PHE m 92 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER m 97 " --> pdb=" O LYS m 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 92 through 97' Processing helix chain 'm' and resid 103 through 125 removed outlier: 3.652A pdb=" N ARG m 107 " --> pdb=" O GLN m 103 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU m 108 " --> pdb=" O PRO m 104 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU m 109 " --> pdb=" O SER m 105 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA m 110 " --> pdb=" O GLN m 106 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA m 124 " --> pdb=" O GLU m 120 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY m 125 " --> pdb=" O ARG m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 133 removed outlier: 5.791A pdb=" N LYS m 133 " --> pdb=" O TRP m 129 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 7 removed outlier: 3.925A pdb=" N THR n 6 " --> pdb=" O PRO n 2 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LYS n 7 " --> pdb=" O SER n 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 2 through 7' Processing helix chain 'n' and resid 41 through 48 removed outlier: 4.553A pdb=" N LYS n 47 " --> pdb=" O ILE n 43 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR n 48 " --> pdb=" O ASN n 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 64 through 69 removed outlier: 4.087A pdb=" N PHE n 68 " --> pdb=" O GLN n 64 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP n 69 " --> pdb=" O GLN n 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 64 through 69' Processing helix chain 'n' and resid 74 through 82 removed outlier: 5.118A pdb=" N TRP n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR n 80 " --> pdb=" O ASP n 76 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU n 81 " --> pdb=" O LYS n 77 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE n 82 " --> pdb=" O LEU n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 94 removed outlier: 4.581A pdb=" N ASP n 88 " --> pdb=" O GLU n 84 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN n 89 " --> pdb=" O ASP n 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR n 90 " --> pdb=" O LYS n 86 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER n 93 " --> pdb=" O GLN n 89 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA n 94 " --> pdb=" O TYR n 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 103 through 108 Processing helix chain 'n' and resid 131 through 142 removed outlier: 3.575A pdb=" N ILE n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 20 removed outlier: 3.679A pdb=" N HIS o 17 " --> pdb=" O THR o 13 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG o 18 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN o 19 " --> pdb=" O LYS o 15 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY o 20 " --> pdb=" O ALA o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 59 removed outlier: 3.707A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS o 59 " --> pdb=" O ALA o 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 20 removed outlier: 4.398A pdb=" N LYS p 13 " --> pdb=" O SER p 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA p 15 " --> pdb=" O ASN p 11 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU p 16 " --> pdb=" O GLN p 12 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL p 17 " --> pdb=" O LYS p 13 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE p 18 " --> pdb=" O LEU p 14 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS p 19 " --> pdb=" O ALA p 15 " (cutoff:3.500A) removed outlier: 3.891A 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 Processing helix chain 'p' and resid 73 through 82 removed outlier: 4.088A pdb=" N THR p 79 " --> pdb=" O ASN p 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 15 through 21 removed outlier: 3.887A pdb=" N ARG q 19 " --> pdb=" O ASN q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 44 removed outlier: 3.503A pdb=" N ARG q 28 " --> pdb=" O SER q 24 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA q 29 " --> pdb=" O PHE q 25 " (cutoff:3.500A) Proline residue: q 30 - end of helix Processing helix chain 'q' and resid 52 through 61 Processing helix chain 'r' and resid 21 through 26 removed outlier: 5.138A pdb=" N HIS r 26 " --> pdb=" O SER r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 78 through 86 removed outlier: 3.607A pdb=" N LEU r 82 " --> pdb=" O ASN r 78 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR r 84 " --> pdb=" O LYS r 80 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU r 85 " --> pdb=" O ASP r 81 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR r 86 " --> pdb=" O LEU r 82 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 116 removed outlier: 3.943A pdb=" N VAL r 107 " --> pdb=" O LYS r 103 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 45 removed outlier: 4.570A pdb=" N PHE s 43 " --> pdb=" O GLN s 39 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR s 44 " --> pdb=" O ASP s 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU s 45 " --> pdb=" O ALA s 41 " (cutoff:3.500A) Processing helix chain 't' and resid 58 through 66 removed outlier: 4.083A pdb=" N TYR t 62 " --> pdb=" O ARG t 58 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA t 63 " --> pdb=" O PRO t 59 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL t 65 " --> pdb=" O GLN t 61 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N SER t 66 " --> pdb=" O TYR t 62 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 58 through 66' Processing helix chain 't' and resid 81 through 113 removed outlier: 3.621A pdb=" N ILE t 100 " --> pdb=" O GLU t 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU t 107 " --> pdb=" O LYS t 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN t 108 " --> pdb=" O VAL t 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU t 110 " --> pdb=" O LYS t 106 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS t 113 " --> pdb=" O THR t 109 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 13 removed outlier: 4.303A pdb=" N THR u 11 " --> pdb=" O TYR u 7 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS u 12 " --> pdb=" O GLU u 8 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER u 13 " --> pdb=" O LEU u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 38 removed outlier: 3.919A pdb=" N SER u 19 " --> pdb=" O GLU u 15 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL u 22 " --> pdb=" O ALA u 18 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU u 36 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER u 37 " --> pdb=" O VAL u 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG u 38 " --> pdb=" O GLN u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 42 through 71 removed outlier: 4.542A pdb=" N THR u 46 " --> pdb=" O PRO u 42 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL u 47 " --> pdb=" O LYS u 43 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG u 48 " --> pdb=" O ILE u 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU u 64 " --> pdb=" O GLU u 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL u 66 " --> pdb=" O GLN u 62 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN u 68 " --> pdb=" O GLU u 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU u 69 " --> pdb=" O ALA u 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS u 71 " --> pdb=" O ARG u 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 77 through 82 removed outlier: 5.494A pdb=" N ALA u 82 " --> pdb=" O LYS u 78 " (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 112 removed outlier: 3.536A pdb=" N GLN u 108 " --> pdb=" O GLN u 104 " (cutoff:3.500A) Proline residue: u 112 - end of helix Processing helix chain 'v' and resid 25 through 30 removed outlier: 4.663A pdb=" N LYS v 29 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS v 30 " --> pdb=" O ILE v 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 25 through 30' Processing helix chain 'v' and resid 34 through 49 removed outlier: 3.915A pdb=" N GLU v 46 " --> pdb=" O SER v 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE v 47 " --> pdb=" O LEU v 43 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 64 removed outlier: 3.617A pdb=" N ARG v 56 " --> pdb=" O PRO v 52 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE v 58 " --> pdb=" O GLU v 54 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP v 59 " --> pdb=" O ARG v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 65 through 78 removed outlier: 3.512A pdb=" N VAL v 72 " --> pdb=" O ARG v 68 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY v 78 " --> pdb=" O LYS v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 97 removed outlier: 3.638A pdb=" N ALA v 85 " --> pdb=" O THR v 81 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL v 87 " --> pdb=" O ALA v 83 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN v 92 " --> pdb=" O GLU v 88 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA v 95 " --> pdb=" O ASN v 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER v 97 " --> pdb=" O ILE v 93 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 11 removed outlier: 4.028A pdb=" N GLY w 9 " --> pdb=" O THR w 5 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS w 10 " --> pdb=" O PRO w 6 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG w 11 " --> pdb=" O SER w 7 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 58 removed outlier: 3.731A pdb=" N HIS w 57 " --> pdb=" O ALA w 53 " (cutoff:3.500A) Processing helix chain 'w' and resid 66 through 77 removed outlier: 4.083A pdb=" N VAL w 70 " --> pdb=" O TYR w 66 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER w 71 " --> pdb=" O LEU w 67 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG w 72 " --> pdb=" O LYS w 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS w 75 " --> pdb=" O SER w 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 7 through 18 removed outlier: 3.742A pdb=" N PHE x 11 " --> pdb=" O ASP x 7 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU x 12 " --> pdb=" O ILE x 8 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU x 13 " --> pdb=" O LYS x 9 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU x 14 " --> pdb=" O GLN x 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR x 15 " --> pdb=" O PHE x 11 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG x 16 " --> pdb=" O LEU x 12 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG x 17 " --> pdb=" O GLU x 13 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA x 18 " --> pdb=" O LEU x 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 7 through 18' Processing helix chain 'x' and resid 58 through 69 removed outlier: 3.978A pdb=" N LYS x 63 " --> pdb=" O ALA x 59 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS x 64 " --> pdb=" O GLY x 60 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE x 66 " --> pdb=" O ALA x 62 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN x 67 " --> pdb=" O LYS x 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER x 68 " --> pdb=" O LYS x 64 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU x 69 " --> pdb=" O LEU x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 21 removed outlier: 3.599A pdb=" N LYS y 15 " --> pdb=" O GLN y 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS y 18 " --> pdb=" O ALA y 14 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG y 21 " --> pdb=" O LYS y 17 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 30 removed outlier: 4.304A pdb=" N ARG y 28 " --> pdb=" O PRO y 24 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG y 30 " --> pdb=" O TRP y 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 24 through 30' Processing helix chain 'z' and resid 79 through 91 removed outlier: 4.116A pdb=" N TYR z 89 " --> pdb=" O LEU z 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 49 removed outlier: 3.548A pdb=" N ARG Q 45 " --> pdb=" O ARG Q 41 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Q 48 " --> pdb=" O ASP Q 44 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLY Q 49 " --> pdb=" O ARG Q 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 34 removed outlier: 3.581A pdb=" N GLN R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS R 34 " --> pdb=" O GLU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 91 removed outlier: 3.519A pdb=" N THR R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG R 87 " --> pdb=" O ILE R 83 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 88 removed outlier: 4.017A pdb=" N LEU V 81 " --> pdb=" O GLU V 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU V 82 " --> pdb=" O SER V 78 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG V 88 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 152 removed outlier: 4.588A pdb=" N ALA V 147 " --> pdb=" O CYS V 143 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR V 150 " --> pdb=" O CYS V 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR V 151 " --> pdb=" O ALA V 147 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR V 152 " --> pdb=" O ARG V 148 " (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: 4.042A pdb=" N LEU V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS V 180 " --> pdb=" O GLN V 176 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.637A pdb=" N VAL V 217 " --> pdb=" O PHE V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 268 removed outlier: 4.770A pdb=" N GLY V 268 " --> pdb=" O ALA V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 305 removed outlier: 3.690A pdb=" N ARG V 303 " --> pdb=" O SER V 299 