Starting phenix.real_space_refine on Mon Dec 11 17:52:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npu_12521/12_2023/7npu_12521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npu_12521/12_2023/7npu_12521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npu_12521/12_2023/7npu_12521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npu_12521/12_2023/7npu_12521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npu_12521/12_2023/7npu_12521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npu_12521/12_2023/7npu_12521.pdb" } resolution = 4.48 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 408 5.16 5 C 40130 2.51 5 N 10825 2.21 5 O 10967 1.98 5 H 64397 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B1 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 GLU 47": "OE1" <-> "OE2" Residue "B2 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B2 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B2 ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 GLU 45": "OE1" <-> "OE2" Residue "B2 GLU 47": "OE1" <-> "OE2" Residue "B3 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B3 ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 GLU 45": "OE1" <-> "OE2" Residue "B3 GLU 47": "OE1" <-> "OE2" Residue "B4 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B4 ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B4 GLU 45": "OE1" <-> "OE2" Residue "B4 GLU 47": "OE1" <-> "OE2" Residue "B5 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B5 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B5 ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B5 GLU 47": "OE1" <-> "OE2" Residue "B6 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B6 GLU 45": "OE1" <-> "OE2" Residue "B6 GLU 47": "OE1" <-> "OE2" Residue "C1 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 19": "OE1" <-> "OE2" Residue "C1 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 GLU 150": "OE1" <-> "OE2" Residue "C1 ASP 157": "OD1" <-> "OD2" Residue "C1 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 GLU 173": "OE1" <-> "OE2" Residue "C1 GLU 187": "OE1" <-> "OE2" Residue "C1 GLU 198": "OE1" <-> "OE2" Residue "C1 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 218": "OE1" <-> "OE2" Residue "C1 ASP 248": "OD1" <-> "OD2" Residue "C1 ASP 258": "OD1" <-> "OD2" Residue "C1 ASP 263": "OD1" <-> "OD2" Residue "C1 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 292": "OE1" <-> "OE2" Residue "C1 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 GLU 296": "OE1" <-> "OE2" Residue "C1 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 ASP 330": "OD1" <-> "OD2" Residue "C1 ASP 331": "OD1" <-> "OD2" Residue "C1 GLU 335": "OE1" <-> "OE2" Residue "C1 GLU 341": "OE1" <-> "OE2" Residue "C1 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ASP 350": "OD1" <-> "OD2" Residue "C1 ASP 368": "OD1" <-> "OD2" Residue "C1 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 ASP 388": "OD1" <-> "OD2" Residue "C1 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ASP 397": "OD1" <-> "OD2" Residue "C1 GLU 403": "OE1" <-> "OE2" Residue "C1 GLU 405": "OE1" <-> "OE2" Residue "C1 GLU 406": "OE1" <-> "OE2" Residue "C1 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 GLU 19": "OE1" <-> "OE2" Residue "C2 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 GLU 150": "OE1" <-> "OE2" Residue "C2 ASP 157": "OD1" <-> "OD2" Residue "C2 PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 GLU 173": "OE1" <-> "OE2" Residue "C2 GLU 187": "OE1" <-> "OE2" Residue "C2 GLU 198": "OE1" <-> "OE2" Residue "C2 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 GLU 218": "OE1" <-> "OE2" Residue "C2 ASP 248": "OD1" <-> "OD2" Residue "C2 ASP 258": "OD1" <-> "OD2" Residue "C2 ASP 263": "OD1" <-> "OD2" Residue "C2 GLU 292": "OE1" <-> "OE2" Residue "C2 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 GLU 296": "OE1" <-> "OE2" Residue "C2 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 ASP 330": "OD1" <-> "OD2" Residue "C2 ASP 331": "OD1" <-> "OD2" Residue "C2 GLU 335": "OE1" <-> "OE2" Residue "C2 GLU 341": "OE1" <-> "OE2" Residue "C2 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ASP 350": "OD1" <-> "OD2" Residue "C2 ASP 368": "OD1" <-> "OD2" Residue "C2 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C2 ASP 388": "OD1" <-> "OD2" Residue "C2 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ASP 397": "OD1" <-> "OD2" Residue "C2 GLU 403": "OE1" <-> "OE2" Residue "C2 GLU 405": "OE1" <-> "OE2" Residue "C2 GLU 406": "OE1" <-> "OE2" Residue "C2 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C2 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 