Starting phenix.real_space_refine on Fri Feb 16 05:52:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9z_15936/02_2024/8b9z_15936_updated.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 S 480 5.16 5 Na 1 4.78 5 C 43415 2.51 5 N 11016 2.21 5 O 11993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ASP 216": "OD1" <-> "OD2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 419": "OD1" <-> "OD2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "F PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ASP 133": "OD1" <-> "OD2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F ASP 207": "OD1" <-> "OD2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 209": "OD1" <-> "OD2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F GLU 304": "OE1" <-> "OE2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ARG 317": "NH1" <-> "NH2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F ASP 373": "OD1" <-> "OD2" Residue "F ASP 377": "OD1" <-> "OD2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F GLU 423": "OE1" <-> "OE2" Residue "F PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 471": "NH1" <-> "NH2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G ASP 148": "OD1" <-> "OD2" Residue "G ASP 151": "OD1" <-> "OD2" Residue "G ASP 159": "OD1" <-> "OD2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "G ASP 178": "OD1" <-> "OD2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "G ARG 280": "NH1" <-> "NH2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G ARG 286": "NH1" <-> "NH2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ASP 369": "OD1" <-> "OD2" Residue "G ARG 373": "NH1" <-> "NH2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G ARG 393": "NH1" <-> "NH2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 448": "OD1" <-> "OD2" Residue "G ASP 452": "OD1" <-> "OD2" Residue "G ASP 465": "OD1" <-> "OD2" Residue "G GLU 493": "OE1" <-> "OE2" Residue "G ASP 496": "OD1" <-> "OD2" Residue "G TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 564": "OE1" <-> "OE2" Residue "G TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 606": "OE1" <-> "OE2" Residue "G ARG 608": "NH1" <-> "NH2" Residue "G TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 643": "OD1" <-> "OD2" Residue "G GLU 666": "OE1" <-> "OE2" Residue "G ASP 687": "OD1" <-> "OD2" Residue "G GLU 692": "OE1" <-> "OE2" Residue "G ARG 694": "NH1" <-> "NH2" Residue "G TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 721": "NH1" <-> "NH2" Residue "G GLU 724": "OE1" <-> "OE2" Residue "H PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 206": "OD1" <-> "OD2" Residue "H PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 221": "OE1" <-> "OE2" Residue "H PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 151": "OD1" <-> "OD2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "J TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "K TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 174": "OE1" <-> "OE2" Residue "L GLU 179": "OE1" <-> "OE2" Residue "L PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 235": "NH1" <-> "NH2" Residue "L PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 424": "NH1" <-> "NH2" Residue "L PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 323": "OE1" <-> "OE2" Residue "M PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 440": "OE1" <-> "OE2" Residue "N PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 303": "OE1" <-> "OE2" Residue "N PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O ASP 107": "OD1" <-> "OD2" Residue "O TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 115": "OD1" <-> "OD2" Residue "O ASP 117": "OD1" <-> "OD2" Residue "O TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 127": "OD1" <-> "OD2" Residue "O TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 162": "NH1" <-> "NH2" Residue "O TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 194": "OD1" <-> "OD2" Residue "O PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 212": "NH1" <-> "NH2" Residue "O TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 219": "NH1" <-> "NH2" Residue "O GLU 225": "OE1" <-> "OE2" Residue "O ARG 249": "NH1" <-> "NH2" Residue "O GLU 254": "OE1" <-> "OE2" Residue "O TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 267": "OD1" <-> "OD2" Residue "O GLU 269": "OE1" <-> "OE2" Residue "O TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 290": "OD1" <-> "OD2" Residue "O GLU 298": "OE1" <-> "OE2" Residue "O GLU 302": "OE1" <-> "OE2" Residue "O ASP 303": "OD1" <-> "OD2" Residue "O ASP 308": "OD1" <-> "OD2" Residue "O PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 313": "OE1" <-> "OE2" Residue "O ASP 315": "OD1" <-> "OD2" Residue "O GLU 329": "OE1" <-> "OE2" Residue "O ARG 354": "NH1" <-> "NH2" Residue "O ASP 356": "OD1" <-> "OD2" Residue "O GLU 359": "OE1" <-> "OE2" Residue "O ARG 362": "NH1" <-> "NH2" Residue "O ASP 365": "OD1" <-> "OD2" Residue "O ASP 372": "OD1" <-> "OD2" Residue "O TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 389": "OD1" <-> "OD2" Residue "O ASP 392": "OD1" <-> "OD2" Residue "O GLU 393": "OE1" <-> "OE2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P ASP 97": "OD1" <-> "OD2" Residue "P ASP 98": "OD1" <-> "OD2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "P ASP 109": "OD1" <-> "OD2" Residue "P ASP 122": "OD1" <-> "OD2" Residue "P GLU 145": "OE1" <-> "OE2" Residue "P ASP 153": "OD1" <-> "OD2" Residue "P GLU 160": "OE1" <-> "OE2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P GLU 168": "OE1" <-> "OE2" Residue "P GLU 172": "OE1" <-> "OE2" Residue "P PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 203": "OE1" <-> "OE2" Residue "P ARG 207": "NH1" <-> "NH2" Residue "P ASP 210": "OD1" <-> "OD2" Residue "P PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 232": "NH1" <-> "NH2" Residue "P TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 243": "NH1" <-> "NH2" Residue "P ASP 274": "OD1" <-> "OD2" Residue "P ARG 280": "NH1" <-> "NH2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 294": "OE1" <-> "OE2" Residue "P ASP 297": "OD1" <-> "OD2" Residue "P ARG 301": "NH1" <-> "NH2" Residue "P ARG 304": "NH1" <-> "NH2" Residue "P ARG 314": "NH1" <-> "NH2" Residue "P TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 320": "OD1" <-> "OD2" Residue "P PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 346": "NH1" <-> "NH2" Residue "P GLU 348": "OE1" <-> "OE2" Residue "P ASP 365": "OD1" <-> "OD2" Residue "P GLU 374": "OE1" <-> "OE2" Residue "P GLU 380": "OE1" <-> "OE2" Residue "P ARG 385": "NH1" <-> "NH2" Residue "P TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 391": "OD1" <-> "OD2" Residue "P GLU 396": "OE1" <-> "OE2" Residue "P PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 398": "OE1" <-> "OE2" Residue "P GLU 407": "OE1" <-> "OE2" Residue "P ASP 410": "OD1" <-> "OD2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q ARG 46": "NH1" <-> "NH2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 77": "OE1" <-> "OE2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "Q GLU 81": "OE1" <-> "OE2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q ARG 147": "NH1" <-> "NH2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q ASP 155": "OD1" <-> "OD2" Residue "Q GLU 163": "OE1" <-> "OE2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "R ASP 35": "OD1" <-> "OD2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ASP 47": "OD1" <-> "OD2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 65": "OE1" <-> "OE2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 91": "OD1" <-> "OD2" Residue "R ASP 104": "OD1" <-> "OD2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 78": "NH1" <-> "NH2" Residue "T TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 87": "OD1" <-> "OD2" Residue "T ASP 90": "OD1" <-> "OD2" Residue "T ASP 103": "OD1" <-> "OD2" Residue "T ASP 107": "OD1" <-> "OD2" Residue "T ASP 110": "OD1" <-> "OD2" Residue "T PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 128": "OD1" <-> "OD2" Residue "T TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 146": "OD1" <-> "OD2" Residue "U ASP 87": "OD1" <-> "OD2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 113": "OE1" <-> "OE2" Residue "U GLU 119": "OE1" <-> "OE2" Residue "U ASP 120": "OD1" <-> "OD2" Residue "U PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 125": "OE1" <-> "OE2" Residue "U ASP 128": "OD1" <-> "OD2" Residue "U ASP 130": "OD1" <-> "OD2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "U TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 152": "OE1" <-> "OE2" Residue "V TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V ASP 41": "OD1" <-> "OD2" Residue "V TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 45": "NH1" <-> "NH2" Residue "V TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 55": "NH1" <-> "NH2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V GLU 85": "OE1" <-> "OE2" Residue "V GLU 101": "OE1" <-> "OE2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ARG 22": "NH1" <-> "NH2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 46": "OD1" <-> "OD2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 68": "NH1" <-> "NH2" Residue "W ASP 72": "OD1" <-> "OD2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W ARG 102": "NH1" <-> "NH2" Residue "W TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 28": "NH1" <-> "NH2" Residue "X GLU 44": "OE1" <-> "OE2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 116": "OD1" <-> "OD2" Residue "X PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 122": "NH1" <-> "NH2" Residue "X TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 130": "NH1" <-> "NH2" Residue "X GLU 144": "OE1" <-> "OE2" Residue "X GLU 158": "OE1" <-> "OE2" Residue "X ASP 159": "OD1" <-> "OD2" Residue "X TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 170": "NH1" <-> "NH2" Residue "X PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 5": "NH1" <-> "NH2" Residue "Y ASP 13": "OD1" <-> "OD2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 39": "OD1" <-> "OD2" Residue "Y PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 129": "OE1" <-> "OE2" Residue "Y PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 158": "OD1" <-> "OD2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Z ASP 13": "OD1" <-> "OD2" Residue "Z ARG 27": "NH1" <-> "NH2" Residue "Z PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 67": "OE1" <-> "OE2" Residue "Z ARG 83": "NH1" <-> "NH2" Residue "Z ASP 84": "OD1" <-> "OD2" Residue "Z PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 89": "NH1" <-> "NH2" Residue "Z ARG 93": "NH1" <-> "NH2" Residue "Z ARG 95": "NH1" <-> "NH2" Residue "Z TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 116": "OE1" <-> "OE2" Residue "Z GLU 124": "OE1" <-> "OE2" Residue "Z PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 140": "OD1" <-> "OD2" Residue "a TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 72": "NH1" <-> "NH2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d ARG 47": "NH1" <-> "NH2" Residue "d PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 77": "OE1" <-> "OE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 87": "NH1" <-> "NH2" Residue "d TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 95": "OD1" <-> "OD2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 116": "NH1" <-> "NH2" Residue "e PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 39": "OE1" <-> "OE2" Residue "e GLU 49": "OE1" <-> "OE2" Residue "e ASP 56": "OD1" <-> "OD2" Residue "e ARG 69": "NH1" <-> "NH2" Residue "e PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "e TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 6": "OD1" <-> "OD2" Residue "f GLU 29": "OE1" <-> "OE2" Residue "f ASP 38": "OD1" <-> "OD2" Residue "g PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ASP 71": "OD1" <-> "OD2" Residue "g PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g ASP 142": "OD1" <-> "OD2" Residue "h PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 56": "OD1" <-> "OD2" Residue "h TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 97": "OE1" <-> "OE2" Residue "h TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "h TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 136": "OE1" <-> "OE2" Residue "h GLU 146": "OE1" <-> "OE2" Residue "h GLU 153": "OE1" <-> "OE2" Residue "h TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 181": "OE1" <-> "OE2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i ASP 45": "OD1" <-> "OD2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 120": "OD1" <-> "OD2" Residue "i ASP 140": "OD1" <-> "OD2" Residue "i GLU 141": "OE1" <-> "OE2" Residue "i ASP 148": "OD1" <-> "OD2" Residue "i TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 73": "OE1" <-> "OE2" Residue "j ASP 92": "OD1" <-> "OD2" Residue "k TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 48": "NH1" <-> "NH2" Residue "k TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 45": "OE1" <-> "OE2" Residue "l TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 67": "OD1" <-> "OD2" Residue "l ASP 68": "OD1" <-> "OD2" Residue "l TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 74": "OD1" <-> "OD2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 88": "OD1" <-> "OD2" Residue "l TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 100": "NH1" <-> "NH2" Residue "l ARG 125": "NH1" <-> "NH2" Residue "l TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 151": "OD1" <-> "OD2" Residue "l ARG 156": "NH1" <-> "NH2" Residue "l PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 9": "OE1" <-> "OE2" Residue "m ARG 13": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 91": "NH1" <-> "NH2" Residue "m TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 99": "NH1" <-> "NH2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 31": "OD1" <-> "OD2" Residue "n TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "n GLU 71": "OE1" <-> "OE2" Residue "n PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 90": "OE1" <-> "OE2" Residue "n ARG 91": "NH1" <-> "NH2" Residue "n GLU 92": "OE1" <-> "OE2" Residue "n TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 119": "OE1" <-> "OE2" Residue "n GLU 124": "OE1" <-> "OE2" Residue "n TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 45": "OE1" <-> "OE2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o ASP 70": "OD1" <-> "OD2" Residue "o PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 91": "OE1" <-> "OE2" Residue "o TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 103": "OE1" <-> "OE2" Residue "o ARG 104": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o GLU 108": "OE1" <-> "OE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o ARG 112": "NH1" <-> "NH2" Residue "p TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 58": "OD1" <-> "OD2" Residue "p GLU 64": "OE1" <-> "OE2" Residue "p ARG 70": "NH1" <-> "NH2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 78": "OE1" <-> "OE2" Residue "p ASP 89": "OD1" <-> "OD2" Residue "p GLU 94": "OE1" <-> "OE2" Residue "p ASP 107": "OD1" <-> "OD2" Residue "p TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 18": "NH1" <-> "NH2" Residue "q TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 53": "OE1" <-> "OE2" Residue "q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 74": "OD1" <-> "OD2" Residue "q TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 98": "NH1" <-> "NH2" Residue "q ASP 99": "OD1" <-> "OD2" Residue "q ARG 102": "NH1" <-> "NH2" Residue "q GLU 120": "OE1" <-> "OE2" Residue "q TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 14": "NH1" <-> "NH2" Residue "r ARG 22": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 43": "OE1" <-> "OE2" Residue "r ASP 46": "OD1" <-> "OD2" Residue "r GLU 65": "OE1" <-> "OE2" Residue "r GLU 74": "OE1" <-> "OE2" Residue "r TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 81": "OE1" <-> "OE2" Residue "s TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 87": "NH1" <-> "NH2" Residue "s PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 92": "OE1" <-> "OE2" Residue "s GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66970 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 956 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 168} Chain: "C" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1726 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3434 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 404} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1679 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 196} Chain: "F" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3381 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 414} Chain: "G" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5146 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 33, 'TRANS': 643} Chain breaks: 1 Chain: "H" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2571 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 305} Chain: "I" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1485 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 175} Chain: "J" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1397 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "K" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 793 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "L" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4606 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 564} Chain: "M" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3617 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 434} Chain: "N" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2796 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 7, 'TRANS': 