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA V 304 " --> pdb=" O VAL V 300 " (cutoff:3.500A) Proline residue: V 305 - end of helix Processing helix chain 'V' and resid 342 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) Processing helix chain 'V' and resid 373 through 378 removed outlier: 4.423A pdb=" N SER V 377 " --> pdb=" O PHE V 373 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN V 378 " --> pdb=" O ILE V 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 373 through 378' Processing helix chain 'V' and resid 381 through 388 removed outlier: 4.012A pdb=" N LEU V 387 " --> pdb=" O LEU V 383 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASN V 388 " --> pdb=" O PHE V 384 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 199 removed outlier: 3.670A pdb=" N GLN W 190 " --> pdb=" O GLU W 186 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU W 191 " --> pdb=" O VAL W 187 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP W 199 " --> pdb=" O VAL W 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 215 removed outlier: 3.819A pdb=" N PHE W 213 " --> pdb=" O ASN W 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG W 214 " --> pdb=" O PRO W 210 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER W 215 " --> pdb=" O LEU W 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 209 through 215' Processing helix chain 'W' and resid 216 through 224 removed outlier: 3.545A pdb=" N ARG W 220 " --> pdb=" O VAL W 216 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS W 223 " --> pdb=" O GLU W 219 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU W 224 " --> pdb=" O ARG W 220 " (cutoff:3.500A) Processing helix chain 'W' and resid 242 through 257 removed outlier: 4.607A pdb=" N ARG W 246 " --> pdb=" O THR W 242 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR W 252 " --> pdb=" O ALA W 248 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 358 removed outlier: 3.624A pdb=" N LEU W 356 " --> pdb=" O THR W 352 " (cutoff:3.500A) Processing helix chain 'W' and resid 400 through 407 removed outlier: 4.126A pdb=" N VAL W 404 " --> pdb=" O LYS W 400 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY W 407 " --> pdb=" O LEU W 403 " (cutoff:3.500A) Processing helix chain 'W' and resid 416 through 429 Proline residue: W 420 - end of helix removed outlier: 3.615A pdb=" N VAL W 424 " --> pdb=" O PRO W 420 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU W 426 " --> pdb=" O GLY W 422 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE W 428 " --> pdb=" O VAL W 424 " (cutoff:3.500A) Proline residue: W 429 - end of helix Processing helix chain 'W' and resid 430 through 438 removed outlier: 3.993A pdb=" N TYR W 437 " --> pdb=" O ILE W 433 " (cutoff:3.500A) Processing helix chain 'W' and resid 456 through 469 removed outlier: 5.695A pdb=" N LEU W 460 " --> pdb=" O THR W 456 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU W 461 " --> pdb=" O ALA W 457 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG W 468 " --> pdb=" O TYR W 464 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY W 469 " --> pdb=" O ALA W 465 " (cutoff:3.500A) Processing helix chain 'W' and resid 481 through 494 removed outlier: 3.846A pdb=" N ARG W 485 " --> pdb=" O PRO W 481 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR W 486 " --> pdb=" O ARG W 482 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE W 487 " --> pdb=" O ALA W 483 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY W 494 " --> pdb=" O ASP W 490 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'X' and resid 23 through 27 Processing sheet with id= 2, first strand: chain 'X' and resid 69 through 73 Processing sheet with id= 3, first strand: chain 'X' and resid 114 through 117 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'X' and resid 158 through 161 removed outlier: 4.264A pdb=" N GLY X 159 " --> pdb=" O PRO X 180 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL X 161 " --> pdb=" O VAL X 182 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.689A pdb=" N GLN D 47 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS D 60 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 86 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 110 through 114 removed outlier: 3.955A pdb=" N THR D 111 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG D 147 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 58 through 64 Processing sheet with id= 8, first strand: chain 'E' and resid 51 through 55 removed outlier: 3.522A pdb=" N VAL E 79 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 98 through 102 removed outlier: 3.533A pdb=" N GLY E 98 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY E 91 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL E 87 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 177 through 182 removed outlier: 5.146A pdb=" N HIS E 177 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 164 " --> pdb=" O HIS E 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 272 through 278 removed outlier: 4.275A pdb=" N HIS E 273 " --> pdb=" O THR E 221 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 84 through 90 removed outlier: 6.460A pdb=" N LEU E 161 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL E 89 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG E 159 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.763A pdb=" N LYS E 201 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 224 through 229 removed outlier: 3.743A pdb=" N GLU F 226 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 228 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR F 209 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N PHE F 247 " --> pdb=" O GLY F 204 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 60 through 66 removed outlier: 3.713A pdb=" N VAL G 53 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 37 through 43 removed outlier: 4.266A pdb=" N THR H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS H 50 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 133 through 138 removed outlier: 7.948A pdb=" N TYR I 133 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS I 82 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER I 113 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASN I 112 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 152 through 155 removed outlier: 6.388A pdb=" N GLY I 152 " --> pdb=" O LEU I 163 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 176 through 179 removed outlier: 3.609A pdb=" N LEU J 150 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 5 through 12 removed outlier: 3.650A pdb=" N VAL K 12 " --> pdb=" O GLN K 51 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLN K 51 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 17 through 20 removed outlier: 6.436A pdb=" N ARG K 23 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 100 through 105 removed outlier: 6.006A pdb=" N LYS K 110 " --> pdb=" O VAL K 128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 132 through 137 removed outlier: 5.093A pdb=" N GLU K 143 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP K 142 " --> pdb=" O TYR K 92 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 86 through 90 Processing sheet with id= 25, first strand: chain 'L' and resid 34 through 37 removed outlier: 5.877A pdb=" N TYR L 34 " --> pdb=" O VAL L 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE L 136 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU L 52 " --> pdb=" O ILE L 135 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN L 133 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 56 through 59 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'L' and resid 189 through 192 removed outlier: 7.691A pdb=" N GLU L 189 " --> pdb=" O LEU L 200 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 49 through 55 removed outlier: 4.882A pdb=" N CYS L 49 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN L 162 " --> pdb=" O ASN L 55 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 45 through 49 removed outlier: 3.778A pdb=" N LYS M 16 " --> pdb=" O VAL M 130 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL M 130 " --> pdb=" O LYS M 16 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER M 22 " --> pdb=" O GLY M 124 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLY M 124 " --> pdb=" O SER M 22 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 89 through 92 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'N' and resid 56 through 59 Processing sheet with id= 32, first strand: chain 'O' and resid 19 through 23 removed outlier: 4.359A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS O 31 " --> pdb=" O ILE O 23 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA O 34 " --> pdb=" O ASP O 47 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'a' and resid 35 through 39 removed outlier: 7.140A pdb=" N VAL a 35 " --> pdb=" O ARG a 65 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE a 61 " --> pdb=" O ALA a 39 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY a 58 " --> pdb=" O ASP a 136 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR a 126 " --> pdb=" O ARG a 68 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR a 129 " --> pdb=" O VAL a 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN a 117 " --> pdb=" O ILE a 133 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'b' and resid 6 through 10 Processing sheet with id= 35, first strand: chain 'c' and resid 16 through 20 removed outlier: 7.012A pdb=" N LYS c 111 " --> pdb=" O LYS c 153 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'c' and resid 116 through 122 removed outlier: 3.669A pdb=" N HIS c 116 " --> pdb=" O VAL c 149 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'd' and resid 79 through 83 removed outlier: 3.588A pdb=" N LEU d 138 " --> pdb=" O THR d 80 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 21 through 25 removed outlier: 6.814A pdb=" N LYS e 21 " --> pdb=" O LYS e 53 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS e 53 " --> pdb=" O LYS e 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP e 23 " --> pdb=" O VAL e 51 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL e 51 " --> pdb=" O TRP e 23 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR e 49 " --> pdb=" O ASP e 25 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'f' and resid 24 through 31 removed outlier: 4.740A pdb=" N GLU f 6 " --> pdb=" O ILE f 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER f 60 " --> pdb=" O ILE f 10 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 88 through 96 removed outlier: 3.584A pdb=" N VAL f 79 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN f 74 " --> pdb=" O ILE f 129 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS f 125 " --> pdb=" O TRP f 78 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 39 through 42 removed outlier: 4.481A pdb=" N LYS g 60 " --> pdb=" O ILE g 42 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 72 through 79 Processing sheet with id= 43, first strand: chain 'h' and resid 62 through 67 removed outlier: 3.641A pdb=" N VAL h 65 " --> pdb=" O PHE h 15 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN h 101 " --> pdb=" O THR h 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR h 16 " --> pdb=" O ASN h 101 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG h 94 " --> pdb=" O ALA h 106 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'i' and resid 21 through 24 removed outlier: 4.436A pdb=" N ALA i 21 " --> pdb=" O ILE i 36 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'i' and resid 56 through 60 removed outlier: 4.662A pdb=" N ASP i 56 " --> pdb=" O VAL i 78 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP i 97 " --> pdb=" O ALA i 82 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA i 82 " --> pdb=" O ASP i 97 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'i' and resid 84 through 87 removed outlier: 4.188A pdb=" N VAL i 91 " --> pdb=" O ARG i 87 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'j' and resid 18 through 22 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'k' and resid 81 through 86 removed outlier: 3.876A pdb=" N LYS k 120 " --> pdb=" O VAL k 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR k 119 " --> pdb=" O ARG k 115 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS k 109 " --> pdb=" O ARG k 125 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'l' and resid 56 through 59 removed outlier: 4.267A pdb=" N GLN l 66 " --> pdb=" O VAL l 58 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'l' and resid 72 through 75 removed outlier: 3.662A pdb=" N SER l 72 " --> pdb=" O GLN l 81 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'l' and resid 86 through 89 removed outlier: 4.082A pdb=" N VAL l 95 " --> pdb=" O LYS l 87 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS l 89 " --> pdb=" O ALA l 93 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA l 93 " --> pdb=" O LYS l 89 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'm' and resid 10 through 13 removed outlier: 3.953A pdb=" N LYS m 21 " --> pdb=" O VAL m 13 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'm' and resid 42 through 45 Processing sheet with id= 54, first strand: chain 'p' and resid 22 through 25 removed outlier: 7.059A pdb=" N LYS p 22 " --> pdb=" O LEU p 93 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU p 93 " --> pdb=" O LYS p 22 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU p 41 " --> pdb=" O ILE p 92 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS p 66 " --> pdb=" O LYS p 40 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 48 through 51 removed outlier: 5.057A pdb=" N ASP q 48 " --> pdb=" O LEU q 89 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL q 8 " --> pdb=" O ARG q 77 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR q 9 " --> pdb=" O VAL q 109 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 71 through 77 Processing sheet with id= 57, first strand: chain 's' and resid 10 through 15 removed outlier: 5.832A pdb=" N LYS s 10 " --> pdb=" O GLU s 33 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU s 29 " --> pdb=" O LEU s 14 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG s 82 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS s 63 " --> pdb=" O ALA s 55 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS s 47 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG s 48 " --> pdb=" O PHE s 101 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 's' and resid 8 through 14 removed outlier: 4.133A pdb=" N ALA s 96 " --> pdb=" O HIS s 13 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 't' and resid 19 through 24 removed outlier: 4.738A pdb=" N LYS t 19 " --> pdb=" O VAL t 35 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL t 35 " --> pdb=" O LYS t 19 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'x' and resid 2 through 5 removed outlier: 4.668A pdb=" N VAL x 55 " --> pdb=" O ILE x 5 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE x 43 " --> pdb=" O LEU x 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN x 40 " --> pdb=" O ASN x 28 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG x 46 " --> pdb=" O THR x 22 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N THR x 22 " --> pdb=" O ARG x 46 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE x 27 " --> pdb=" O LEU x 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'z' and resid 100 through 103 removed outlier: 6.234A pdb=" N LYS z 93 " --> pdb=" O LYS z 124 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Q' and resid 2 through 5 Processing sheet with id= 63, first strand: chain 'Q' and resid 7 through 10 removed outlier: 8.025A pdb=" N GLN Q 22 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 47 through 50 removed outlier: 4.837A pdb=" N ILE R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY R 53 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS R 62 " --> pdb=" O CYS R 57 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 52 through 58 removed outlier: 4.937A pdb=" N ARG V 113 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP V 99 " --> pdb=" O THR V 117 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 188 through 192 removed outlier: 3.811A pdb=" N SER V 189 " --> pdb=" O PHE V 200 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG V 156 " --> pdb=" O TYR V 240 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE V 242 " --> pdb=" O ARG V 156 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR V 239 " --> pdb=" O ILE V 229 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS V 223 " --> pdb=" O SER V 245 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'V' and resid 274 through 277 removed outlier: 4.058A pdb=" N GLN V 292 " --> pdb=" O ASP V 287 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'V' and resid 315 through 320 removed outlier: 3.950A pdb=" N ASP V 367 " --> pdb=" O VAL V 320 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'V' and resid 322 through 325 Processing sheet with id= 70, first strand: chain 'W' and resid 230 through 236 removed outlier: 3.596A pdb=" N VAL W 201 " --> pdb=" O ALA W 230 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU W 200 " --> pdb=" O ASN W 338 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET W 384 " --> pdb=" O ILE W 337 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY W 343 " --> pdb=" O CYS W 388 " (cutoff:3.500A) 1734 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2429 hydrogen bonds 4044 hydrogen bond angles 0 basepair planarities 993 basepair parallelities 1610 stacking parallelities Total time for adding SS restraints: 207.91 Time building geometry restraints manager: 52.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 26681 1.34 - 1.46: 50580 1.46 - 1.58: 57087 1.58 - 1.71: 6941 1.71 - 1.83: 184 Bond restraints: 141473 Sorted by residual: bond pdb=" C1' GNP W 701 " pdb=" C2' GNP W 701 " ideal model delta sigma weight residual 1.273 1.521 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3' GNP W 701 " pdb=" C4' GNP W 701 " ideal model delta sigma weight residual 1.285 1.518 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1' GNP W 701 " pdb=" O4' GNP W 701 " ideal model delta sigma weight residual 1.564 1.430 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C2' GNP W 701 " pdb=" C3' GNP W 701 " ideal model delta sigma weight residual 1.651 1.518 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C2 GNP W 701 " pdb=" N2 GNP W 701 " ideal model delta sigma weight residual 1.483 1.354 0.129 2.00e-02 2.50e+03 4.13e+01 ... (remaining 141468 not shown) Histogram of bond angle deviations from ideal: 96.51 - 104.37: 14592 104.37 - 112.24: 74798 112.24 - 120.11: 63325 120.11 - 127.98: 49525 127.98 - 135.85: 5901 Bond angle restraints: 208141 Sorted by residual: angle pdb=" C ARG j 80 " pdb=" N PRO j 81 " pdb=" CA PRO j 81 " ideal model delta sigma weight residual 119.84 131.76 -11.92 1.25e+00 6.40e-01 9.09e+01 angle pdb=" C4' U A3078 " pdb=" C3' U A3078 " pdb=" O3' U A3078 " ideal model delta sigma weight residual 109.40 123.17 -13.77 1.50e+00 4.44e-01 8.42e+01 angle pdb=" C PRO b 109 " pdb=" N PRO b 110 " pdb=" CA PRO b 110 " ideal model delta sigma weight residual 120.38 129.58 -9.20 1.03e+00 9.43e-01 7.97e+01 angle pdb=" N PRO b 110 " pdb=" CA PRO b 110 " pdb=" C PRO b 110 " ideal model delta sigma weight residual 110.70 121.25 -10.55 1.22e+00 6.72e-01 7.48e+01 angle pdb=" O3' U A 979 " pdb=" C3' U A 979 " pdb=" C2' U A 979 " ideal model delta sigma weight residual 109.50 122.10 -12.60 1.50e+00 4.44e-01 7.05e+01 ... (remaining 208136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 73837 35.99 - 71.98: 3377 71.98 - 107.98: 229 107.98 - 143.97: 27 143.97 - 179.96: 62 Dihedral angle restraints: 77532 sinusoidal: 56282 harmonic: 21250 Sorted by residual: dihedral pdb=" C5' U A3351 " pdb=" C4' U A3351 " pdb=" C3' U A3351 " pdb=" O3' U A3351 " ideal model delta sinusoidal sigma weight residual 147.00 71.69 75.31 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" C4' U A3351 " pdb=" C3' U A3351 " pdb=" C2' U A3351 " pdb=" C1' U A3351 " ideal model delta sinusoidal sigma weight residual -35.00 34.18 -69.18 1 8.00e+00 1.56e-02 9.67e+01 dihedral pdb=" C4' U A2513 " pdb=" C3' U A2513 " pdb=" C2' U A2513 " pdb=" C1' U A2513 " ideal model delta sinusoidal