333} Chain: "O" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3007 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 19, 'TRANS': 348} Chain: "P" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3032 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 21, 'TRANS': 355} Chain: "Q" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1214 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "R" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 716 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "T" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 615 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "U" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "V" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "W" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 968 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "X" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1383 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "Y" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1277 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 9, 'TRANS': 157} Chain: "Z" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1201 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 12, 'TRANS': 133} Chain: "a" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 601 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 519 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "d" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "e" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "f" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 429 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "g" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 883 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "h" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1234 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "i" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1302 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 11, 'TRANS': 149} Chain: "j" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 541 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 6, 'TRANS': 59} Chain: "k" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 671 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "l" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1215 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 14, 'TRANS': 131} Chain: "m" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 892 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "n" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1152 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "o" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 937 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "p" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1266 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain: "q" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1118 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain: "r" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 9, 'TRANS': 79} Chain breaks: 1 Chain: "s" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 456 Classifications: {'peptide': 62} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 54} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 118 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'3PE': 1, 'CDL': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' NA': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PE': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "L" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "M" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'DGT': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'CDL': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "Y" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "d" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "h" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1906 SG CYS B 161 79.990 87.507 100.217 1.00 67.08 S ATOM 2137 SG CYS B 191 83.516 89.026 95.519 1.00 65.47 S ATOM 1399 SG CYS B 96 86.358 88.636 101.174 1.00 75.55 S ATOM 1405 SG CYS B 97 82.195 93.361 100.064 1.00 73.74 S ATOM 8373 SG CYS E 128 104.195 58.735 34.024 1.00 95.29 S ATOM 8407 SG CYS E 133 107.191 58.207 32.173 1.00 95.52 S ATOM 8688 SG CYS E 169 104.179 54.092 36.199 1.00 94.85 S ATOM 8711 SG CYS E 173 107.159 53.157 35.088 1.00 99.00 S ATOM 11996 SG CYS F 397 94.892 52.698 56.743 1.00 67.52 S ATOM 12016 SG CYS F 400 97.435 55.494 52.490 1.00 69.60 S ATOM 12338 SG CYS F 440 97.464 49.450 51.696 1.00 73.09 S ATOM 11977 SG CYS F 394 91.869 52.409 51.009 1.00 72.86 S ATOM 13444 SG CYS G 147 83.841 65.143 69.544 1.00 65.06 S ATOM 13383 SG CYS G 138 86.022 71.264 69.501 1.00 57.28 S ATOM 13404 SG CYS G 141 80.454 69.641 66.734 1.00 60.74 S ATOM 13806 SG CYS G 193 82.214 56.859 62.137 1.00 63.17 S ATOM 13782 SG CYS G 190 83.130 61.617 57.705 1.00 60.78 S ATOM 13830 SG CYS G 196 78.046 57.648 57.711 1.00 67.01 S ATOM 14159 SG CYS G 240 78.959 61.687 62.679 1.00 65.02 S ATOM 12883 SG CYS G 74 86.769 50.948 63.143 1.00 67.48 S ATOM 12968 SG CYS G 85 89.387 53.477 64.994 1.00 66.96 S ATOM 12993 SG CYS G 88 91.181 48.708 66.880 1.00 69.15 S ATOM 13094 SG CYS G 102 88.775 47.207 65.071 1.00 70.81 S ATOM 21354 SG CYS I 160 85.509 84.433 87.685 1.00 60.73 S ATOM 21328 SG CYS I 157 80.561 88.773 88.371 1.00 60.10 S ATOM 21375 SG CYS I 163 82.907 86.600 82.815 1.00 59.13 S ATOM 21100 SG CYS I 128 79.422 82.789 86.885 1.00 58.06 S ATOM 21404 SG CYS I 167 83.371 84.736 74.408 1.00 59.26 S ATOM 21030 SG CYS I 118 77.032 84.498 73.216 1.00 60.21 S ATOM 21072 SG CYS I 124 79.160 82.569 78.846 1.00 57.85 S ATOM 21049 SG CYS I 121 81.139 79.190 74.240 1.00 57.34 S ATOM 42734 SG CYS R 87 85.130 82.981 58.747 1.00 75.61 S ATOM 42910 SG CYS R 111 82.911 82.399 59.974 1.00 70.13 S ATOM 42932 SG CYS R 114 82.880 85.776 60.031 1.00 71.19 S Time building chain proxies: 26.32, per 1000 atoms: 0.39 Number of scatterers: 66970 At special positions: 0 Unit cell: (141.48, 192.832, 298.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 480 16.00 P 36 15.00 Na 1 11.00 O 11993 8.00 N 11016 7.00 C 43415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS X 80 " - pdb=" SG CYS X 113 " distance=2.04 Simple disulfide: pdb=" SG CYS X 90 " - pdb=" SG CYS X 103 " distance=2.03 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.38 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 128 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 173 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 169 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 85 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 88 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 102 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 74 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 161 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 191 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 96 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 97 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 400 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 394 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 440 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 397 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 134 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 141 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 147 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 138 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 193 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 190 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 196 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 240 " pdb=" SF4 I 301 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 163 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 157 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 128 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 160 " pdb=" SF4 I 302 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 124 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 121 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 167 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 118 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 96 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 114 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 111 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " Number of angles added : 3 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 356 helices and 25 sheets defined 52.8% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 removed outlier: 3.807A pdb=" N MET A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 80 removed outlier: 3.591A pdb=" N LEU A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 4.845A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 removed outlier: 3.647A pdb=" N ILE A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 67 through 85 Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 136 through 148 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 195 through 210 Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.623A pdb=" N TRP B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.582A pdb=" N ALA C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 104 removed outlier: 3.741A pdb=" N VAL C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Proline residue: C 97 - end of helix removed outlier: 3.552A pdb=" N ASP C 104 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.522A pdb=" N ASN C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR C 168 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 175 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR C 176 " --> pdb=" O TRP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'D' and resid 46 through 52 removed outlier: 4.248A pdb=" N GLN D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 125 through 131 removed outlier: 3.947A pdb=" N GLU D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Proline residue: D 139 - end of helix removed outlier: 3.859A pdb=" N ASP D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 143 " --> pdb=" O PRO D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.546A pdb=" N GLU D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 199 Processing helix chain 'D' and resid 203 through 222 removed outlier: 4.092A pdb=" N GLU D 211 " --> pdb=" O TRP D 207 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 267 removed outlier: 3.676A pdb=" N LYS D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.634A pdb=" N ASN D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.762A pdb=" N GLY D 300 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'D' and resid 331 through 355 removed outlier: 3.672A pdb=" N ASP D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN D 351 " --> pdb=" O ARG D 347 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 376 No H-bonds generated for 'chain 'D' and resid 373 through 376' Processing helix chain 'D' and resid 380 through 391 Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.855A pdb=" N HIS D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.506A pdb=" N LYS E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 4.456A pdb=" N ILE E 73 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Proline residue: E 74 - end of helix removed outlier: 3.976A pdb=" N ARG E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.663A pdb=" N VAL E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 191 through 202 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 68 through 74 Processing helix chain 'F' and resid 80 through 86 Processing helix chain 'F' and resid 88 through 98 Processing helix chain 'F' and resid 110 through 118 removed outlier: 4.241A pdb=" N MET F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN F 118 " --> pdb=" O TRP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 147 removed outlier: 3.619A pdb=" N MET F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 164 Processing helix chain 'F' and resid 178 through 193 Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 219 through 222 Processing helix chain 'F' and resid 224 through 231 Processing helix chain 'F' and resid 250 through 252 No H-bonds generated for 'chain 'F' and resid 250 through 252' Processing helix chain 'F' and resid 260 through 272 Proline residue: F 267 - end of helix removed outlier: 3.525A pdb=" N CYS F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 279 Processing helix chain 'F' and resid 311 through 318 removed outlier: 3.544A pdb=" N HIS F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 354 through 360 removed outlier: 3.778A pdb=" N ALA F 360 " --> pdb=" O GLY F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 392 removed outlier: 3.528A pdb=" N LEU F 385 " --> pdb=" O ALA F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 416 removed outlier: 4.100A pdb=" N ILE F 404 " --> pdb=" O CYS F 400 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY F 405 " --> pdb=" O ARG F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 434 removed outlier: 3.504A pdb=" N ILE F 430 " --> pdb=" O LEU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 473 Proline residue: F 449 - end of helix removed outlier: 3.669A pdb=" N ARG F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) Proline residue: F 459 - end of helix Processing helix chain 'G' and resid 59 through 66 removed outlier: 3.939A pdb=" N ILE G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 130 Processing helix chain 'G' and resid 138 through 140 No H-bonds generated for 'chain 'G' and resid 138 through 140' Processing helix chain 'G' and resid 148 through 155 Processing helix chain 'G' and resid 164 through 167 removed outlier: 3.541A pdb=" N ASN G 167 " --> pdb=" O THR G 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 164 through 167' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 195 through 202 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 233 through 239 Processing helix chain 'G' and resid 302 through 305 No H-bonds generated for 'chain 'G' and resid 302 through 305' Processing helix chain 'G' and resid 310 through 312 No H-bonds generated for 'chain 'G' and resid 310 through 312' Processing helix chain 'G' and resid 333 through 347 removed outlier: 3.698A pdb=" N ALA G 343 " --> pdb=" O ALA G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 373 Processing helix chain 'G' and resid 389 through 391 No H-bonds generated for 'chain 'G' and resid 389 through 391' Processing helix chain 'G' and resid 393 through 396 removed outlier: 4.003A pdb=" N TYR G 396 " --> pdb=" O ARG G 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 393 through 396' Processing helix chain 'G' and resid 402 through 407 removed outlier: 4.264A pdb=" N GLU G 406 " --> pdb=" O ILE G 402 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 402 through 407' Processing helix chain 'G' and resid 418 through 421 No H-bonds generated for 'chain 'G' and resid 418 through 421' Processing helix chain 'G' and resid 423 through 435 removed outlier: 3.542A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 468 removed outlier: 3.644A pdb=" N CYS G 467 " --> pdb=" O LYS G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 479 removed outlier: 4.122A pdb=" N VAL G 476 " --> pdb=" O ALA G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 493 Processing helix chain 'G' and resid 495 through 511 removed outlier: 4.138A pdb=" N ALA G 498 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL G 504 " --> pdb=" O HIS G 501 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS G 508 " --> pdb=" O ALA G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 534 removed outlier: 4.253A pdb=" N GLY G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 546 removed outlier: 3.624A pdb=" N VAL G 544 " --> pdb=" O GLN G 541 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS G 545 " --> pdb=" O THR G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 584 No H-bonds generated for 'chain 'G' and resid 581 through 584' Processing helix chain 'G' and resid 595 through 597 No H-bonds generated for 'chain 'G' and resid 595 through 597' Processing helix chain 'G' and resid 625 through 636 removed outlier: 3.575A pdb=" N LEU G 629 " --> pdb=" O ASP G 625 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU G 634 " --> pdb=" O ARG G 630 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 635 " --> pdb=" O ALA G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 655 Processing helix chain 'G' and resid 657 through 660 Processing helix chain 'G' and resid 694 through 697 No H-bonds generated for 'chain 'G' and resid 694 through 697' Processing helix chain 'G' and resid 701 through 704 No H-bonds generated for 'chain 'G' and resid 701 through 704' Processing helix chain 'G' and resid 707 through 726 Processing helix chain 'H' and resid 2 through 38 removed outlier: 3.709A pdb=" N PHE H 6 " --> pdb=" O PHE H 2 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE H 7 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 59 Proline residue: H 55 - end of helix Processing helix chain 'H' and resid 75 through 95 Proline residue: H 82 - end of helix removed outlier: 4.446A pdb=" N TRP H 93 " --> pdb=" O SER H 89 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 130 removed outlier: 4.273A pdb=" N VAL H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 123 " --> pdb=" O GLY H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 164 removed outlier: 3.520A pdb=" N GLN H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER H 152 " --> pdb=" O SER H 148 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE H 164 " --> pdb=" O PHE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 