sigma weight residual -35.00 32.07 -67.07 1 8.00e+00 1.56e-02 9.16e+01 ... (remaining 77529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 21965 0.141 - 0.282: 4108 0.282 - 0.424: 51 0.424 - 0.565: 12 0.565 - 0.706: 9 Chirality restraints: 26145 Sorted by residual: chirality pdb=" C3' A A2593 " pdb=" C4' A A2593 " pdb=" O3' A A2593 " pdb=" C2' A A2593 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C3' U A3269 " pdb=" C4' U A3269 " pdb=" O3' U A3269 " pdb=" C2' U A3269 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C3' U A1716 " pdb=" C4' U A1716 " pdb=" O3' U A1716 " pdb=" C2' U A1716 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.63 2.00e-01 2.50e+01 9.91e+00 ... (remaining 26142 not shown) Planarity restraints: 13457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP W 701 " 0.294 2.00e-02 2.50e+03 5.02e-01 5.67e+03 pdb=" C2' GNP W 701 " -0.346 2.00e-02 2.50e+03 pdb=" C3' GNP W 701 " -0.528 2.00e-02 2.50e+03 pdb=" C4' GNP W 701 " 0.429 2.00e-02 2.50e+03 pdb=" C5' GNP W 701 " -0.214 2.00e-02 2.50e+03 pdb=" N9 GNP W 701 " -0.750 2.00e-02 2.50e+03 pdb=" O2' GNP W 701 " 0.519 2.00e-02 2.50e+03 pdb=" O3' GNP W 701 " -0.223 2.00e-02 2.50e+03 pdb=" O4' GNP W 701 " 0.820 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS V 143 " 0.117 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO V 144 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO V 144 " 0.117 5.00e-02 4.00e+02 pdb=" CD PRO V 144 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A1315 " -0.051 2.00e-02 2.50e+03 2.61e-02 1.54e+01 pdb=" N1 U A1315 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U A1315 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U A1315 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U A1315 " 0.012 2.00e-02 2.50e+03 pdb=" C4 U A1315 " 0.010 2.00e-02 2.50e+03 pdb=" O4 U A1315 " -0.040 2.00e-02 2.50e+03 pdb=" C5 U A1315 " 0.012 2.00e-02 2.50e+03 pdb=" C6 U A1315 " 0.009 2.00e-02 2.50e+03 ... (remaining 13454 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.14: 54 2.14 - 2.89: 42043 2.89 - 3.64: 226083 3.64 - 4.39: 438923 4.39 - 5.14: 629501 Nonbonded interactions: 1336604 Sorted by model distance: nonbonded pdb=" O2' C A1556 " pdb=" OP1 A A1557 " model vdw 1.390 2.440 nonbonded pdb=" O4 U A2434 " pdb=" N1 A A2595 " model vdw 1.447 2.496 nonbonded pdb=" O ALA W 265 " pdb=" O6 GNP W 701 " model vdw 1.447 3.040 nonbonded pdb=" CD2 LEU V 291 " pdb=" CG2 VAL V 334 " model vdw 1.518 3.880 nonbonded pdb=" O4 U A2410 " pdb=" N1 A A2801 " model vdw 1.609 2.496 ... (remaining 1336599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 17.580 Check model and map are aligned: 1.390 Set scattering table: 0.830 Process input model: 451.390 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.330 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 479.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 0.248 141473 Z= 0.462 Angle : 1.135 28.493 208141 Z= 0.749 Chirality : 0.095 0.706 26145 Planarity : 0.007 0.502 13457 Dihedral : 17.391 179.962 63780 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 2.23 % Allowed : 8.10 % Favored : 89.67 % Rotamer Outliers : 6.32 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.08), residues: 6959 helix: -2.98 (0.08), residues: 2045 sheet: -2.41 (0.16), residues: 793 loop : -2.64 (0.08), residues: 4121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1829 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1460 time to evaluate : 6.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 369 outliers final: 96 residues processed: 1713 average time/residue: 1.3878 time to fit residues: 3953.3693 Evaluate side-chains 979 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 883 time to evaluate : 6.659 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 1 residues processed: 96 average time/residue: 1.1406 time to fit residues: 208.0313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 869 optimal weight: 3.9990 chunk 780 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 526 optimal weight: 3.9990 chunk 417 optimal weight: 0.9980 chunk 807 optimal weight: 0.4980 chunk 312 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 chunk 600 optimal weight: 8.9990 chunk 935 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 50 HIS X 95 GLN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 HIS D 24 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 211 HIS E 3 HIS E 173 GLN E 198 HIS E 211 GLN E 243 HIS E 259 HIS E 279 ASN E 319 ASN F 58 HIS F 221 ASN F 296 GLN F 361 HIS G 40 HIS G 63 GLN H 80 ASN H 138 GLN I 64 GLN I 104 GLN I 159 GLN K 8 GLN K 9 GLN K 125 ASN K 163 GLN L 12 GLN L 51 HIS L 59 GLN L 209 ASN M 109 HIS ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN b 31 GLN c 50 GLN c 172 GLN d 9 GLN d 58 ASN d 73 GLN e 36 ASN f 63 GLN f 89 ASN f 138 GLN g 66 ASN g 103 GLN h 52 ASN j 42 GLN j 58 HIS l 4 GLN m 36 HIS m 57 HIS n 74 ASN o 43 HIS o 48 HIS p 36 GLN q 15 ASN q 57 GLN q 105 GLN r 52 GLN r 104 ASN u 59 ASN x 40 GLN x 67 GLN V 66 GLN V 163 GLN V 231 GLN ** W 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 406 ASN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 442 GLN W 500 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 141473 Z= 0.271 Angle : 0.705 21.015 208141 Z= 0.363 Chirality : 0.043 0.419 26145 Planarity : 0.006 0.099 13457 Dihedral : 15.624 179.957 49915 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 1.02 % Allowed : 5.22 % Favored : 93.76 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.64 (0.09), residues: 6959 helix: -1.02 (0.10), residues: 2180 sheet: -1.72 (0.15), residues: 986 loop : -2.24 (0.09), residues: 3793 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 942 time to evaluate : 6.502 Fit side-chains revert: symmetry clash outliers start: 224 outliers final: 119 residues processed: 1108 average time/residue: 1.3110 time to fit residues: 2497.8837 Evaluate side-chains 924 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 805 time to evaluate : 6.463 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 1 residues processed: 119 average time/residue: 1.0197 time to fit residues: 239.