175 removed outlier: 3.694A pdb=" N TYR H 175 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 186 through 200 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing helix chain 'H' and resid 224 through 249 Processing helix chain 'H' and resid 258 through 274 Processing helix chain 'H' and resid 282 through 291 removed outlier: 4.302A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 314 removed outlier: 3.523A pdb=" N TYR H 300 " --> pdb=" O PHE H 296 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU H 302 " --> pdb=" O LEU H 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 removed outlier: 3.644A pdb=" N ASP I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.711A pdb=" N ARG I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY I 74 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 186 through 188 No H-bonds generated for 'chain 'I' and resid 186 through 188' Processing helix chain 'I' and resid 192 through 201 Processing helix chain 'I' and resid 203 through 211 Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 23 through 44 removed outlier: 3.570A pdb=" N GLY J 42 " --> pdb=" O CYS J 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET J 44 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 72 Processing helix chain 'J' and resid 82 through 100 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 134 through 137 Processing helix chain 'J' and resid 141 through 163 removed outlier: 3.633A pdb=" N ASN J 150 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE J 154 " --> pdb=" O TYR J 151 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE J 159 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL J 160 " --> pdb=" O ILE J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 8 through 22 Processing helix chain 'K' and resid 28 through 52 removed outlier: 3.685A pdb=" N LEU K 33 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU K 36 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL K 39 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE K 43 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU K 50 " --> pdb=" O PHE K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 85 removed outlier: 3.631A pdb=" N VAL K 68 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU K 73 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE K 77 " --> pdb=" O GLY K 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS K 85 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 6 through 31 removed outlier: 3.851A pdb=" N VAL L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 80 removed outlier: 4.321A pdb=" N GLU L 79 " --> pdb=" O PHE L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 106 Processing helix chain 'L' and resid 110 through 128 removed outlier: 3.828A pdb=" N LEU L 114 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY L 116 " --> pdb=" O SER L 112 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR L 125 " --> pdb=" O GLY L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 164 removed outlier: 4.050A pdb=" N GLY L 150 " --> pdb=" O SER L 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 159 " --> pdb=" O LEU L 155 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR L 164 " --> pdb=" O TRP L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 172 No H-bonds generated for 'chain 'L' and resid 169 through 172' Processing helix chain 'L' and resid 180 through 197 removed outlier: 3.535A pdb=" N LEU L 191 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS L 196 " --> pdb=" O ALA L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 211 removed outlier: 3.540A pdb=" N TRP L 205 " --> pdb=" O PHE L 202 " (cutoff:3.500A) Proline residue: L 207 - end of helix removed outlier: 3.523A pdb=" N ALA L 211 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 220 Processing helix chain 'L' and resid 225 through 242 removed outlier: 3.890A pdb=" N GLY L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL L 230 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE L 239 " --> pdb=" O ARG L 235 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 240 " --> pdb=" O PHE L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 265 removed outlier: 3.876A pdb=" N ASN L 265 " --> pdb=" O GLY L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 291 removed outlier: 3.605A pdb=" N LEU L 284 " --> pdb=" O SER L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 321 removed outlier: 3.502A pdb=" N LEU L 310 " --> pdb=" O LEU L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 337 No H-bonds generated for 'chain 'L' and resid 334 through 337' Processing helix chain 'L' and resid 339 through 353 removed outlier: 3.766A pdb=" N SER L 348 " --> pdb=" O CYS L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 373 removed outlier: 3.997A pdb=" N SER L 363 " --> pdb=" O ALA L 359 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET L 366 " --> pdb=" O TYR L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 402 removed outlier: 3.518A pdb=" N THR L 388 " --> pdb=" O TYR L 384 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER L 395 " --> pdb=" O THR L 391 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 444 removed outlier: 4.009A pdb=" N GLY L 425 " --> pdb=" O ILE L 421 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET L 426 " --> pdb=" O MET L 422 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY L 428 " --> pdb=" O ARG L 424 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU L 429 " --> pdb=" O GLY L 425 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET L 432 " --> pdb=" O GLY L 428 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE L 434 " --> pdb=" O LEU L 430 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY L 437 " --> pdb=" O SER L 433 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER L 438 " --> pdb=" O ILE L 434 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP L 442 " --> pdb=" O SER L 438 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU L 443 " --> pdb=" O MET L 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 476 removed outlier: 4.838A pdb=" N LEU L 460 " --> pdb=" O TYR L 456 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR L 461 " --> pdb=" O MET L 457 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU L 462 " --> pdb=" O LYS L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 485 through 488 No H-bonds generated for 'chain 'L' and resid 485 through 488' Processing helix chain 'L' and resid 490 through 507 removed outlier: 3.692A pdb=" N MET L 499 " --> pdb=" O PHE L 495 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP L 500 " --> pdb=" O LEU L 496 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE L 501 " --> pdb=" O GLY L 497 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET L 502 " --> pdb=" O SER L 498 " (cutoff:3.500A) Proline residue: L 503 - end of helix Processing helix chain 'L' and resid 511 through 524 removed outlier: 3.560A pdb=" N LEU L 515 " --> pdb=" O ILE L 511 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN L 519 " --> pdb=" O LEU L 515 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 532 No H-bonds generated for 'chain 'L' and resid 529 through 532' Processing helix chain 'L' and resid 535 through 553 removed outlier: 3.519A pdb=" N MET L 544 " --> pdb=" O GLN L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 576 Processing helix chain 'M' and resid 2 through 15 Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 21 through 37 removed outlier: 3.859A pdb=" N GLN M 25 " --> pdb=" O TYR M 21 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE M 26 " --> pdb=" O TRP M 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET M 27 " --> pdb=" O MET M 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER M 32 " --> pdb=" O MET M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 75 removed outlier: 3.532A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU M 73 " --> pdb=" O CYS M 69 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 81 Processing helix chain 'M' and resid 86 through 105 Processing helix chain 'M' and resid 109 through 130 removed outlier: 3.692A pdb=" N SER M 118 " --> pdb=" O LEU M 114 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU M 120 " --> pdb=" O PHE M 116 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE M 121 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Proline residue: M 122 - end of helix Processing helix chain 'M' and resid 134 through 165 removed outlier: 3.683A pdb=" N LEU M 137 " --> pdb=" O PRO M 134 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA M 139 " --> pdb=" O ARG M 136 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU M 141 " --> pdb=" O GLN M 138 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR M 142 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU M 143 " --> pdb=" O GLY M 140 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR M 146 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR M 147 " --> pdb=" O LEU M 144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU M 148 " --> pdb=" O PHE M 145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU M 149 " --> pdb=" O TYR M 146 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU M 152 " --> pdb=" O LEU M 149 " (cutoff:3.500A) Proline residue: M 153 - end of helix removed outlier: 3.624A pdb=" N TYR M 160 " --> pdb=" O GLY M 157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN M 163 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE M 165 " --> pdb=" O MET M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 175 removed outlier: 4.129A pdb=" N ASN M 175 " --> pdb=" O TYR M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 185 removed outlier: 3.522A pdb=" N PHE M 185 " --> pdb=" O ASP M 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 181 through 185' Processing helix chain 'M' and resid 189 through 194 removed outlier: 4.071A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 200 No H-bonds generated for 'chain 'M' and resid 198 through 200' Processing helix chain 'M' and resid 204 through 210 Processing helix chain 'M' and resid 213 through 221 Processing helix chain 'M' and resid 223 through 234 removed outlier: 3.753A pdb=" N GLY M 227 " --> pdb=" O MET M 223 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 265 removed outlier: 4.096A pdb=" N LYS M 244 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR M 245 " --> pdb=" O MET M 241 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE M 247 " --> pdb=" O LEU M 243 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL M 248 " --> pdb=" O LYS M 244 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP M 249 " --> pdb=" O TYR M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 291 removed outlier: 3.505A pdb=" N VAL M 279 " --> pdb=" O ALA M 275 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 325 removed outlier: 3.646A pdb=" N ARG M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'M' and resid 341 through 354 removed outlier: 3.819A pdb=" N LEU M 345 " --> pdb=" O PRO M 341 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TRP M 346 " --> pdb=" O SER M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 376 removed outlier: 3.728A pdb=" N TYR M 368 " --> pdb=" O LEU M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 403 removed outlier: 3.956A pdb=" N LEU M 383 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU M 384 " --> pdb=" O MET M 381 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 387 " --> pdb=" O LEU M 384 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER M 391 " --> pdb=" O SER M 388 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR M 394 " --> pdb=" O SER M 391 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU M 396 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER M 400 " --> pdb=" O TYR M 397 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE M 401 " --> pdb=" O LEU M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 436 Proline residue: M 431 - end of helix removed outlier: 4.951A pdb=" N ILE M 436 " --> pdb=" O LEU M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 443 Processing helix chain 'N' and resid 5 through 22 Processing helix chain 'N' and resid 27 through 45 removed outlier: 3.529A pdb=" N LEU N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) Proline residue: N 43 - end of helix Processing helix chain 'N' and resid 51 through 81 removed outlier: 3.826A pdb=" N GLU N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 105 removed outlier: 3.707A pdb=" N ILE N 97 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 110 No H-bonds generated for 'chain 'N' and resid 108 through 110' Processing helix chain 'N' and resid 112 through 117 removed outlier: 3.515A pdb=" N ASN N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 130 Processing helix chain 'N' and resid 132 through 141 removed outlier: 4.232A pdb=" N ALA N 136 " --> pdb=" O GLN N 133 " (cutoff:3.500A) Proline residue: N 137 - end of helix Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.886A pdb=" N GLY N 165 " --> pdb=" O GLY N 161 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN N 167 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 190 Processing helix chain 'N' and resid 195 through 218 removed outlier: 3.657A pdb=" N PHE N 213 " --> pdb=" O PHE N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 228 removed outlier: 3.718A pdb=" N PHE N 227 " --> pdb=" O LEU N 223 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 247 removed outlier: 3.613A pdb=" N MET N 242 " --> pdb=" O PHE N 238 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN N 243 " --> pdb=" O THR N 239 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE N 244 " --> pdb=" O LEU N 240 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU N 245 " --> pdb=" O PHE N 241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER N 246 " --> pdb=" O MET N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 266 Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 272 through 295 removed outlier: 3.650A pdb=" N LEU N 283 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE N 284 " --> pdb=" O MET N 280 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER N 295 " --> pdb=" O ARG N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 314 through 335 removed outlier: 3.530A pdb=" N ILE N 322 " --> pdb=" O ASN N 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE N 326 " --> pdb=" O ILE N 322 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU N 331 " --> pdb=" O SER N 327 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE N 332 " --> pdb=" O ILE N 328 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU N 333 " --> pdb=" O PHE N 329 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE N 334 " --> pdb=" O GLY N 330 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER N 335 " --> pdb=" O LEU N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 46 No H-bonds generated for 'chain 'O' and resid 43 through 46' Processing helix chain 'O' and resid 66 through 69 No H-bonds generated for 'chain 'O' and resid 66 through 69' Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 116 through 120 removed outlier: 3.593A pdb=" N TYR O 120 " --> pdb=" O ASP O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 133 Proline residue: O 133 - end of helix Processing helix chain 'O' and resid 137 through 139 No H-bonds generated for 'chain 'O' and resid 137 through 139' Processing helix chain 'O' and resid 144 through 149 Processing helix chain 'O' and resid 154 through 181 removed outlier: 3.553A pdb=" N ALA O 157 " --> pdb=" O ASP O 154 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG O 167 " --> pdb=" O TYR O 164 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER O 180 " --> pdb=" O HIS O 177 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR O 181 " --> pdb=" O VAL O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 203 removed outlier: 4.162A pdb=" N PHE O 195 " --> pdb=" O TYR O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 225 removed outlier: 4.519A pdb=" N GLY O 224 " --> pdb=" O GLN O 220 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU O 225 " --> pdb=" O ASN O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 249 removed outlier: 3.675A pdb=" N LYS O 247 " --> pdb=" O LYS O 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG O 249 " --> pdb=" O GLN O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 256 Processing helix chain 'O' and resid 262 through 274 Processing helix chain 'O' and resid 276 through 282 removed outlier: 4.433A pdb=" N THR O 282 " --> pdb=" O LYS O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 306 removed outlier: 3.636A pdb=" N ARG O 306 " --> pdb=" O GLU O 302 " (cutoff:3.500A) Processing helix chain 'O' and resid 311 through 313 No H-bonds generated for 'chain 'O' and resid 311 through 313' Processing helix chain 'O' and resid 329 through 341 Processing helix chain 'O' and resid 343 through 348 Processing helix chain 'O' and resid 364 through 376 Processing helix chain 'O' and resid 388 through 390 No H-bonds generated for 'chain 'O' and resid 388 through 390' Processing helix chain 'O' and resid 395 through 397 No H-bonds generated for 'chain 'O' and resid 395 through 397' Processing helix chain 'P' and resid 48 through 50 No H-bonds generated for 'chain 'P' and resid 48 through 50' Processing helix chain 'P' and resid 74 through 86 removed outlier: 4.156A pdb=" N TYR P 78 " --> pdb=" O PHE P 74 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER P 86 " --> pdb=" O LYS P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 106 removed outlier: 4.423A pdb=" N ARG P 103 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU P 104 " --> pdb=" O