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 519 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 778 optimal weight: 9.9990 chunk 636 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 937 optimal weight: 6.9990 chunk 1012 optimal weight: 10.0000 chunk 834 optimal weight: 9.9990 chunk 929 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 751 optimal weight: 0.3980 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 95 GLN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 218 HIS E 371 GLN F 116 ASN F 260 GLN I 104 GLN J 59 GLN L 133 GLN M 39 GLN N 120 GLN N 129 ASN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 GLN f 157 GLN g 127 GLN g 134 GLN h 25 ASN i 28 ASN k 94 GLN l 120 GLN m 36 HIS n 89 GLN o 43 HIS p 36 GLN u 62 GLN v 63 ASN V 66 GLN V 163 GLN W 375 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.186 141473 Z= 0.399 Angle : 0.775 21.409 208141 Z= 0.396 Chirality : 0.046 0.329 26145 Planarity : 0.006 0.077 13457 Dihedral : 15.602 179.862 49915 Min Nonbonded Distance : 0.877 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.62 % Favored : 91.54 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -2.44 (0.09), residues: 6959 helix: -0.79 (0.10), residues: 2189 sheet: -1.44 (0.15), residues: 1007 loop : -2.23 (0.09), residues: 3763 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 843 time to evaluate : 6.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 111 residues processed: 1010 average time/residue: 1.2359 time to fit residues: 2130.4625 Evaluate side-chains 866 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 755 time to evaluate : 6.467 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 1 residues processed: 111 average time/residue: 0.9563 time to fit residues: 208.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 925 optimal weight: 5.9990 chunk 704 optimal weight: 2.9990 chunk 486 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 447 optimal weight: 8.9990 chunk 629 optimal weight: 4.9990 chunk 940 optimal weight: 4.9990 chunk 995 optimal weight: 0.4980 chunk 491 optimal weight: 0.6980 chunk 891 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 86 ASN X 145 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN E 279 ASN F 5 GLN F 291 ASN F 361 HIS I 104 GLN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS K 157 ASN K 163 GLN L 59 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS d 126 GLN g 127 GLN i 7 GLN i 28 ASN l 120 GLN m 36 HIS n 40 HIS n 67 HIS u 62 GLN V 66 GLN V 203 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 473 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 141473 Z= 0.175 Angle : 0.581 21.717 208141 Z= 0.300 Chirality : 0.037 0.295 26145 Planarity : 0.004 0.059 13457 Dihedral : 15.075 179.698 49915 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.03 % Favored : 94.18 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.84 (0.09), residues: 6959 helix: -0.08 (0.11), residues: 2188 sheet: -1.05 (0.15), residues: 1038 loop : -2.03 (0.09), residues: 3733 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 839 time to evaluate : 6.657 Fit side-chains revert: symmetry clash outliers start: 118 outliers final: 59 residues processed: 921 average time/residue: 1.2957 time to fit residues: 2048.8098 Evaluate side-chains 819 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 760 time to evaluate : 6.485 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 1 residues processed: 59 average time/residue: 0.9640 time to fit residues: 117.5135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 829 optimal weight: 1.9990 chunk 565 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 741 optimal weight: 8.9990 chunk 410 optimal weight: 0.8980 chunk 849 optimal weight: 8.9990 chunk 688 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 508 optimal weight: 10.0000 chunk 893 optimal weight: 0.5980 chunk 251 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 21 ASN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN X 187 ASN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 260 GLN K 9 GLN K 163 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 GLN g 127 GLN g 134 GLN p 36 GLN s 42 GLN u 62 GLN Q 47 GLN V 54 ASN V 66 GLN W 375 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 141473 Z= 0.269 Angle : 0.634 21.700 208141 Z= 0.324 Chirality : 0.039 0.315 26145 Planarity : 0.005 0.059 13457 Dihedral : 15.057 179.833 49915 Min Nonbonded Distance : 1.063 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.77 % Favored : 92.44 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -1.77 (0.09), residues: 6959 helix: -0.05 (0.11), residues: 2204 sheet: -0.93 (0.16), residues: 1004 loop : -2.00 (0.09), residues: 3751 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 770 time to evaluate : 6.551 Fit side-chains revert: symmetry clash outliers start: 132 outliers final: 69 residues processed: 855 average time/residue: 1.3007 time to fit residues: 1904.2902 Evaluate side-chains 813 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 744 time to evaluate : 6.474 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 1 residues processed: 69 average time/residue: 0.9891 time to fit residues: 139.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 334 optimal weight: 10.0000 chunk 896 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 584 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 996 optimal weight: 20.0000 chunk 827 optimal weight: 6.9990 chunk 461 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 523 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 145 ASN X 157 GLN X 162 HIS ** X 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS E 139 GLN E 184 ASN E 279 ASN F 9 HIS F 213 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN n 89 GLN p 36 GLN s 42 GLN t 3 GLN V 163 GLN W 375 GLN ** W 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.136 141473 Z= 0.441 Angle : 0.771 21.356 208141 Z= 0.388 Chirality : 0.046 0.318 26145 Planarity : 0.006 0.079 13457 Dihedral : 15.363 179.922 49915 Min Nonbonded Distance : 1.008 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.33 % Favored : 91.92 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -2.08 (0.09), residues: 6959 helix: -0.42 (0.11), residues: 2224 sheet: -1.03 (0.16), residues: 1011 loop : -2.13 (0.09), residues: 3724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 752 time to evaluate : 5.883 Fit side-chains outliers start: 157 outliers final: 85 residues processed: 865 average time/residue: 1.2384 time to fit residues: 1834.4313 Evaluate side-chains 801 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 716 time to evaluate : 6.500 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 85 outliers final: 1 residues processed: 85 average time/residue: 0.9454 time to fit residues: 161.2428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 960 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 567 optimal weight: 10.0000 chunk 727 optimal weight: 6.9990 chunk 563 optimal weight: 5.9990 chunk 838 optimal weight: 2.9990 chunk 556 optimal weight: 0.9980 chunk 992 optimal weight: 20.0000 chunk 621 optimal weight: 2.9990 chunk 605 optimal weight: 4.9990 chunk 458 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN ** X 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 213 ASN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 134 GLN n 89 GLN p 36 GLN s 42 GLN V 203 GLN W 413 GLN W 442 