ASP P 100 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL P 106 " --> pdb=" O ILE P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 129 removed outlier: 3.639A pdb=" N ASP P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA P 129 " --> pdb=" O SER P 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 154 No H-bonds generated for 'chain 'P' and resid 151 through 154' Processing helix chain 'P' and resid 157 through 169 Processing helix chain 'P' and resid 196 through 211 Processing helix chain 'P' and resid 248 through 251 Processing helix chain 'P' and resid 261 through 273 Processing helix chain 'P' and resid 292 through 302 Processing helix chain 'P' and resid 322 through 333 Processing helix chain 'P' and resid 339 through 341 No H-bonds generated for 'chain 'P' and resid 339 through 341' Processing helix chain 'P' and resid 344 through 351 removed outlier: 3.502A pdb=" N ARG P 349 " --> pdb=" O ALA P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 366 Processing helix chain 'P' and resid 373 through 380 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 382 through 384 No H-bonds generated for 'chain 'P' and resid 382 through 384' Processing helix chain 'P' and resid 408 through 414 removed outlier: 3.538A pdb=" N LEU P 412 " --> pdb=" O ALA P 408 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 44 Processing helix chain 'Q' and resid 47 through 57 Processing helix chain 'Q' and resid 69 through 72 No H-bonds generated for 'chain 'Q' and resid 69 through 72' Processing helix chain 'Q' and resid 76 through 81 Processing helix chain 'Q' and resid 127 through 130 Processing helix chain 'Q' and resid 138 through 148 Processing helix chain 'Q' and resid 169 through 171 No H-bonds generated for 'chain 'Q' and resid 169 through 171' Processing helix chain 'R' and resid 34 through 37 No H-bonds generated for 'chain 'R' and resid 34 through 37' Processing helix chain 'R' and resid 51 through 56 Processing helix chain 'R' and resid 68 through 74 removed outlier: 3.585A pdb=" N GLU R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'T' and resid 72 through 85 Processing helix chain 'T' and resid 108 through 122 removed outlier: 4.085A pdb=" N ASP T 120 " --> pdb=" O MET T 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 131 No H-bonds generated for 'chain 'T' and resid 128 through 131' Processing helix chain 'T' and resid 137 through 145 Processing helix chain 'U' and resid 72 through 85 Processing helix chain 'U' and resid 108 through 122 Processing helix chain 'U' and resid 130 through 133 Processing helix chain 'U' and resid 137 through 147 Processing helix chain 'V' and resid 20 through 36 Processing helix chain 'V' and resid 43 through 61 removed outlier: 3.582A pdb=" N LYS V 53 " --> pdb=" O GLU V 49 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER V 58 " --> pdb=" O GLN V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 72 Processing helix chain 'V' and resid 77 through 97 removed outlier: 3.605A pdb=" N ASN V 86 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU V 87 " --> pdb=" O GLN V 83 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP V 97 " --> pdb=" O LYS V 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 46 Proline residue: W 41 - end of helix removed outlier: 3.597A pdb=" N MET W 45 " --> pdb=" O PRO W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 66 Processing helix chain 'W' and resid 73 through 91 removed outlier: 3.523A pdb=" N LEU W 87 " --> pdb=" O GLY W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 103 removed outlier: 3.570A pdb=" N MET W 101 " --> pdb=" O LYS W 97 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR W 103 " --> pdb=" O HIS W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 121 Processing helix chain 'X' and resid 12 through 15 No H-bonds generated for 'chain 'X' and resid 12 through 15' Processing helix chain 'X' and resid 24 through 29 Processing helix chain 'X' and resid 31 through 51 removed outlier: 3.666A pdb=" N LYS X 36 " --> pdb=" O PHE X 32 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN X 37 " --> pdb=" O HIS X 33 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN X 40 " --> pdb=" O LYS X 36 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ALA X 41 " --> pdb=" O GLN X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 78 removed outlier: 4.469A pdb=" N ALA X 60 " --> pdb=" O ALA X 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR X 66 " --> pdb=" O LYS X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 93 Processing helix chain 'X' and resid 104 through 117 Processing helix chain 'Y' and resid 8 through 10 No H-bonds generated for 'chain 'Y' and resid 8 through 10' Processing helix chain 'Y' and resid 17 through 42 removed outlier: 3.728A pdb=" N TYR Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 81 removed outlier: 3.992A pdb=" N LEU Y 53 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY Y 54 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Proline residue: Y 62 - end of helix removed outlier: 3.648A pdb=" N ALA Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 104 removed outlier: 3.556A pdb=" N PHE Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA Y 96 " --> pdb=" O GLY Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 36 through 101 removed outlier: 3.606A pdb=" N LEU Z 56 " --> pdb=" O GLY Z 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL Z 74 " --> pdb=" O SER Z 70 " (cutoff:3.500A) Proline residue: Z 77 - end of helix removed outlier: 4.050A pdb=" N ARG Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG Z 93 " --> pdb=" O ARG Z 89 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA Z 99 " --> pdb=" O ARG Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 136 Processing helix chain 'Z' and resid 141 through 148 removed outlier: 3.704A pdb=" N ARG Z 147 " --> pdb=" O SER Z 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 30 removed outlier: 3.603A pdb=" N ILE a 5 " --> pdb=" O TRP a 2 " (cutoff:3.500A) Proline residue: a 7 - end of helix removed outlier: 3.753A pdb=" N VAL a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE a 11 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE a 12 " --> pdb=" O ALA a 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU a 16 " --> pdb=" O THR a 13 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.766A pdb=" N MET a 23 " --> pdb=" O ILE a 20 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR a 24 " --> pdb=" O TYR a 21 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP a 27 " --> pdb=" O TYR a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 54 Processing helix chain 'a' and resid 64 through 66 No H-bonds generated for 'chain 'a' and resid 64 through 66' Processing helix chain 'b' and resid 12 through 19 Processing helix chain 'b' and resid 21 through 46 Processing helix chain 'b' and resid 66 through 70 removed outlier: 4.020A pdb=" N LYS b 70 " --> pdb=" O PRO b 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 66 through 70' Processing helix chain 'd' and resid 7 through 11 Processing helix chain 'd' and resid 23 through 45 removed outlier: 4.633A pdb=" N ASN d 27 " --> pdb=" O SER d 23 " (cutoff:3.500A) Proline residue: d 28 - end of helix removed outlier: 3.541A pdb=" N ASN d 43 " --> pdb=" O ALA d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 93 removed outlier: 3.695A pdb=" N GLU d 77 " --> pdb=" O GLN d 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 107 No H-bonds generated for 'chain 'd' and resid 105 through 107' Processing helix chain 'e' and resid 10 through 15 Processing helix chain 'e' and resid 28 through 41 Processing helix chain 'e' and resid 43 through 49 removed outlier: 4.165A pdb=" N ARG e 48 " --> pdb=" O GLU e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 Processing helix chain 'e' and resid 64 through 82 removed outlier: 4.176A pdb=" N ALA e 72 " --> pdb=" O MET e 68 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 32 Proline residue: f 15 - end of helix removed outlier: 3.543A pdb=" N ILE f 21 " --> pdb=" O GLY f 18 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU f 25 " --> pdb=" O GLY f 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP f 26 " --> pdb=" O HIS f 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 84 Processing helix chain 'g' and resid 88 through 95 Processing helix chain 'g' and resid 104 through 119 removed outlier: 3.581A pdb=" N LEU g 114 " --> pdb=" O GLY g 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 140 through 143 No H-bonds generated for 'chain 'g' and resid 140 through 143' Processing helix chain 'h' and resid 53 through 83 Proline residue: h 72 - end of helix Processing helix chain 'h' and resid 100 through 103 Processing helix chain 'h' and resid 107 through 115 Processing helix chain 'h' and resid 120 through 154 removed outlier: 3.565A pdb=" N ALA h 138 " --> pdb=" O GLU h 134 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP h 145 " --> pdb=" O ARG h 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU h 146 " --> pdb=" O LEU h 142 " (cutoff:3.500A) Processing helix chain 'h' and resid 168 through 183 removed outlier: 3.527A pdb=" N LEU h 183 " --> pdb=" O GLU h 179 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 22 removed outlier: 3.795A pdb=" N VAL i 22 " --> pdb=" O GLY i 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 19 through 22' Processing helix chain 'i' and resid 24 through 28 Processing helix chain 'i' and resid 33 through 46 Processing helix chain 'i' and resid 56 through 61 removed outlier: 3.762A pdb=" N LEU i 60 " --> pdb=" O PRO i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 70 Processing helix chain 'i' and resid 72 through 85 removed outlier: 3.822A pdb=" N VAL i 77 " --> pdb=" O PRO i 73 " (cutoff:3.500A) Proline residue: i 83 - end of helix Processing helix chain 'i' and resid 87 through 116 removed outlier: 3.536A pdb=" N LEU i 101 " --> pdb=" O THR i 97 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 154 No H-bonds generated for 'chain 'i' and resid 152 through 154' Processing helix chain 'j' and resid 42 through 65 removed outlier: 3.801A pdb=" N LEU j 49 " --> pdb=" O LYS j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 79 through 81 No H-bonds generated for 'chain 'j' and resid 79 through 81' Processing helix chain 'k' and resid 14 through 16 No H-bonds generated for 'chain 'k' and resid 14 through 16' Processing helix chain 'k' and resid 19 through 21 No H-bonds generated for 'chain 'k' and resid 19 through 21' Processing helix chain 'k' and resid 23 through 35 removed outlier: 3.652A pdb=" N VAL k 28 " --> pdb=" O GLN k 24 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA k 31 " --> pdb=" O GLU k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 49 removed outlier: 3.541A pdb=" N TRP k 47 " --> pdb=" O ASN k 44 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 54 No H-bonds generated for 'chain 'k' and resid 51 through 54' Processing helix chain 'k' and resid 57 through 66 Processing helix chain 'k' and resid 69 through 85 Processing helix chain 'l' and resid 33 through 35 No H-bonds generated for 'chain 'l' and resid 33 through 35' Processing helix chain 'l' and resid 45 through 55 removed outlier: 3.517A pdb=" N ALA l 50 " --> pdb=" O LYS l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 86 No H-bonds generated for 'chain 'l' and resid 84 through 86' Processing helix chain 'l' and resid 128 through 148 removed outlier: 3.854A pdb=" N PHE l 132 " --> pdb=" O ASN l 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU l 145 " --> pdb=" O GLY l 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 29 removed outlier: 3.689A pdb=" N LEU m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 37 removed outlier: 3.512A pdb=" N THR m 37 " --> pdb=" O TYR m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 56 removed outlier: 3.599A pdb=" N VAL m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 61 No H-bonds generated for 'chain 'm' and resid 59 through 61' Processing helix chain 'm' and resid 67 through 75 Processing helix chain 'm' and resid 77 through 100 removed outlier: 3.534A pdb=" N LYS m 97 " --> pdb=" O GLY m 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR m 98 " --> pdb=" O ARG m 94 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 48 removed outlier: 3.524A pdb=" N PHE n 47 " --> pdb=" O LEU n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 72 removed outlier: 3.520A pdb=" N ARG n 60 " --> pdb=" O GLY n 56 " (cutoff:3.500A) Processing helix chain 'n' and resid 97 through 102 Processing helix chain 'n' and resid 105 through 133 removed outlier: 3.863A pdb=" N GLN n 110 " --> pdb=" O LEU n 106 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR n 111 " --> pdb=" O GLU n 107 " (cutoff:3.500A) Proline residue: n 112 - end of helix removed outlier: 3.553A pdb=" N LYS n 123 " --> pdb=" O GLU n 119 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR n 127 " --> pdb=" O LYS n 123 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 9 Processing helix chain 'o' and resid 41 through 46 Processing helix chain 'o' and resid 51 through 53 No H-bonds generated for 'chain 'o' and resid 51 through 53' Processing helix chain 'o' and resid 58 through 71 Processing helix chain 'o' and resid 75 through 112 removed outlier: 5.467A pdb=" N HIS o 80 " --> pdb=" O LYS o 77 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR o 85 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU o 89 " --> pdb=" O LEU o 86 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR o 90 " --> pdb=" O THR o 87 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG o 102 " --> pdb=" O GLU o 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU o 107 " --> pdb=" O ARG o 104 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN o 110 " --> pdb=" O LEU o 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 29 removed outlier: 3.559A pdb=" N SER p 14 " --> pdb=" O SER p 10 " (cutoff:3.500A) Proline residue: p 22 - end of helix Processing helix chain 'p' and resid 31 through 34 No H-bonds generated for 'chain 'p' and resid 31 through 34' Processing helix chain 'p' and resid 51 through 53 No H-bonds generated for 'chain 'p' and resid 51 through 53' Processing helix chain 'p' and resid 60 through 93 removed outlier: 3.673A pdb=" N VAL p 80 " --> pdb=" O ASP p 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU p 92 " --> pdb=" O GLU p 88 " (cutoff:3.500A) Processing helix chain 'p' and resid 99 through 119 Proline residue: p 104 - end of helix Processing helix chain 'p' and resid 129 through 146 Processing helix chain 'q' and resid 9 through 20 Processing helix chain 'q' and resid 22 through 33 Processing helix chain 'q' and resid 59 through 61 No H-bonds generated for 'chain 'q' and resid 59 through 61' Processing helix chain 'q' and resid 77 through 79 No H-bonds generated for 'chain 'q' and resid 77 through 79' Processing helix chain 'q' and resid 82 through 88 removed outlier: 4.316A pdb=" N GLY q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TRP q 87 " --> pdb=" O GLU q 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 98 No H-bonds generated for 'chain 'q' and resid 96 through 98' Processing helix chain 'r' and resid 10 through 20 Processing helix chain 'r' and resid 57 through 60 No H-bonds generated for 'chain 'r' and resid 57 through 60' Processing helix chain 'r' and resid 63 through 65 No H-bonds generated for 'chain 'r' and resid 63 through 65' Processing helix chain 'r' and resid 72 through 77 removed outlier: 3.712A pdb=" N GLN r 76 " --> pdb=" O LEU r 72 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS r 77 " --> pdb=" O VAL r 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 72 through 77' Processing helix chain 's' and resid 55 through 57 No H-bonds generated for 'chain 's' and resid 55 through 57' Processing helix chain 's' and resid 80 through 83 Processing helix chain 's' and resid 89 through 99 removed outlier: 3.737A pdb=" N VAL s 95 " --> pdb=" O ALA s 91 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU s 96 " --> pdb=" O GLU s 92 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA s 98 " --> pdb=" O GLU s 94 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS s 99 " --> pdb=" O VAL s 95 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.728A pdb=" N TRP B 154 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL B 130 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 156 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 186 " --> pdb=" O SER B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 112 through 120 removed outlier: 6.560A pdb=" N ASN C 133 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE C 116 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL C 131 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY C 118 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU C 129 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 86 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS C 146 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 88 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N TYR C 148 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ILE C 90 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 210 through 215 removed outlier: 3.656A pdb=" N ARG C 220 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 85 through 89 removed outlier: 3.773A pdb=" N ARG D 113 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP D 107 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 399 through 407 removed outlier: 3.646A pdb=" N THR D 403 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 413 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 426 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 162 through 167 removed outlier: 6.852A pdb=" N TYR E 123 " --> pdb=" O THR E 163 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER E 165 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE E 125 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL E 167 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL E 127 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS E 128 " --> pdb=" O MET E 178 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N MET E 178 " --> pdb=" O CYS E 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 254 through 259 removed outlier: 3.517A pdb=" N THR F 256 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA F 168 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL F 130 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR F 170 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA F 132 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR F 172 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP F 209 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE F 171 " --> pdb=" O ASP F 209 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE F 211 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE F 173 " --> pdb=" O PHE F 211 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS F 213 " --> pdb=" O ILE F 173 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 301 through 306 removed outlier: 5.983A pdb=" N ILE F 369 " --> pdb=" O SER F 294 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 42 through 46 Processing sheet with id= J, first strand: chain 'G' and resid 183 through 185 Processing sheet with id= K, first strand: chain 'G' and resid 260 through 265 removed outlier: 3.897A pdb=" N ARG G 286 " --> pdb=" O SER G 278 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 320 through 322 Processing sheet with id= M, first strand: chain 'G' and resid 378 through 380 removed outlier: 4.478A pdb=" N VAL G 378 " --> pdb=" O ILE G 351 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL G 550 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE G 354 " --> pdb=" O VAL G 550 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE G 552 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE G 571 " --> pdb=" O LEU G 551 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU G 553 " --> pdb=" O PHE G 571 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL G 573 " --> pdb=" O LEU G 553 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA G 588 " --> pdb=" O TYR G 574 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY G 576 " --> pdb=" O ALA G 588 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU G 590 " --> pdb=" O GLY G 576 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 439 through 443 Processing sheet with id= O, first strand: chain 'G' and resid 601 through 603 Processing sheet with id= P, first strand: chain 'I' and resid 106 through 108 Processing sheet with id= Q, first strand: chain 'I' and resid 133 through 139 removed outlier: 5.877A pdb=" N GLU I 138 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR I 147 " --> pdb=" O GLU I 138 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 35 through 44 removed outlier: 6.902A pdb=" N ILE L 49 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER L 43 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N MET L 47 " --> pdb=" O SER L 43 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'O' and resid 285 through 289 removed outlier: 6.409A pdb=" N VAL O 185 " --> pdb=" O ILE O 85 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL O 87 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU O 187 " --> pdb=" O VAL O 87 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY O 89 " --> pdb=" O LEU O 187 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU O 109 " --> pdb=" O VAL O 186 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 65 through 67 removed outlier: 6.586A pdb=" N GLN P 89 " --> pdb=" O ALA P 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS P 116 " --> pdb=" O LEU P 92 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 135 through 138 removed outlier: 6.692A pdb=" N ARG P 173 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN P 138 " --> pdb=" O ARG P 173 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE P 175 " --> pdb=" O ASN P 138 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR P 216 " --> pdb=" O HIS P 176 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Q' and resid 151 through 154 removed outlier: 3.690A pdb=" N VAL Q 133 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'R' and resid 78 through 80 Processing sheet with id= X, first strand: chain 'R' and resid 84 through 87 Processing sheet with id= Y, first strand: chain 'q' and resid 63 through 66 removed outlier: 6.669A pdb=" N GLU q 53 " --> pdb=" O LEU q 41 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU q 41 " --> pdb=" O GLU q 53 " (cutoff:3.500A) 2670 hydrogen bonds defined for protein. 7155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.82 Time building geometry restraints manager: 24.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.37: 22914 1.37 - 1.60: 44824 1.60 - 1.83: 833 1.83 - 2.05: 0 2.05 - 2.28: 80 Bond restraints: 68651 Sorted by residual: bond pdb=" C1' DGT O 501 " pdb=" O4' DGT O 501 " ideal model delta sigma weight residual 1.536 1.302 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1 UQ9 H 501 " pdb=" C6 UQ9 H 501 " ideal model delta sigma weight residual 1.345 1.542 -0.197 2.00e-02 2.50e+03 9.66e+01 bond pdb=" C3 UQ9 H 501 " pdb=" C4 UQ9 H 501 " ideal model delta sigma weight residual 1.340 1.525 -0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" C5N NDP P 501 " pdb=" C6N NDP P 501 " ideal model delta sigma weight residual 1.337 1.545 -0.208 2.40e-02 1.74e+03 7.53e+01 bond pdb=" C1' DGT O 501 " pdb=" C2' DGT O 501 " ideal model delta sigma weight residual 1.362 1.531 -0.169 2.00e-02 2.50e+03 7.18e+01 ... (remaining 68646 not shown) Histogram of bond angle deviations from ideal: 72.88 - 86.06: 76 86.06 - 99.23: 22 99.23 - 112.41: 35964 112.41 - 125.58: 55474 125.58 - 138.75: 1265 Bond angle restraints: 92801 Sorted by residual: angle pdb=" CA3 CDL h 202 " pdb=" OA5 CDL h 202 " pdb=" PA1 CDL h 202 " ideal model delta sigma weight residual 121.27 112.53 8.74 1.00e+00 1.00e+00 7.64e+01 angle pdb=" C51 CDL P 502 " pdb=" CB5 CDL P 502 " pdb=" OB6 CDL P 502 " ideal model delta sigma weight residual 111.33 122.09 -10.76 1.32e+00 5.72e-01 6.62e+01 angle pdb=" C11 CDL h 202 " pdb=" CA5 CDL h 202 " pdb=" OA6 CDL h 202 " ideal model delta sigma weight residual 111.33 121.38 -10.05 1.32e+00 5.72e-01 5.78e+01 angle pdb=" C1' DGT O 501 " pdb=" N9 DGT O 501 " pdb=" C8 DGT O 501 " ideal model delta sigma weight residual 116.68 138.75 -22.07 3.00e+00 1.11e-01 5.41e+01 angle pdb=" O1X NDP P 501 " pdb=" P2B NDP P 501 " pdb=" O3X NDP P 501 " ideal model delta sigma weight residual 117.46 109.35 8.11 1.17e+00 7.36e-01 4.83e+01 ... (remaining 92796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 40161 34.20 - 68.41: 954 68.41 - 102.61: 80 102.61 - 136.82: 11 136.82 - 171.02: 12 Dihedral angle restraints: 41218 sinusoidal: 17424 harmonic: 23794 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 88.90 168.69 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA PHE N 297 " pdb=" C PHE N 297 " pdb=" N MET N 298 " pdb=" CA MET N 298 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CB CYS X 90 " pdb=" SG CYS X 90 " pdb=" SG CYS X 103 " pdb=" CB CYS X 103 " ideal model delta sinusoidal sigma weight residual 93.00 140.19 -47.19 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 41215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.208: 9926 4.208 - 8.416: 0 8.416 - 12.624: 0 12.624 - 16.832: 0 16.832 - 21.040: 16 Chirality restraints: 9942 Sorted by residual: chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.49 21.04 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.46 21.01 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 I 301 " pdb=" S2 SF4 I 301 " pdb=" S3 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False -10.55 10.45 -21.01 2.00e-01 2.50e+01 1.10e+04 ... (remaining 9939 not shown) Planarity restraints: 11646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGT O 501 " 0.255 2.00e-02 2.50e+03 5.55e-01 6.16e+03 pdb=" C2' DGT O 501 " -0.949 2.00e-02 2.50e+03 pdb=" C3' DGT O 501 " -0.391 2.00e-02 2.50e+03 pdb=" C4' DGT O 501 " 0.376 2.00e-02 2.50e+03 pdb=" C5' DGT O 501 " -0.424 2.00e-02 2.50e+03 pdb=" N9 DGT O 501 " -0.187 2.00e-02 2.50e+03 pdb=" O3' DGT O 501 " 0.417 2.00e-02 2.50e+03 pdb=" O4' DGT O 501 " 0.903 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP P 501 " -0.378 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C3N NDP P 501 " -0.197 2.00e-02 2.50e+03 pdb=" C4N NDP P 501 " 0.008 2.00e-02 2.50e+03 pdb=" C7N NDP P 501 " 0.244 2.00e-02 2.50e+03 pdb=" N1N NDP P 501 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN g 52 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO g 53 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO g 53 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO g 53 " 0.049 5.00e-02 4.00e+02 ... (remaining 11643 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 491 2.52 - 3.12: 55805 3.12 - 3.71: 105400 3.71 - 4.31: 155587 4.31 - 4.90: 255583 Nonbonded interactions: 572866 Sorted by model distance: nonbonded pdb=" OH TYR h 124 " pdb=" OE1 GLU p 64 " model vdw 1.929 2.440 nonbonded pdb=" OH TYR L 517 " pdb=" O ALA m 75 " model vdw 1.932 2.440 nonbonded pdb=" OG SER N 178 " pdb=" OH TYR N 289 " model vdw 1.983 2.440 nonbonded pdb=" OD1 ASN I 191 " pdb=" OH TYR q 122 " model vdw 1.997 2.440 nonbonded pdb=" O GLY Y 32 " pdb=" OG SER Y 36 " model vdw 2.023 2.440 ... (remaining 572861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 70 through 146 or resid 201)) } 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 21.160 Check model and map are aligned: 0.800 Set scattering table: 0.460 Process input model: 161.240 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.008 0.273 68651 Z= 0.506 Angle : 0.857 22.074 92801 Z= 0.406 Chirality : 0.842 21.040 9942 Planarity : 0.007 0.555 11646 Dihedral : 15.276 171.024 25934 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.09), residues: 8085 helix: 0.07 (0.08), residues: 4162 sheet: -1.33 (0.26), residues: 379 loop : -0.58 (0.11), residues: 3544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 167 HIS 0.018 0.002 HIS h 129 PHE 0.039 0.002 PHE A 96 TYR 0.044 0.002 TYR P 390 ARG 0.018 0.001 ARG d 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 902 time to evaluate : 5.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6839 (tm-30) REVERT: B 151 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7493 (mm-30) REVERT: F 164 MET cc_start: 0.8515 (mpp) cc_final: 0.8191 (mtm) REVERT: G 308 CYS cc_start: 0.8375 (p) cc_final: 0.8167 (p) REVERT: H 209 GLU cc_start: 0.7275 (tp30) cc_final: 0.7025 (tp30) REVERT: H 284 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8604 (mmtm) REVERT: K 88 ASP cc_start: 0.8479 (p0) cc_final: 0.8212 (p0) REVERT: L 32 ASP cc_start: 0.8672 (t0) cc_final: 0.8400 (t70) REVERT: L 161 MET cc_start: 0.8518 (ttt) cc_final: 0.8310 (ttt) REVERT: L 403 MET cc_start: 0.8900 (mpp) cc_final: 0.8691 (mpp) REVERT: L 426 MET cc_start: 0.7938 (mtp) cc_final: 0.7567 (mtp) REVERT: L 540 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7448 (tm-30) REVERT: M 12 ILE cc_start: 0.8730 (mt) cc_final: 0.8501 (mt) REVERT: N 64 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8724 (mm-40) REVERT: N 329 PHE cc_start: 0.8609 (m-80) cc_final: 0.8353 (m-80) REVERT: O 390 MET cc_start: 0.7463 (mmp) cc_final: 0.7215 (tpp) REVERT: R 91 ASP cc_start: 0.8564 (t0) cc_final: 0.8334 (t0) REVERT: T 88 LYS cc_start: 0.8499 (mttt) cc_final: 0.8178 (mttt) REVERT: T 107 ASP cc_start: 0.8368 (m-30) cc_final: 0.8162 (m-30) REVERT: U 119 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7951 (mt-10) REVERT: U 143 TYR cc_start: 0.8983 (t80) cc_final: 0.8776 (t80) REVERT: W 46 ASP cc_start: 0.8607 (t0) cc_final: 0.8399 (t0) REVERT: X 58 CYS cc_start: 0.8038 (p) cc_final: 0.7259 (m) REVERT: Y 89 TYR cc_start: 0.8541 (m-80) cc_final: 0.8197 (m-80) REVERT: a 4 GLU cc_start: 0.8309 (mp0) cc_final: 0.7401 (mp0) REVERT: a 29 LEU cc_start: 0.9308 (tp) cc_final: 0.8875 (mm) REVERT: b 70 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8620 (mtmm) REVERT: d 11 LEU cc_start: 0.9525 (mm) cc_final: 0.9296 (mm) REVERT: e 68 MET cc_start: 0.8970 (ttp) cc_final: 0.8767 (ttt) REVERT: h 116 ILE cc_start: 0.9314 (mm) cc_final: 0.9016 (mt) REVERT: h 120 ASP cc_start: 0.8155 (t70) cc_final: 0.7952 (t0) REVERT: j 55 MET cc_start: 0.9106 (ttp) cc_final: 0.8745 (ttp) REVERT: l 61 GLU cc_start: 0.8097 (mp0) cc_final: 0.7791 (mp0) REVERT: l 104 GLU cc_start: 0.8683 (tt0) cc_final: 0.8336 (tt0) REVERT: l 139 MET cc_start: 0.8930 (mmm) cc_final: 0.8236 (ttp) REVERT: q 76 ASP cc_start: 0.8479 (m-30) cc_final: 0.7809 (m-30) outliers start: 0 outliers final: 0 residues processed: 902 average time/residue: 0.6752 time to fit residues: 1048.0758 Evaluate side-chains 705 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 705 time to evaluate : 5.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 673 optimal weight: 0.9990 chunk 604 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 206 optimal weight: 0.3980 chunk 407 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 624 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 379 optimal weight: 0.8980 chunk 464 optimal weight: 1.9990 chunk 723 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 GLN C 243 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN E 213 ASN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN F 292 ASN F 328 ASN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN I 81 HIS ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 554 ASN ** M 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN N 265 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 376 ASN Q 87 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN d 57 HIS d 88 HIS ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 106 HIS ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 108 GLN ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.273 68651 Z= 0.492 Angle : 1.340 50.888 92801 Z= 0.852 Chirality : 0.256 6.541 9942 Planarity : 0.004 0.057 11646 Dihedral : 12.997 171.641 9989 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 0.72 % Allowed : 5.66 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.09), residues: 8085 helix: 0.92 (0.08), residues: 4164 sheet: -0.97 (0.26), residues: 390 loop : -0.29 (0.11), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 152 HIS 0.005 0.001 HIS R 96 PHE 0.026 0.001 PHE L 307 TYR 0.030 0.001 TYR T 86 ARG 0.008 0.000 ARG h 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 835 time to evaluate : 5.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 126 ASP cc_start: 0.8346 (t0) cc_final: 0.8052 (t0) REVERT: B 151 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7509 (mm-30) REVERT: E 178 MET cc_start: 0.8314 (ppp) cc_final: 0.7853 (ppp) REVERT: F 159 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8775 (mp) REVERT: G 308 CYS cc_start: 0.8317 (p) cc_final: 0.8099 (p) REVERT: H 96 MET cc_start: 0.8538 (tmm) cc_final: 0.8316 (ttt) REVERT: H 106 ASN cc_start: 0.8100 (m-40) cc_final: 0.7890 (m-40) REVERT: H 234 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8182 (tm-30) REVERT: H 280 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8585 (t80) REVERT: H 284 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8626 (mmtm) REVERT: J 44 MET cc_start: 0.8502 (ptt) cc_final: 0.8147 (ptt) REVERT: J 172 MET cc_start: 0.8470 (tmm) cc_final: 0.8106 (tmm) REVERT: K 88 ASP cc_start: 0.8395 (p0) cc_final: 0.8118 (p0) REVERT: L 161 MET cc_start: 0.8576 (ttt) cc_final: 0.8369 (ttt) REVERT: L 176 MET cc_start: 0.8249 (mmt) cc_final: 0.8029 (mmm) REVERT: L 403 MET cc_start: 0.8894 (mpp) cc_final: 0.8503 (mpp) REVERT: L 540 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7383 (tm-30) REVERT: M 1 MET cc_start: 0.7169 (tpp) cc_final: 0.6928 (tpp) REVERT: M 186 CYS cc_start: 0.8279 (m) cc_final: 0.7871 (t) REVERT: M 241 MET cc_start: 0.8597 (mmm) cc_final: 0.8076 (mmm) REVERT: M 269 ASP cc_start: 0.7779 (t0) cc_final: 0.7508 (t0) REVERT: N 64 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8801 (mm-40) REVERT: N 329 PHE cc_start: 0.8466 (m-80) cc_final: 0.7994 (m-80) REVERT: O 45 MET cc_start: 0.8706 (mpp) cc_final: 0.8159 (mpp) REVERT: O 390 MET cc_start: 0.7508 (mmp) cc_final: 0.7231 (tpp) REVERT: U 77 GLU cc_start: 0.8520 (tt0) cc_final: 0.8282 (tt0) REVERT: W 46 ASP cc_start: 0.8512 (t0) cc_final: 0.8280 (t0) REVERT: W 54 GLU cc_start: 0.7947 (pm20) cc_final: 0.7402 (mp0) REVERT: X 92 ASP cc_start: 0.8642 (t0) cc_final: 0.8206 (t0) REVERT: Y 89 TYR cc_start: 0.8644 (m-80) cc_final: 0.8300 (m-80) REVERT: a 4 GLU cc_start: 0.8106 (mp0) cc_final: 0.7738 (mp0) REVERT: a 29 LEU cc_start: 0.9219 (tp) cc_final: 0.8836 (mm) REVERT: b 19 GLU cc_start: 0.7149 (tt0) cc_final: 0.6590 (tt0) REVERT: b 70 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8578 (mtmm) REVERT: e 99 ASP cc_start: 0.7924 (t0) cc_final: 0.7581 (t0) REVERT: h 116 ILE cc_start: 0.9276 (mm) cc_final: 0.8994 (mp) REVERT: j 55 MET cc_start: 0.9109 (ttp) cc_final: 0.8792 (ttp) REVERT: l 61 GLU cc_start: 0.8033 (mp0) cc_final: 0.7719 (mp0) REVERT: l 104 GLU cc_start: 0.8716 (tt0) cc_final: 0.8377 (tt0) REVERT: l 139 MET cc_start: 0.8958 (mmm) cc_final: 0.8153 (ttp) REVERT: m 96 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7813 (tm-30) REVERT: n 117 LYS cc_start: 0.8902 (tttt) cc_final: 0.8580 (tptp) REVERT: p 134 MET cc_start: 0.8785 (tpp) cc_final: 0.8538 (mmp) REVERT: p 143 GLU cc_start: 0.8961 (tt0) cc_final: 0.8741 (tt0) REVERT: q 110 ASP cc_start: 0.8056 (m-30) cc_final: 0.7841 (t0) outliers start: 51 outliers final: 27 residues processed: 855 average time/residue: 0.6173 time to fit residues: 920.8541 Evaluate side-chains 733 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 704 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain H residue 280 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain L residue 331 MET Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 56 PHE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain q residue 19 GLU Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain s residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 402 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 602 optimal weight: 6.9990 chunk 492 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 725 optimal weight: 10.0000 chunk 783 optimal weight: 9.9990 chunk 645 optimal weight: 4.9990 chunk 719 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 581 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN F 200 ASN G 84 ASN ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN J 33 GLN J 117 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 354 ASN ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 HIS N 216 ASN O 153 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN d 43 ASN ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.231 68651 Z= 0.574 Angle : 1.362 50.731 92801 Z= 0.861 Chirality : 0.258 6.437 9942 Planarity : 0.004 0.057 11646 Dihedral : 12.681 168.543 9989 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 1.38 % Allowed : 8.85 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 8085 helix: 0.96 (0.08), residues: 4177 sheet: -0.96 (0.26), residues: 390 loop : -0.33 (0.11), residues: 3518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 167 HIS 0.010 0.001 HIS o 59 PHE 0.022 0.002 PHE J 66 TYR 0.039 0.002 TYR b 45 ARG 0.010 0.001 ARG M 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 719 time to evaluate : 5.