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 141473 Z= 0.207 Angle : 0.598 21.481 208141 Z= 0.307 Chirality : 0.037 0.341 26145 Planarity : 0.005 0.057 13457 Dihedral : 14.980 179.934 49915 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.15 % Favored : 93.07 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -1.72 (0.09), residues: 6959 helix: -0.02 (0.11), residues: 2213 sheet: -0.85 (0.16), residues: 1002 loop : -1.97 (0.09), residues: 3744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 769 time to evaluate : 6.513 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 28 residues processed: 815 average time/residue: 1.2354 time to fit residues: 1721.2665 Evaluate side-chains 751 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 723 time to evaluate : 6.558 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.9830 time to fit residues: 59.9671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 614 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 chunk 592 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 631 optimal weight: 3.9990 chunk 676 optimal weight: 0.9990 chunk 490 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 780 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 ASN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 213 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 122 ASN g 54 HIS g 127 GLN p 36 GLN s 42 GLN t 3 GLN V 181 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 141473 Z= 0.290 Angle : 0.646 20.966 208141 Z= 0.329 Chirality : 0.039 0.296 26145 Planarity : 0.005 0.056 13457 Dihedral : 15.033 179.421 49915 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.13 % Favored : 92.15 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -1.75 (0.09), residues: 6959 helix: -0.07 (0.11), residues: 2222 sheet: -0.81 (0.16), residues: 1033 loop : -2.00 (0.09), residues: 3704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 735 time to evaluate : 6.598 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 49 residues processed: 779 average time/residue: 1.2510 time to fit residues: 1661.3245 Evaluate side-chains 765 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 716 time to evaluate : 6.504 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.9864 time to fit residues: 99.2195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 903 optimal weight: 0.0970 chunk 951 optimal weight: 10.0000 chunk 867 optimal weight: 8.9990 chunk 925 optimal weight: 7.9990 chunk 950 optimal weight: 2.9990 chunk 556 optimal weight: 6.9990 chunk 403 optimal weight: 0.9980 chunk 726 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 835 optimal weight: 1.9990 chunk 874 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN X 187 ASN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 213 ASN F 296 GLN N 103 ASN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN p 36 GLN s 42 GLN t 3 GLN V 181 HIS V 269 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 141473 Z= 0.208 Angle : 0.586 20.762 208141 Z= 0.300 Chirality : 0.036 0.255 26145 Planarity : 0.004 0.055 13457 Dihedral : 14.880 179.627 49915 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.08 % Favored : 93.20 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.58 (0.09), residues: 6959 helix: 0.11 (0.11), residues: 2214 sheet: -0.75 (0.16), residues: 1019 loop : -1.91 (0.09), residues: 3726 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 756 time to evaluate : 6.627 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 778 average time/residue: 1.3010 time to fit residues: 1727.0881 Evaluate side-chains 741 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 726 time to evaluate : 6.455 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 1.0252 time to fit residues: 36.3750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 921 optimal weight: 0.5980 chunk 607 optimal weight: 7.9990 chunk 978 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 464 optimal weight: 0.6980 chunk 680 optimal weight: 7.9990 chunk 1026 optimal weight: 9.9990 chunk 944 optimal weight: 6.9990 chunk 817 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 631 optimal weight: 4.9990 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 ASN D 47 GLN E 184 ASN E 279 ASN F 260 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 122 ASN g 127 GLN s 42 GLN z 90 ASN V 181 HIS W 375 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 141473 Z= 0.312 Angle : 0.657 20.379 208141 Z= 0.333 Chirality : 0.040 0.264 26145 Planarity : 0.005 0.057 13457 Dihedral : 15.010 179.953 49915 Min Nonbonded Distance : 1.029 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.33 % Favored : 92.00 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.72 (0.09), residues: 6959 helix: -0.06 (0.11), residues: 2224 sheet: -0.79 (0.16), residues: 1029 loop : -1.98 (0.09), residues: 3706 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13918 Ramachandran restraints generated. 6959 Oldfield, 0 Emsley, 6959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 729 time to evaluate : 6.566 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 747 average time/residue: 1.3203 time to fit residues: 1686.9081 Evaluate side-chains 741 residues out of total 5927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 719 time to evaluate : 6.628 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 1.0549 time to fit residues: 51.8884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 501 optimal weight: 6.9990 chunk 649 optimal weight: 0.9990 chunk 870 optimal weight: 4.9990 chunk 250 optimal weight: 30.0000 chunk 753 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 818 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 840 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN D 47 GLN E 184 ASN E 279 ASN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 127 GLN s 42 GLN ** t 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.137792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109770 restraints weight = 184433.227| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.05 r_work: 0.2898 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 141473 Z= 0.304 Angle : 0.657 19.946 208141 Z= 0.334 Chirality : 0.040 0.265 26145 Planarity : 0.005 0.063 13457 Dihedral : 15.023 179.816 49915 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.93 % Favored : 92.43 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % 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: -1.76 (0.09), residues: 6959 helix: -0.10 (0.11), residues: 2223 sheet: -0.80 (0.16), residues: 1006 loop : -1.99 (0.09), residues: 3730 =============================================================================== Job complete usr+sys time: 31378.21 seconds wall clock time: 549 minutes 39.46 seconds (32979.46 seconds total)