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 178 MET cc_start: 0.8320 (ppp) cc_final: 0.7747 (ppp) REVERT: F 159 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8770 (mp) REVERT: G 308 CYS cc_start: 0.8397 (p) cc_final: 0.8171 (p) REVERT: H 234 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8239 (tm-30) REVERT: H 284 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8702 (mmtm) REVERT: J 44 MET cc_start: 0.8579 (ptt) cc_final: 0.8133 (ptt) REVERT: J 172 MET cc_start: 0.8649 (tmm) cc_final: 0.8276 (tmm) REVERT: K 88 ASP cc_start: 0.8405 (p0) cc_final: 0.8086 (p0) REVERT: L 141 MET cc_start: 0.8738 (tpt) cc_final: 0.8531 (tpp) REVERT: L 298 MET cc_start: 0.8515 (tpt) cc_final: 0.8302 (tpt) REVERT: L 403 MET cc_start: 0.8975 (mpp) cc_final: 0.8257 (mpp) REVERT: L 540 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7412 (tm-30) REVERT: M 186 CYS cc_start: 0.8195 (m) cc_final: 0.7906 (t) REVERT: M 282 MET cc_start: 0.8724 (tpp) cc_final: 0.8501 (mmp) REVERT: N 64 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8796 (mm-40) REVERT: N 175 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8270 (tpp) REVERT: N 262 VAL cc_start: 0.9332 (t) cc_final: 0.9114 (p) REVERT: O 45 MET cc_start: 0.8737 (mpp) cc_final: 0.8154 (mpp) REVERT: O 390 MET cc_start: 0.7672 (mmp) cc_final: 0.7408 (tpp) REVERT: Q 41 LYS cc_start: 0.8818 (tptt) cc_final: 0.8540 (tmtt) REVERT: Q 131 MET cc_start: 0.8732 (tpt) cc_final: 0.8373 (tpp) REVERT: T 88 LYS cc_start: 0.8044 (mttt) cc_final: 0.7838 (mptt) REVERT: W 46 ASP cc_start: 0.8578 (t0) cc_final: 0.8338 (t0) REVERT: X 92 ASP cc_start: 0.8799 (t0) cc_final: 0.8433 (t0) REVERT: Y 89 TYR cc_start: 0.8751 (m-80) cc_final: 0.8346 (m-80) REVERT: Y 162 ASN cc_start: 0.8606 (t0) cc_final: 0.8353 (t0) REVERT: a 4 GLU cc_start: 0.8144 (mp0) cc_final: 0.7782 (mp0) REVERT: a 29 LEU cc_start: 0.9250 (tp) cc_final: 0.8892 (mm) REVERT: b 19 GLU cc_start: 0.7219 (tt0) cc_final: 0.6640 (tt0) REVERT: b 70 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8484 (mtmm) REVERT: f 39 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8467 (mttp) REVERT: h 116 ILE cc_start: 0.9324 (mm) cc_final: 0.9057 (mp) REVERT: j 55 MET cc_start: 0.9117 (ttp) cc_final: 0.8584 (ttp) REVERT: l 61 GLU cc_start: 0.8104 (mp0) cc_final: 0.7687 (mp0) REVERT: l 104 GLU cc_start: 0.8719 (tt0) cc_final: 0.8415 (tt0) REVERT: l 139 MET cc_start: 0.8881 (mmm) cc_final: 0.8130 (ttp) REVERT: m 96 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7785 (tm-30) REVERT: n 12 LYS cc_start: 0.8959 (ptmm) cc_final: 0.8680 (ttpp) REVERT: n 117 LYS cc_start: 0.8962 (tttt) cc_final: 0.8660 (tptp) REVERT: p 134 MET cc_start: 0.8920 (tpp) cc_final: 0.8622 (mmp) REVERT: p 143 GLU cc_start: 0.8974 (tt0) cc_final: 0.8747 (tt0) REVERT: q 110 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7881 (t0) REVERT: s 94 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8279 (mm-30) outliers start: 98 outliers final: 63 residues processed: 780 average time/residue: 0.6385 time to fit residues: 872.9101 Evaluate side-chains 745 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 678 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 331 MET Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 105 GLN Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 56 PHE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 130 GLN Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain d residue 42 ILE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 39 LYS Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 149 ILE Chi-restraints excluded: chain h residue 74 THR Chi-restraints excluded: chain i residue 17 ILE Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain p residue 34 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain q residue 110 ASP Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 78 GLN Chi-restraints excluded: chain s residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 716 optimal weight: 0.9990 chunk 545 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 486 optimal weight: 3.9990 chunk 727 optimal weight: 10.0000 chunk 770 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 689 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN G 192 HIS ** G 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN O 204 GLN W 67 HIS e 20 ASN ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** h 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.236 68651 Z= 0.507 Angle : 1.330 50.697 92801 Z= 0.848 Chirality : 0.256 6.379 9942 Planarity : 0.004 0.058 11646 Dihedral : 12.449 171.243 9989 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.82 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 10.30 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8085 helix: 1.11 (0.08), residues: 4164 sheet: -0.84 (0.26), residues: 392 loop : -0.25 (0.11), residues: 3529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 173 HIS 0.008 0.001 HIS h 170 PHE 0.023 0.001 PHE H 296 TYR 0.038 0.001 TYR T 86 ARG 0.009 0.000 ARG k 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 729 time to evaluate : 6.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 178 MET cc_start: 0.8314 (ppp) cc_final: 0.7714 (ppp) REVERT: F 159 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8754 (mp) REVERT: F 297 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8740 (m) REVERT: G 70 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8859 (mp) REVERT: G 148 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8673 (t0) REVERT: G 308 CYS cc_start: 0.8366 (p) cc_final: 0.8155 (p) REVERT: H 234 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8271 (tm-30) REVERT: J 44 MET cc_start: 0.8581 (ptt) cc_final: 0.8173 (ptt) REVERT: J 172 MET cc_start: 0.8658 (tmm) cc_final: 0.8242 (tmm) REVERT: K 88 ASP cc_start: 0.8409 (p0) cc_final: 0.8103 (p0) REVERT: L 298 MET cc_start: 0.8479 (tpt) cc_final: 0.8254 (tpt) REVERT: L 403 MET cc_start: 0.8991 (mpp) cc_final: 0.8225 (mpp) REVERT: L 540 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7497 (tm-30) REVERT: M 186 CYS cc_start: 0.8266 (m) cc_final: 0.7888 (t) REVERT: M 241 MET cc_start: 0.8597 (mmm) cc_final: 0.8214 (mmm) REVERT: M 282 MET cc_start: 0.8710 (tpp) cc_final: 0.8475 (mmp) REVERT: M 443 MET cc_start: 0.7958 (ttt) cc_final: 0.7707 (ttt) REVERT: N 64 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8791 (mm-40) REVERT: N 262 VAL cc_start: 0.9334 (t) cc_final: 0.9119 (p) REVERT: N 323 MET cc_start: 0.8034 (mmp) cc_final: 0.7784 (mmp) REVERT: O 45 MET cc_start: 0.8748 (mpp) cc_final: 0.8175 (mpp) REVERT: O 108 MET cc_start: 0.8940 (mmt) cc_final: 0.8729 (mmp) REVERT: O 390 MET cc_start: 0.7656 (mmp) cc_final: 0.7416 (tpp) REVERT: Q 41 LYS cc_start: 0.8825 (tptt) cc_final: 0.8524 (tmtt) REVERT: R 62 TYR cc_start: 0.8583 (m-80) cc_final: 0.8217 (m-80) REVERT: U 77 GLU cc_start: 0.8562 (tt0) cc_final: 0.8271 (tt0) REVERT: V 79 GLU cc_start: 0.7504 (tt0) cc_final: 0.7269 (tt0) REVERT: W 46 ASP cc_start: 0.8572 (t0) cc_final: 0.8306 (t0) REVERT: X 92 ASP cc_start: 0.8809 (t0) cc_final: 0.8441 (t0) REVERT: Y 66 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: Y 89 TYR cc_start: 0.8733 (m-80) cc_final: 0.8264 (m-80) REVERT: Y 162 ASN cc_start: 0.8646 (t0) cc_final: 0.8248 (t0) REVERT: a 4 GLU cc_start: 0.8114 (mp0) cc_final: 0.7718 (mp0) REVERT: a 29 LEU cc_start: 0.9213 (tp) cc_final: 0.8885 (mm) REVERT: b 70 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8489 (mtmm) REVERT: e 76 GLU cc_start: 0.8259 (tp30) cc_final: 0.7900 (tp30) REVERT: e 99 ASP cc_start: 0.7956 (t0) cc_final: 0.7672 (t0) REVERT: f 39 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8470 (mttp) REVERT: h 116 ILE cc_start: 0.9299 (mm) cc_final: 0.9028 (mp) REVERT: k 43 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8143 (ttp-110) REVERT: l 61 GLU cc_start: 0.8139 (mp0) cc_final: 0.7701 (mp0) REVERT: l 104 GLU cc_start: 0.8684 (tt0) cc_final: 0.8403 (tt0) REVERT: l 139 MET cc_start: 0.8893 (mmm) cc_final: 0.8125 (ttp) REVERT: m 96 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7786 (tm-30) REVERT: n 117 LYS cc_start: 0.8961 (tttt) cc_final: 0.8618 (tptp) REVERT: p 88 GLU cc_start: 0.8556 (tp30) cc_final: 0.7833 (mm-30) REVERT: p 134 MET cc_start: 0.8852 (tpp) cc_final: 0.8523 (mmp) REVERT: s 94 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8252 (mm-30) outliers start: 117 outliers final: 64 residues processed: 796 average time/residue: 0.6162 time to fit residues: 861.1243 Evaluate side-chains 763 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 692 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain L residue 331 MET Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 130 GLN Chi-restraints excluded: chain a residue 30 MET Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain d residue 42 ILE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 39 LYS Chi-restraints excluded: chain g residue 149 ILE Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain i residue 17 ILE Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 43 ARG Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 78 GLN Chi-restraints excluded: chain s residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 641 optimal weight: 5.9990 chunk 437 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 573 optimal weight: 0.9990 chunk 317 optimal weight: 2.9990 chunk 657 optimal weight: 0.0020 chunk 532 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 393 optimal weight: 1.9990 chunk 691 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN F 118 ASN G 372 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 257 GLN P 266 GLN e 20 ASN ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 42 HIS ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.239 68651 Z= 0.475 Angle : 1.314 50.633 92801 Z= 0.842 Chirality : 0.256 6.362 9942 Planarity : 0.004 0.056 11646 Dihedral : 12.162 174.136 9989 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.77 % Favored : 97.22 % Rotamer: Outliers : 1.81 % Allowed : 11.03 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.10), residues: 8085 helix: 1.23 (0.08), residues: 4175 sheet: -0.67 (0.26), residues: 388 loop : -0.21 (0.11), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 173 HIS 0.006 0.001 HIS h 170 PHE 0.022 0.001 PHE L 307 TYR 0.022 0.001 TYR H 149 ARG 0.010 0.000 ARG k 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 753 time to evaluate : 6.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 342 MET cc_start: 0.7920 (mtt) cc_final: 0.7628 (mtt) REVERT: E 178 MET cc_start: 0.8285 (ppp) cc_final: 0.7741 (ppp) REVERT: F 159 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8810 (mp) REVERT: F 297 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8734 (m) REVERT: G 70 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8835 (mp) REVERT: G 320 MET cc_start: 0.8549 (mtp) cc_final: 0.8345 (mtt) REVERT: H 4 MET cc_start: 0.7607 (ppp) cc_final: 0.7346 (ppp) REVERT: H 66 GLU cc_start: 0.6966 (pm20) cc_final: 0.6716 (pm20) REVERT: H 151 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8830 (p) REVERT: H 234 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8280 (tm-30) REVERT: J 44 MET cc_start: 0.8534 (ptt) cc_final: 0.8216 (ptt) REVERT: J 172 MET cc_start: 0.8625 (tmm) cc_final: 0.8175 (tmm) REVERT: K 88 ASP cc_start: 0.8357 (p0) cc_final: 0.8052 (p0) REVERT: L 298 MET cc_start: 0.8339 (tpt) cc_final: 0.8134 (tpt) REVERT: L 403 MET cc_start: 0.8983 (mpp) cc_final: 0.8150 (mpp) REVERT: L 427 MET cc_start: 0.8459 (mmt) cc_final: 0.8243 (mmt) REVERT: L 526 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7301 (t0) REVERT: L 540 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7494 (tm-30) REVERT: M 111 MET cc_start: 0.8553 (mmm) cc_final: 0.7940 (mmm) REVERT: M 186 CYS cc_start: 0.8250 (m) cc_final: 0.7875 (t) REVERT: M 241 MET cc_start: 0.8602 (mmm) cc_final: 0.8221 (mmm) REVERT: M 282 MET cc_start: 0.8690 (tpp) cc_final: 0.8446 (mmt) REVERT: M 443 MET cc_start: 0.8125 (ttt) cc_final: 0.7868 (ttt) REVERT: N 64 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8774 (mm-40) REVERT: N 262 VAL cc_start: 0.9332 (t) cc_final: 0.9118 (p) REVERT: N 323 MET cc_start: 0.8022 (mmp) cc_final: 0.7784 (mmp) REVERT: O 45 MET cc_start: 0.8749 (mpp) cc_final: 0.8145 (mpp) REVERT: O 390 MET cc_start: 0.7644 (mmp) cc_final: 0.7429 (tpp) REVERT: Q 41 LYS cc_start: 0.8803 (tptt) cc_final: 0.8531 (tmtt) REVERT: R 62 TYR cc_start: 0.8559 (m-80) cc_final: 0.8164 (m-80) REVERT: U 77 GLU cc_start: 0.8551 (tt0) cc_final: 0.8327 (tt0) REVERT: W 46 ASP cc_start: 0.8606 (t0) cc_final: 0.8357 (t0) REVERT: X 92 ASP cc_start: 0.8783 (t0) cc_final: 0.8557 (t0) REVERT: Y 66 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: Y 89 TYR cc_start: 0.8718 (m-80) cc_final: 0.8285 (m-80) REVERT: Y 162 ASN cc_start: 0.8709 (t0) cc_final: 0.8437 (t0) REVERT: a 4 GLU cc_start: 0.8093 (mp0) cc_final: 0.7645 (mp0) REVERT: a 29 LEU cc_start: 0.9205 (tp) cc_final: 0.8870 (mm) REVERT: b 70 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8447 (mtmm) REVERT: d 18 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6220 (tm-30) REVERT: d 110 GLU cc_start: 0.8461 (pm20) cc_final: 0.8255 (pm20) REVERT: e 76 GLU cc_start: 0.8205 (tp30) cc_final: 0.7916 (tp30) REVERT: e 99 ASP cc_start: 0.7990 (t0) cc_final: 0.7673 (t0) REVERT: f 33 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7883 (mmt) REVERT: f 39 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8394 (mttp) REVERT: h 116 ILE cc_start: 0.9266 (mm) cc_final: 0.8999 (mp) REVERT: j 63 LEU cc_start: 0.9499 (mm) cc_final: 0.9267 (mm) REVERT: l 61 GLU cc_start: 0.8118 (mp0) cc_final: 0.7701 (mp0) REVERT: l 104 GLU cc_start: 0.8683 (tt0) cc_final: 0.8388 (tt0) REVERT: l 139 MET cc_start: 0.8891 (mmm) cc_final: 0.8080 (ttp) REVERT: m 96 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7710 (tm-30) REVERT: m 106 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8841 (mmmm) REVERT: n 117 LYS cc_start: 0.8934 (tttt) cc_final: 0.8652 (tptp) REVERT: o 9 MET cc_start: 0.7534 (tmm) cc_final: 0.7080 (tmm) REVERT: p 88 GLU cc_start: 0.8499 (tp30) cc_final: 0.7937 (mm-30) REVERT: p 134 MET cc_start: 0.8876 (tpp) cc_final: 0.8588 (mmp) REVERT: s 94 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8251 (mm-30) outliers start: 128 outliers final: 70 residues processed: 832 average time/residue: 0.6007 time to fit residues: 876.8508 Evaluate side-chains 789 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 711 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 130 GLN Chi-restraints excluded: chain Y residue 164 THR Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 39 LYS Chi-restraints excluded: chain g residue 149 ILE Chi-restraints excluded: chain i residue 17 ILE Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain l residue 165 SER Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 72 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 78 GLN Chi-restraints excluded: chain s residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 259 optimal weight: 0.9990 chunk 693 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 452 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 771 optimal weight: 9.9990 chunk 640 optimal weight: 1.9990 chunk 357 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 404 optimal weight: 0.0000 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN H 299 ASN J 33 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 HIS ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 GLN M 371 ASN ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 167 ASN P 266 GLN P 343 HIS Q 54 ASN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN n 110 GLN ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 68651 Z= 0.467 Angle : 1.310 50.599 92801 Z= 0.840 Chirality : 0.255 6.345 9942 Planarity : 0.004 0.054 11646 Dihedral : 11.889 177.219 9989 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.79 % Allowed : 11.82 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 8085 helix: 1.32 (0.08), residues: 4173 sheet: -0.59 (0.26), residues: 393 loop : -0.17 (0.11), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 218 HIS 0.006 0.001 HIS h 170 PHE 0.026 0.001 PHE i 69 TYR 0.022 0.001 TYR i 143 ARG 0.013 0.000 ARG k 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 756 time to evaluate : 6.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9437 (m) cc_final: 0.9234 (p) REVERT: B 151 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7682 (mm-30) REVERT: E 178 MET cc_start: 0.8278 (ppp) cc_final: 0.7721 (ppp) REVERT: F 159 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8790 (mp) REVERT: F 297 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8747 (m) REVERT: H 150 GLU cc_start: 0.8399 (tp30) cc_final: 0.8046 (tp30) REVERT: H 234 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8242 (tm-30) REVERT: J 44 MET cc_start: 0.8514 (ptt) cc_final: 0.8193 (ptt) REVERT: J 172 MET cc_start: 0.8610 (tmm) cc_final: 0.8045 (tmm) REVERT: K 88 ASP cc_start: 0.8344 (p0) cc_final: 0.8032 (p0) REVERT: L 298 MET cc_start: 0.8299 (tpt) cc_final: 0.7909 (tpt) REVERT: L 403 MET cc_start: 0.8952 (mpp) cc_final: 0.8125 (mpp) REVERT: L 499 MET cc_start: 0.8289 (mtp) cc_final: 0.7905 (ttm) REVERT: L 526 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7336 (t0) REVERT: L 540 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7499 (tm-30) REVERT: M 116 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8391 (t80) REVERT: M 186 CYS cc_start: 0.8250 (m) cc_final: 0.7876 (t) REVERT: M 241 MET cc_start: 0.8622 (mmm) cc_final: 0.8255 (mmm) REVERT: M 282 MET cc_start: 0.8722 (tpp) cc_final: 0.8453 (mmt) REVERT: N 64 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8767 (mm-40) REVERT: N 262 VAL cc_start: 0.9348 (t) cc_final: 0.9137 (p) REVERT: N 297 PHE cc_start: 0.8361 (m-10) cc_final: 0.8143 (m-10) REVERT: N 323 MET cc_start: 0.8050 (mmp) cc_final: 0.7804 (mmp) REVERT: O 45 MET cc_start: 0.8784 (mpp) cc_final: 0.8139 (mpp) REVERT: O 366 ASP cc_start: 0.8090 (m-30) cc_final: 0.7865 (m-30) REVERT: O 390 MET cc_start: 0.7638 (mmp) cc_final: 0.7404 (tpp) REVERT: P 317 MET cc_start: 0.8734 (ttp) cc_final: 0.8521 (ttp) REVERT: Q 41 LYS cc_start: 0.8818 (tptt) cc_final: 0.8543 (tmtt) REVERT: Q 98 THR cc_start: 0.8436 (p) cc_final: 0.7962 (m) REVERT: R 62 TYR cc_start: 0.8513 (m-80) cc_final: 0.8047 (m-80) REVERT: V 81 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8647 (mp) REVERT: V 87 GLU cc_start: 0.8187 (tp30) cc_final: 0.7754 (tp30) REVERT: W 46 ASP cc_start: 0.8599 (t0) cc_final: 0.8371 (t0) REVERT: X 92 ASP cc_start: 0.8760 (t0) cc_final: 0.8515 (t0) REVERT: Y 64 MET cc_start: 0.8235 (mtp) cc_final: 0.7969 (mtm) REVERT: Y 66 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7880 (mtt) REVERT: Y 89 TYR cc_start: 0.8710 (m-80) cc_final: 0.8276 (m-80) REVERT: Y 162 ASN cc_start: 0.8543 (t0) cc_final: 0.8284 (t0) REVERT: Z 153 TRP cc_start: 0.8001 (m-10) cc_final: 0.7751 (m-10) REVERT: a 1 MET cc_start: 0.7650 (tpp) cc_final: 0.7122 (tpp) REVERT: a 4 GLU cc_start: 0.8090 (mp0) cc_final: 0.7887 (mp0) REVERT: a 29 LEU cc_start: 0.9175 (tp) cc_final: 0.8831 (mm) REVERT: b 70 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8438 (mtmm) REVERT: d 50 VAL cc_start: 0.8935 (m) cc_final: 0.8679 (t) REVERT: e 76 GLU cc_start: 0.8184 (tp30) cc_final: 0.7884 (tp30) REVERT: e 99 ASP cc_start: 0.7967 (t0) cc_final: 0.7645 (t0) REVERT: f 33 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7839 (mmt) REVERT: h 116 ILE cc_start: 0.9242 (mm) cc_final: 0.8971 (mp) REVERT: j 55 MET cc_start: 0.9074 (ttp) cc_final: 0.8575 (ttp) REVERT: j 63 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9261 (mm) REVERT: k 43 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8072 (ttp-110) REVERT: l 61 GLU cc_start: 0.8121 (mp0) cc_final: 0.7705 (mp0) REVERT: l 104 GLU cc_start: 0.8719 (tt0) cc_final: 0.8476 (tt0) REVERT: l 139 MET cc_start: 0.8875 (mmm) cc_final: 0.8108 (ttp) REVERT: m 96 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7700 (tm-30) REVERT: o 9 MET cc_start: 0.7582 (tmm) cc_final: 0.7327 (tmm) REVERT: p 88 GLU cc_start: 0.8440 (tp30) cc_final: 0.8106 (mm-30) REVERT: p 134 MET cc_start: 0.8870 (tpp) cc_final: 0.8611 (mmm) REVERT: s 94 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8257 (mm-30) outliers start: 127 outliers final: 86 residues processed: 837 average time/residue: 0.6064 time to fit residues: 893.8863 Evaluate side-chains 809 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 714 time to evaluate : 5.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 331 MET Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 343 MET Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 164 THR Chi-restraints excluded: chain a residue 40 ASP Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain j residue 63 LEU Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 43 ARG Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 165 SER Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain p residue 78 GLU Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 72 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 78 GLN Chi-restraints excluded: chain s residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 743 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 439 optimal weight: 10.0000 chunk 563 optimal weight: 4.9990 chunk 436 optimal weight: 5.9990 chunk 649 optimal weight: 0.9980 chunk 430 optimal weight: 4.9990 chunk 768 optimal weight: 9.9990 chunk 480 optimal weight: 0.0670 chunk 468 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN H 219 ASN J 33 GLN L 85 ASN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 HIS ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 519 GLN ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 257 GLN ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 HIS ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 129 HIS ** h 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 69 HIS ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.234 68651 Z= 0.520 Angle : 1.331 50.663 92801 Z= 0.849 Chirality : 0.256 6.364 9942 Planarity : 0.004 0.056 11646 Dihedral : 11.888 179.103 9989 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.01 % Allowed : 12.13 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 8085 helix: 1.29 (0.08), residues: 4179 sheet: -0.60 (0.25), residues: 398 loop : -0.16 (0.11), residues: 3508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 173 HIS 0.007 0.001 HIS h 170 PHE 0.022 0.001 PHE d 21 TYR 0.036 0.001 TYR m 83 ARG 0.013 0.000 ARG k 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 707 time to evaluate : 6.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9453 (m) cc_final: 0.9229 (p) REVERT: B 76 ASP cc_start: 0.8165 (t0) cc_final: 0.7816 (t0) REVERT: E 62 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9083 (tp) REVERT: E 178 MET cc_start: 0.8301 (ppp) cc_final: 0.7746 (ppp) REVERT: F 159 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8795 (mp) REVERT: F 297 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8808 (m) REVERT: G 320 MET cc_start: 0.8358 (mtt) cc_final: 0.8144 (mtp) REVERT: H 150 GLU cc_start: 0.8436 (tp30) cc_final: 0.8082 (tp30) REVERT: H 151 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8811 (p) REVERT: H 188 MET cc_start: 0.7108 (mtm) cc_final: 0.6857 (mtt) REVERT: H 234 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8240 (tm-30) REVERT: J 44 MET cc_start: 0.8587 (ptt) cc_final: 0.8196 (ptt) REVERT: J 172 MET cc_start: 0.8597 (tmm) cc_final: 0.7970 (tmm) REVERT: K 88 ASP cc_start: 0.8387 (p0) cc_final: 0.8050 (p0) REVERT: L 267 GLU cc_start: 0.8148 (tt0) cc_final: 0.7802 (tt0) REVERT: L 403 MET cc_start: 0.8974 (mpp) cc_final: 0.8137 (mpp) REVERT: L 526 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7333 (t0) REVERT: L 540 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7590 (tm-30) REVERT: M 116 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8415 (t80) REVERT: M 186 CYS cc_start: 0.8264 (m) cc_final: 0.7890 (t) REVERT: M 241 MET cc_start: 0.8660 (mmm) cc_final: 0.8314 (mmm) REVERT: M 282 MET cc_start: 0.8723 (tpp) cc_final: 0.8456 (mmt) REVERT: M 443 MET cc_start: 0.7978 (ttt) cc_final: 0.7726 (ttt) REVERT: N 64 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8793 (mm-40) REVERT: N 262 VAL cc_start: 0.9364 (t) cc_final: 0.9149 (p) REVERT: N 297 PHE cc_start: 0.8399 (m-10) cc_final: 0.8143 (m-10) REVERT: N 323 MET cc_start: 0.8024 (mmp) cc_final: 0.7771 (mmp) REVERT: O 45 MET cc_start: 0.8797 (mpp) cc_final: 0.8156 (mpp) REVERT: O 366 ASP cc_start: 0.8146 (m-30) cc_final: 0.7917 (m-30) REVERT: O 390 MET cc_start: 0.7650 (mmp) cc_final: 0.7428 (tpp) REVERT: Q 41 LYS cc_start: 0.8808 (tptt) cc_final: 0.8530 (tmtt) REVERT: Q 98 THR cc_start: 0.8507 (p) cc_final: 0.8012 (m) REVERT: U 77 GLU cc_start: 0.8569 (tt0) cc_final: 0.8252 (tt0) REVERT: V 81 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8749 (mp) REVERT: V 87 GLU cc_start: 0.8323 (tp30) cc_final: 0.7956 (tp30) REVERT: W 46 ASP cc_start: 0.8613 (t0) cc_final: 0.8367 (t0) REVERT: X 92 ASP cc_start: 0.8798 (t0) cc_final: 0.8564 (t0) REVERT: Y 47 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7554 (mm-40) REVERT: Y 66 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7907 (mtt) REVERT: Y 162 ASN cc_start: 0.8583 (t0) cc_final: 0.8350 (t0) REVERT: Z 153 TRP cc_start: 0.7990 (m-10) cc_final: 0.7618 (m-10) REVERT: a 1 MET cc_start: 0.7789 (tpp) cc_final: 0.7407 (tpp) REVERT: a 4 GLU cc_start: 0.8107 (mp0) cc_final: 0.7858 (mp0) REVERT: a 29 LEU cc_start: 0.9182 (tp) cc_final: 0.8787 (mm) REVERT: b 70 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8460 (mtmm) REVERT: e 36 GLU cc_start: 0.7983 (tp30) cc_final: 0.7685 (tp30) REVERT: e 76 GLU cc_start: 0.8205 (tp30) cc_final: 0.7890 (tp30) REVERT: e 99 ASP cc_start: 0.7965 (t0) cc_final: 0.7644 (t0) REVERT: f 33 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7700 (mmt) REVERT: f 39 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8361 (mttp) REVERT: h 116 ILE cc_start: 0.9283 (mm) cc_final: 0.9032 (mp) REVERT: j 55 MET cc_start: 0.9110 (ttp) cc_final: 0.8608 (ttp) REVERT: k 43 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8154 (ttp-110) REVERT: l 61 GLU cc_start: 0.8136 (mp0) cc_final: 0.7686 (mp0) REVERT: l 104 GLU cc_start: 0.8636 (tt0) cc_final: 0.8366 (tt0) REVERT: l 139 MET cc_start: 0.8861 (mmm) cc_final: 0.8113 (ttp) REVERT: m 96 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7708 (tm-30) REVERT: o 9 MET cc_start: 0.7704 (tmm) cc_final: 0.7408 (tmm) REVERT: p 88 GLU cc_start: 0.8396 (tp30) cc_final: 0.8080 (mm-30) REVERT: p 134 MET cc_start: 0.8820 (tpp) cc_final: 0.8604 (mmm) REVERT: s 55 LEU cc_start: 0.8727 (mp) cc_final: 0.8430 (mp) REVERT: s 61 LYS cc_start: 0.6196 (tptt) cc_final: 0.5496 (mttp) REVERT: s 92 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7628 (mm-30) outliers start: 142 outliers final: 100 residues processed: 805 average time/residue: 0.6022 time to fit residues: 855.4151 Evaluate side-chains 810 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 699 time to evaluate : 5.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 105 GLN Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 164 THR Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 40 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 39 LYS Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain h residue 67 MET Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain i residue 17 ILE Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 43 ARG Chi-restraints excluded: chain l residue 165 SER Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain p residue 34 ASN Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 72 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 78 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 475 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 458 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 488 optimal weight: 0.9990 chunk 523 optimal weight: 6.9990 chunk 379 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 603 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN H 67 GLN ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 HIS ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 257 GLN ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN e 20 ASN ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 170 HIS ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.239 68651 Z= 0.467 Angle : 1.313 50.591 92801 Z= 0.841 Chirality : 0.256 6.347 9942 Planarity : 0.004 0.055 11646 Dihedral : 11.666 177.403 9989 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.60 % Allowed : 12.78 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 8085 helix: 1.36 (0.08), residues: 4178 sheet: -0.53 (0.26), residues: 395 loop : -0.15 (0.11), residues: 3512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 173 HIS 0.005 0.001 HIS L 221 PHE 0.031 0.001 PHE H 218 TYR 0.025 0.001 TYR m 83 ARG 0.013 0.000 ARG k 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 740 time to evaluate : 6.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9422 (m) cc_final: 0.9203 (p) REVERT: B 76 ASP cc_start: 0.8090 (t0) cc_final: 0.7783 (t0) REVERT: B 77 ASP cc_start: 0.8409 (t0) cc_final: 0.8195 (t70) REVERT: B 151 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7703 (mm-30) REVERT: E 62 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9078 (tp) REVERT: E 178 MET cc_start: 0.8273 (ppp) cc_final: 0.7697 (ppp) REVERT: F 159 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8795 (mp) REVERT: F 297 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8758 (m) REVERT: F 337 SER cc_start: 0.8098 (m) cc_final: 0.7810 (p) REVERT: G 320 MET cc_start: 0.8327 (mtt) cc_final: 0.8123 (mtp) REVERT: H 29 LEU cc_start: 0.9050 (tp) cc_final: 0.8824 (tt) REVERT: H 150 GLU cc_start: 0.8436 (tp30) cc_final: 0.7997 (tp30) REVERT: H 234 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8248 (tm-30) REVERT: H 281 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7237 (tmm-80) REVERT: I 66 MET cc_start: 0.8148 (ttt) cc_final: 0.7943 (ttt) REVERT: J 44 MET cc_start: 0.8520 (ptt) cc_final: 0.8193 (ptt) REVERT: J 172 MET cc_start: 0.8557 (tmm) cc_final: 0.7921 (tmm) REVERT: K 54 ASN cc_start: 0.8775 (t0) cc_final: 0.8397 (t0) REVERT: K 88 ASP cc_start: 0.8342 (p0) cc_final: 0.8026 (p0) REVERT: L 79 GLU cc_start: 0.8632 (tt0) cc_final: 0.7922 (tp30) REVERT: L 176 MET cc_start: 0.8453 (mmt) cc_final: 0.8145 (mmm) REVERT: L 221 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6222 (m90) REVERT: L 259 MET cc_start: 0.8398 (tmm) cc_final: 0.8155 (tmm) REVERT: L 267 GLU cc_start: 0.8206 (tt0) cc_final: 0.7845 (tt0) REVERT: L 403 MET cc_start: 0.8948 (mpp) cc_final: 0.8121 (mpp) REVERT: L 526 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7374 (t0) REVERT: L 540 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7563 (tm-30) REVERT: M 116 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8399 (t80) REVERT: M 186 CYS cc_start: 0.8251 (m) cc_final: 0.7874 (t) REVERT: M 241 MET cc_start: 0.8629 (mmm) cc_final: 0.8281 (mmm) REVERT: N 64 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8782 (mm-40) REVERT: N 262 VAL cc_start: 0.9355 (t) cc_final: 0.9137 (p) REVERT: N 297 PHE cc_start: 0.8251 (m-10) cc_final: 0.8018 (m-10) REVERT: N 323 MET cc_start: 0.8059 (mmp) cc_final: 0.7811 (mmp) REVERT: O 45 MET cc_start: 0.8806 (mpp) cc_final: 0.8183 (mpp) REVERT: O 390 MET cc_start: 0.7657 (mmp) cc_final: 0.7404 (tpp) REVERT: P 243 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7463 (mmt90) REVERT: Q 41 LYS cc_start: 0.8811 (tptt) cc_final: 0.8520 (tmtt) REVERT: Q 98 THR cc_start: 0.8291 (p) cc_final: 0.7773 (m) REVERT: Q 131 MET cc_start: 0.8658 (tpp) cc_final: 0.8335 (tpt) REVERT: R 62 TYR cc_start: 0.8508 (m-80) cc_final: 0.7950 (m-80) REVERT: U 77 GLU cc_start: 0.8571 (tt0) cc_final: 0.8241 (tt0) REVERT: V 81 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8927 (mp) REVERT: V 87 GLU cc_start: 0.8393 (tp30) cc_final: 0.7893 (tp30) REVERT: W 46 ASP cc_start: 0.8597 (t0) cc_final: 0.8396 (t0) REVERT: X 92 ASP cc_start: 0.8780 (t0) cc_final: 0.8512 (t0) REVERT: Y 47 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7656 (mm-40) REVERT: Y 64 MET cc_start: 0.8223 (mtp) cc_final: 0.7961 (mtm) REVERT: Y 66 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7913 (mtt) REVERT: Y 162 ASN cc_start: 0.8553 (t0) cc_final: 0.8329 (t0) REVERT: Z 153 TRP cc_start: 0.7958 (m-10) cc_final: 0.7637 (m-10) REVERT: a 1 MET cc_start: 0.7710 (tpp) cc_final: 0.7375 (tpp) REVERT: a 4 GLU cc_start: 0.8104 (mp0) cc_final: 0.7861 (mp0) REVERT: a 29 LEU cc_start: 0.9097 (tp) cc_final: 0.8684 (mm) REVERT: b 70 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8539 (mtmm) REVERT: d 50 VAL cc_start: 0.8958 (m) cc_final: 0.8698 (t) REVERT: d 110 GLU cc_start: 0.8517 (pm20) cc_final: 0.8278 (pm20) REVERT: e 36 GLU cc_start: 0.8035 (tp30) cc_final: 0.7685 (tp30) REVERT: e 44 GLU cc_start: 0.7637 (pm20) cc_final: 0.7128 (pm20) REVERT: e 76 GLU cc_start: 0.8059 (tp30) cc_final: 0.7725 (tp30) REVERT: e 99 ASP cc_start: 0.7969 (t0) cc_final: 0.7650 (t0) REVERT: f 3 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7437 (mm) REVERT: f 31 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7074 (mp0) REVERT: f 33 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7475 (mmt) REVERT: g 118 GLU cc_start: 0.8202 (pp20) cc_final: 0.7935 (pp20) REVERT: h 116 ILE cc_start: 0.9251 (mm) cc_final: 0.8989 (mp) REVERT: j 55 MET cc_start: 0.9088 (ttp) cc_final: 0.8605 (ttp) REVERT: k 43 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8114 (ttp-110) REVERT: l 61 GLU cc_start: 0.8149 (mp0) cc_final: 0.7712 (mp0) REVERT: l 104 GLU cc_start: 0.8632 (tt0) cc_final: 0.8381 (tt0) REVERT: l 139 MET cc_start: 0.8848 (mmm) cc_final: 0.8208 (ttp) REVERT: m 96 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7764 (tp30) REVERT: n 117 LYS cc_start: 0.8935 (tttt) cc_final: 0.8623 (tttm) REVERT: o 9 MET cc_start: 0.7719 (tmm) cc_final: 0.7442 (tmm) REVERT: p 88 GLU cc_start: 0.8378 (tp30) cc_final: 0.8112 (mm-30) REVERT: p 134 MET cc_start: 0.8807 (tpp) cc_final: 0.8490 (mmp) REVERT: s 61 LYS cc_start: 0.6161 (tptt) cc_final: 0.5524 (mttp) REVERT: s 94 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8258 (mm-30) outliers start: 113 outliers final: 86 residues processed: 818 average time/residue: 0.6175 time to fit residues: 890.4067 Evaluate side-chains 815 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 716 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 281 ARG Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 221 HIS Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 526 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 243 ARG Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 130 GLN Chi-restraints excluded: chain Y residue 164 THR Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 40 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 35 MET Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain h residue 67 MET Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 43 ARG Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 165 SER Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 72 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 78 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 698 optimal weight: 6.9990 chunk 735 optimal weight: 0.9990 chunk 671 optimal weight: 6.9990 chunk 715 optimal weight: 4.9990 chunk 430 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 chunk 562 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 646 optimal weight: 9.9990 chunk 677 optimal weight: 10.0000 chunk 713 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN F 193 GLN H 219 ASN J 33 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 266 GLN ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.235 68651 Z= 0.521 Angle : 1.336 50.665 92801 Z= 0.850 Chirality : 0.256 6.365 9942 Planarity : 0.004 0.058 11646 Dihedral : 11.655 176.493 9989 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.69 % Allowed : 12.72 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 8085 helix: 1.33 (0.08), residues: 4161 sheet: -0.52 (0.26), residues: 398 loop : -0.15 (0.11), residues: 3526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 173 HIS 0.016 0.001 HIS L 221 PHE 0.020 0.001 PHE f 19 TYR 0.050 0.001 TYR H 149 ARG 0.014 0.000 ARG k 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 711 time to evaluate : 6.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8180 (t70) cc_final: 0.7945 (t0) REVERT: A 34 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8362 (pt0) REVERT: A 92 THR cc_start: 0.9433 (m) cc_final: 0.9210 (p) REVERT: B 76 ASP cc_start: 0.8215 (t0) cc_final: 0.7875 (t0) REVERT: E 62 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9101 (tp) REVERT: E 178 MET cc_start: 0.8298 (ppp) cc_final: 0.7739 (ppp) REVERT: F 159 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8798 (mp) REVERT: F 297 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8793 (m) REVERT: G 320 MET cc_start: 0.8357 (mtt) cc_final: 0.8146 (mtp) REVERT: H 150 GLU cc_start: 0.8439 (tp30) cc_final: 0.8067 (tp30) REVERT: H 234 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8224 (tm-30) REVERT: H 281 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7313 (tmm-80) REVERT: J 1 MET cc_start: 0.5907 (tpt) cc_final: 0.5655 (mmt) REVERT: J 44 MET cc_start: 0.8601 (ptt) cc_final: 0.8211 (ptt) REVERT: J 172 MET cc_start: 0.8592 (tmm) cc_final: 0.7866 (tmm) REVERT: K 88 ASP cc_start: 0.8414 (p0) cc_final: 0.8088 (p0) REVERT: L 79 GLU cc_start: 0.8628 (tt0) cc_final: 0.7959 (tp30) REVERT: L 176 MET cc_start: 0.8474 (mmt) cc_final: 0.8011 (mmm) REVERT: L 259 MET cc_start: 0.8408 (tmm) cc_final: 0.7789 (tmm) REVERT: L 267 GLU cc_start: 0.8282 (tt0) cc_final: 0.7912 (tt0) REVERT: L 403 MET cc_start: 0.8976 (mpp) cc_final: 0.8126 (mpp) REVERT: L 540 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7588 (tm-30) REVERT: M 116 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8390 (t80) REVERT: M 186 CYS cc_start: 0.8269 (m) cc_final: 0.7904 (t) REVERT: M 241 MET cc_start: 0.8673 (mmm) cc_final: 0.8340 (mmm) REVERT: M 443 MET cc_start: 0.7869 (ttt) cc_final: 0.7634 (ttt) REVERT: N 64 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8797 (mm-40) REVERT: N 262 VAL cc_start: 0.9371 (t) cc_final: 0.9160 (p) REVERT: N 323 MET cc_start: 0.8040 (mmp) cc_final: 0.7785 (mmp) REVERT: O 45 MET cc_start: 0.8812 (mpp) cc_final: 0.8188 (mpp) REVERT: O 390 MET cc_start: 0.7657 (mmp) cc_final: 0.7435 (tpp) REVERT: P 243 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7442 (mmt90) REVERT: Q 41 LYS cc_start: 0.8802 (tptt) cc_final: 0.8505 (tmtt) REVERT: Q 98 THR cc_start: 0.8453 (p) cc_final: 0.7927 (m) REVERT: R 62 TYR cc_start: 0.8493 (m-80) cc_final: 0.7945 (m-80) REVERT: U 77 GLU cc_start: 0.8585 (tt0) cc_final: 0.8308 (tt0) REVERT: V 87 GLU cc_start: 0.8490 (tp30) cc_final: 0.8139 (tp30) REVERT: W 46 ASP cc_start: 0.8590 (t0) cc_final: 0.8356 (t0) REVERT: X 92 ASP cc_start: 0.8793 (t0) cc_final: 0.8537 (t0) REVERT: Y 47 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7537 (mm-40) REVERT: Y 66 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: Y 162 ASN cc_start: 0.8593 (t0) cc_final: 0.8345 (t0) REVERT: a 1 MET cc_start: 0.7748 (tpp) cc_final: 0.7409 (tpp) REVERT: a 4 GLU cc_start: 0.8115 (mp0) cc_final: 0.7851 (mp0) REVERT: a 29 LEU cc_start: 0.9121 (tp) cc_final: 0.8725 (mm) REVERT: a 30 MET cc_start: 0.8285 (ttm) cc_final: 0.7938 (ttp) REVERT: b 70 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8546 (mtmm) REVERT: d 110 GLU cc_start: 0.8502 (pm20) cc_final: 0.8243 (pm20) REVERT: e 36 GLU cc_start: 0.8001 (tp30) cc_final: 0.7654 (tp30) REVERT: e 76 GLU cc_start: 0.8105 (tp30) cc_final: 0.7766 (tp30) REVERT: f 31 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7099 (mp0) REVERT: f 33 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7472 (mmt) REVERT: h 116 ILE cc_start: 0.9291 (mm) cc_final: 0.9033 (mp) REVERT: j 55 MET cc_start: 0.9114 (ttp) cc_final: 0.8622 (ttp) REVERT: k 43 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8148 (ttp-110) REVERT: l 61 GLU cc_start: 0.8143 (mp0) cc_final: 0.7703 (mp0) REVERT: l 104 GLU cc_start: 0.8604 (tt0) cc_final: 0.8345 (tt0) REVERT: l 139 MET cc_start: 0.8853 (mmm) cc_final: 0.8251 (ttp) REVERT: m 96 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7788 (tm-30) REVERT: o 9 MET cc_start: 0.7730 (tmm) cc_final: 0.7445 (tmm) REVERT: p 88 GLU cc_start: 0.8365 (tp30) cc_final: 0.8099 (mm-30) REVERT: p 134 MET cc_start: 0.8845 (tpp) cc_final: 0.8491 (mmp) REVERT: s 61 LYS cc_start: 0.6197 (tptt) cc_final: 0.5549 (mttp) outliers start: 120 outliers final: 96 residues processed: 795 average time/residue: 0.6191 time to fit residues: 867.6012 Evaluate side-chains 805 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 700 time to evaluate : 5.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 281 ARG Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 355 MET Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 243 ARG Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 164 THR Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 40 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 35 MET Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain h residue 67 MET Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 43 ARG Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 165 SER Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 72 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 470 optimal weight: 3.9990 chunk 756 optimal weight: 7.9990 chunk 462 optimal weight: 10.0000 chunk 359 optimal weight: 1.9990 chunk 526 optimal weight: 4.9990 chunk 794 optimal weight: 10.0000 chunk 730 optimal weight: 5.9990 chunk 632 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 488 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 HIS ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 266 GLN V 40 GLN ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 42 HIS ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 68651 Z= 0.475 Angle : 1.320 50.588 92801 Z= 0.844 Chirality : 0.256 6.351 9942 Planarity : 0.004 0.060 11646 Dihedral : 11.486 177.144 9989 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.57 % Allowed : 13.03 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 8085 helix: 1.37 (0.08), residues: 4183 sheet: -0.45 (0.26), residues: 389 loop : -0.15 (0.11), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 306 HIS 0.008 0.001 HIS L 221 PHE 0.028 0.001 PHE i 69 TYR 0.047 0.001 TYR H 149 ARG 0.014 0.000 ARG k 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16170 Ramachandran restraints generated. 8085 Oldfield, 0 Emsley, 8085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 723 time to evaluate : 6.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9438 (m) cc_final: 0.9224 (p) REVERT: B 76 ASP cc_start: 0.8174 (t0) cc_final: 0.7704 (t0) REVERT: E 62 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9097 (tp) REVERT: E 178 MET cc_start: 0.8270 (ppp) cc_final: 0.7694 (ppp) REVERT: F 117 MET cc_start: 0.7920 (ttm) cc_final: 0.7212 (ttm) REVERT: F 159 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (mp) REVERT: F 297 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8753 (m) REVERT: F 337 SER cc_start: 0.8070 (m) cc_final: 0.7796 (p) REVERT: G 320 MET cc_start: 0.8333 (mtt) cc_final: 0.8128 (mtp) REVERT: H 150 GLU cc_start: 0.8429 (tp30) cc_final: 0.8046 (tp30) REVERT: H 234 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8248 (tm-30) REVERT: I 66 MET cc_start: 0.8191 (ttt) cc_final: 0.7950 (ttt) REVERT: J 44 MET cc_start: 0.8549 (ptt) cc_final: 0.8164 (ptt) REVERT: J 172 MET cc_start: 0.8581 (tmm) cc_final: 0.8165 (tmm) REVERT: K 54 ASN cc_start: 0.8770 (t0) cc_final: 0.8269 (t0) REVERT: K 88 ASP cc_start: 0.8364 (p0) cc_final: 0.8047 (p0) REVERT: L 79 GLU cc_start: 0.8614 (tt0) cc_final: 0.8010 (tp30) REVERT: L 82 MET cc_start: 0.8830 (ppp) cc_final: 0.8171 (ppp) REVERT: L 176 MET cc_start: 0.8464 (mmt) cc_final: 0.7978 (mmm) REVERT: L 221 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6222 (m90) REVERT: L 259 MET cc_start: 0.8394 (tmm) cc_final: 0.7827 (tmm) REVERT: L 267 GLU cc_start: 0.8305 (tt0) cc_final: 0.7943 (tt0) REVERT: L 403 MET cc_start: 0.8952 (mpp) cc_final: 0.8041 (mpp) REVERT: L 540 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7562 (tm-30) REVERT: M 116 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8381 (t80) REVERT: M 186 CYS cc_start: 0.8253 (m) cc_final: 0.7890 (t) REVERT: M 241 MET cc_start: 0.8631 (mmm) cc_final: 0.8297 (mmm) REVERT: M 443 MET cc_start: 0.7882 (ttt) cc_final: 0.7610 (ttt) REVERT: N 64 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8794 (mm-40) REVERT: N 262 VAL cc_start: 0.9358 (t) cc_final: 0.9138 (p) REVERT: N 297 PHE cc_start: 0.8240 (m-10) cc_final: 0.7990 (m-80) REVERT: N 323 MET cc_start: 0.8061 (mmp) cc_final: 0.7806 (mmp) REVERT: O 45 MET cc_start: 0.8815 (mpp) cc_final: 0.8209 (mpp) REVERT: O 163 MET cc_start: 0.9018 (mmt) cc_final: 0.8798 (mmt) REVERT: O 390 MET cc_start: 0.7658 (mmp) cc_final: 0.7406 (tpp) REVERT: P 243 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7461 (mmt90) REVERT: Q 41 LYS cc_start: 0.8788 (tptt) cc_final: 0.8492 (tmtt) REVERT: R 62 TYR cc_start: 0.8436 (m-80) cc_final: 0.7927 (m-80) REVERT: U 77 GLU cc_start: 0.8584 (tt0) cc_final: 0.8246 (tt0) REVERT: V 87 GLU cc_start: 0.8428 (tp30) cc_final: 0.8080 (tp30) REVERT: X 92 ASP cc_start: 0.8778 (t0) cc_final: 0.8510 (t0) REVERT: Y 47 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7647 (mm-40) REVERT: Y 66 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7923 (mtt) REVERT: Y 162 ASN cc_start: 0.8571 (t0) cc_final: 0.8255 (t0) REVERT: Z 153 TRP cc_start: 0.7955 (m-10) cc_final: 0.7624 (m-10) REVERT: a 1 MET cc_start: 0.7705 (tpp) cc_final: 0.7390 (tpp) REVERT: a 4 GLU cc_start: 0.8122 (mp0) cc_final: 0.7858 (mp0) REVERT: a 29 LEU cc_start: 0.8985 (tp) cc_final: 0.8382 (mt) REVERT: d 50 VAL cc_start: 0.8971 (m) cc_final: 0.8707 (t) REVERT: d 110 GLU cc_start: 0.8497 (pm20) cc_final: 0.8238 (pm20) REVERT: e 35 MET cc_start: 0.7474 (ttm) cc_final: 0.7212 (mtt) REVERT: e 36 GLU cc_start: 0.8018 (tp30) cc_final: 0.7639 (tp30) REVERT: e 44 GLU cc_start: 0.7644 (pm20) cc_final: 0.7151 (pm20) REVERT: e 76 GLU cc_start: 0.7997 (tp30) cc_final: 0.7698 (tp30) REVERT: e 99 ASP cc_start: 0.7924 (t0) cc_final: 0.7685 (t0) REVERT: f 31 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7089 (mp0) REVERT: f 33 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7734 (mmt) REVERT: g 118 GLU cc_start: 0.8207 (pp20) cc_final: 0.7911 (pp20) REVERT: h 116 ILE cc_start: 0.9253 (mm) cc_final: 0.8997 (mp) REVERT: k 43 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8110 (ttp-110) REVERT: l 61 GLU cc_start: 0.8137 (mp0) cc_final: 0.7718 (mp0) REVERT: l 104 GLU cc_start: 0.8603 (tt0) cc_final: 0.8356 (tt0) REVERT: l 139 MET cc_start: 0.8845 (mmm) cc_final: 0.8132 (ttp) REVERT: m 96 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7771 (tp30) REVERT: n 117 LYS cc_start: 0.8934 (tttt) cc_final: 0.8597 (tttm) REVERT: o 9 MET cc_start: 0.7685 (tmm) cc_final: 0.7443 (tmm) REVERT: p 88 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (mm-30) REVERT: p 134 MET cc_start: 0.8835 (tpp) cc_final: 0.8480 (mmp) REVERT: s 61 LYS cc_start: 0.6287 (tptt) cc_final: 0.5682 (mttp) REVERT: s 94 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8317 (mm-30) outliers start: 111 outliers final: 88 residues processed: 799 average time/residue: 0.6082 time to fit residues: 858.8330 Evaluate side-chains 807 residues out of total 7081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 709 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 448 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 163 CYS Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 221 HIS Chi-restraints excluded: chain L residue 290 SER Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 116 PHE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 310 CYS Chi-restraints excluded: chain M residue 355 MET Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain N residue 89 ASN Chi-restraints excluded: chain N residue 214 MET Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 399 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 243 ARG Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 62 GLU Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 151 ASP Chi-restraints excluded: chain Y residue 66 MET Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 164 THR Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 40 ASP Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain d residue 4 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 41 PHE Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 24 TYR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 35 MET Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain i residue 66 ILE Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 43 ARG Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 165 SER Chi-restraints excluded: chain m residue 6 GLU Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain n residue 16 CYS Chi-restraints excluded: chain n residue 52 SER Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 99 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain p residue 88 GLU Chi-restraints excluded: chain q residue 10 LEU Chi-restraints excluded: chain q residue 72 ASN Chi-restraints excluded: chain q residue 83 GLU Chi-restraints excluded: chain r residue 32 ASP Chi-restraints excluded: chain r residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 502 optimal weight: 8.9990 chunk 673 optimal weight: 0.0370 chunk 193 optimal weight: 4.9990 chunk 582 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 633 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 650 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN H 54 GLN J 33 GLN L 132 GLN L 221 HIS ** L 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS p 42 HIS ** r 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049237 restraints weight = 254099.109| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.68 r_work: 0.2861 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 68651 Z= 0.458 Angle : 1.315 50.541 92801 Z= 0.842 Chirality : 0.255 6.334 9942 Planarity : 0.004 0.062 11646 Dihedral : 11.255 179.767 9989 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.20 % Allowed : 13.44 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.10), residues: 8085 helix: 1.39 (0.08), residues: 4200 sheet: -0.36 (0.26), residues: 388 loop : -0.10 (0.11), residues: 3497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 49 HIS 0.024 0.001 HIS L 221 PHE 0.022 0.001 PHE L 307 TYR 0.046 0.001 TYR H 149 ARG 0.014 0.000 ARG k 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14998.83 seconds wall clock time: 265 minutes 44.89 seconds (15944.89 seconds total)