GLU 19": "OE1" <-> "OE2" Residue "C3 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 GLU 150": "OE1" <-> "OE2" Residue "C3 ASP 157": "OD1" <-> "OD2" Residue "C3 PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 GLU 173": "OE1" <-> "OE2" Residue "C3 ASP 185": "OD1" <-> "OD2" Residue "C3 GLU 187": "OE1" <-> "OE2" Residue "C3 GLU 198": "OE1" <-> "OE2" Residue "C3 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 GLU 218": "OE1" <-> "OE2" Residue "C3 ASP 248": "OD1" <-> "OD2" Residue "C3 ASP 258": "OD1" <-> "OD2" Residue "C3 ASP 263": "OD1" <-> "OD2" Residue "C3 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 GLU 292": "OE1" <-> "OE2" Residue "C3 GLU 296": "OE1" <-> "OE2" Residue "C3 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 ASP 330": "OD1" <-> "OD2" Residue "C3 ASP 331": "OD1" <-> "OD2" Residue "C3 GLU 335": "OE1" <-> "OE2" Residue "C3 GLU 341": "OE1" <-> "OE2" Residue "C3 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ASP 350": "OD1" <-> "OD2" Residue "C3 ASP 368": "OD1" <-> "OD2" Residue "C3 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C3 ASP 388": "OD1" <-> "OD2" Residue "C3 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ASP 397": "OD1" <-> "OD2" Residue "C3 GLU 403": "OE1" <-> "OE2" Residue "C3 GLU 405": "OE1" <-> "OE2" Residue "C3 GLU 406": "OE1" <-> "OE2" Residue "C3 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C3 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 GLU 19": "OE1" <-> "OE2" Residue "C4 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 GLU 150": "OE1" <-> "OE2" Residue "C4 ASP 157": "OD1" <-> "OD2" Residue "C4 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 GLU 173": "OE1" <-> "OE2" Residue "C4 GLU 187": "OE1" <-> "OE2" Residue "C4 GLU 198": "OE1" <-> "OE2" Residue "C4 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 GLU 218": "OE1" <-> "OE2" Residue "C4 ASP 248": "OD1" <-> "OD2" Residue "C4 ASP 258": "OD1" <-> "OD2" Residue "C4 ASP 263": "OD1" <-> "OD2" Residue "C4 GLU 292": "OE1" <-> "OE2" Residue "C4 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 GLU 296": "OE1" <-> "OE2" Residue "C4 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 ASP 330": "OD1" <-> "OD2" Residue "C4 ASP 331": "OD1" <-> "OD2" Residue "C4 GLU 335": "OE1" <-> "OE2" Residue "C4 GLU 341": "OE1" <-> "OE2" Residue "C4 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ASP 350": "OD1" <-> "OD2" Residue "C4 ASP 368": "OD1" <-> "OD2" Residue "C4 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C4 ASP 388": "OD1" <-> "OD2" Residue "C4 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ASP 397": "OD1" <-> "OD2" Residue "C4 GLU 403": "OE1" <-> "OE2" Residue "C4 GLU 405": "OE1" <-> "OE2" Residue "C4 GLU 406": "OE1" <-> "OE2" Residue "C4 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C4 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 GLU 19": "OE1" <-> "OE2" Residue "C5 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 GLU 150": "OE1" <-> "OE2" Residue "C5 ASP 157": "OD1" <-> "OD2" Residue "C5 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 GLU 173": "OE1" <-> "OE2" Residue "C5 GLU 187": "OE1" <-> "OE2" Residue "C5 GLU 198": "OE1" <-> "OE2" Residue "C5 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 GLU 218": "OE1" <-> "OE2" Residue "C5 ASP 248": "OD1" <-> "OD2" Residue "C5 ASP 258": "OD1" <-> "OD2" Residue "C5 ASP 263": "OD1" <-> "OD2" Residue "C5 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 GLU 292": "OE1" <-> "OE2" Residue "C5 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 GLU 296": "OE1" <-> "OE2" Residue "C5 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 ASP 330": "OD1" <-> "OD2" Residue "C5 ASP 331": "OD1" <-> "OD2" Residue "C5 GLU 335": "OE1" <-> "OE2" Residue "C5 GLU 341": "OE1" <-> "OE2" Residue "C5 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ASP 350": "OD1" <-> "OD2" Residue "C5 ASP 368": "OD1" <-> "OD2" Residue "C5 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C5 ASP 388": "OD1" <-> "OD2" Residue "C5 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ASP 397": "OD1" <-> "OD2" Residue "C5 GLU 403": "OE1" <-> "OE2" Residue "C5 GLU 405": "OE1" <-> "OE2" Residue "C5 GLU 406": "OE1" <-> "OE2" Residue "C5 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C5 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 GLU 19": "OE1" <-> "OE2" Residue "C6 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 GLU 150": "OE1" <-> "OE2" Residue "C6 ASP 157": "OD1" <-> "OD2" Residue "C6 ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 GLU 173": "OE1" <-> "OE2" Residue "C6 GLU 187": "OE1" <-> "OE2" Residue "C6 GLU 198": "OE1" <-> "OE2" Residue "C6 PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 GLU 218": "OE1" <-> "OE2" Residue "C6 ASP 248": "OD1" <-> "OD2" Residue "C6 ASP 258": "OD1" <-> "OD2" Residue "C6 ASP 263": "OD1" <-> "OD2" Residue "C6 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 GLU 292": "OE1" <-> "OE2" Residue "C6 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 GLU 296": "OE1" <-> "OE2" Residue "C6 ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 ASP 330": "OD1" <-> "OD2" Residue "C6 ASP 331": "OD1" <-> "OD2" Residue "C6 GLU 335": "OE1" <-> "OE2" Residue "C6 GLU 341": "OE1" <-> "OE2" Residue "C6 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 ASP 350": "OD1" <-> "OD2" Residue "C6 ASP 368": "OD1" <-> "OD2" Residue "C6 ARG 378": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C6 ASP 388": "OD1" <-> "OD2" Residue "C6 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 ASP 397": "OD1" <-> "OD2" Residue "C6 GLU 403": "OE1" <-> "OE2" Residue "C6 GLU 405": "OE1" <-> "OE2" Residue "C6 GLU 406": "OE1" <-> "OE2" Residue "C6 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C6 ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ASP 38": "OD1" <-> "OD2" Residue "D1 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 GLU 60": "OE1" <-> "OE2" Residue "D1 ASP 80": "OD1" <-> "OD2" Residue "D1 GLU 92": "OE1" <-> "OE2" Residue "D1 ASP 94": "OD1" <-> "OD2" Residue "D1 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ASP 108": "OD1" <-> "OD2" Residue "D1 GLU 110": "OE1" <-> "OE2" Residue "D1 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 GLU 117": "OE1" <-> "OE2" Residue "D1 ASP 126": "OD1" <-> "OD2" Residue "D1 ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ASP 135": "OD1" <-> "OD2" Residue "D1 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ASP 195": "OD1" <-> "OD2" Residue "D1 ASP 202": "OD1" <-> "OD2" Residue "D1 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 GLU 321": "OE1" <-> "OE2" Residue "D1 ASP 348": "OD1" <-> "OD2" Residue "D1 ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ASP 380": "OD1" <-> "OD2" Residue "D1 TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ASP 409": "OD1" <-> "OD2" Residue "D1 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 GLU 434": "OE1" <-> "OE2" Residue "D1 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 GLU 479": "OE1" <-> "OE2" Residue "D1 TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 501": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ASP 38": "OD1" <-> "OD2" Residue "D2 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ASP 80": "OD1" <-> "OD2" Residue "D2 GLU 92": "OE1" <-> "OE2" Residue "D2 ASP 94": "OD1" <-> "OD2" Residue "D2 ASP 97": "OD1" <-> "OD2" Residue "D2 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 GLU 117": "OE1" <-> "OE2" Residue "D2 ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 ASP 135": "OD1" <-> "OD2" Residue "D2 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ASP 202": "OD1" <-> "OD2" Residue "D2 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D2 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ASP 348": "OD1" <-> "OD2" Residue "D2 ASP 380": "OD1" <-> "OD2" Residue "D2 ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D2 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ASP 38": "OD1" <-> "OD2" Residue "D3 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 GLU 60": "OE1" <-> "OE2" Residue "D3 ASP 80": "OD1" <-> "OD2" Residue "D3 GLU 92": "OE1" <-> "OE2" Residue "D3 ASP 94": "OD1" <-> "OD2" Residue "D3 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ASP 108": "OD1" <-> "OD2" Residue "D3 GLU 110": "OE1" <-> "OE2" Residue "D3 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 GLU 117": "OE1" <-> "OE2" Residue "D3 ASP 126": "OD1" <-> "OD2" Residue "D3 ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ASP 195": "OD1" <-> "OD2" Residue "D3 ASP 202": "OD1" <-> "OD2" Residue "D3 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 ASP 348": "OD1" <-> "OD2" Residue "D3 ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D3 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 GLU 479": "OE1" <-> "OE2" Residue "D3 TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D3 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 ASP 38": "OD1" <-> "OD2" Residue "D4 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ASP 80": "OD1" <-> "OD2" Residue "D4 GLU 92": "OE1" <-> "OE2" Residue "D4 ASP 94": "OD1" <-> "OD2" Residue "D4 ASP 97": "OD1" <-> "OD2" Residue "D4 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ASP 135": "OD1" <-> "OD2" Residue "D4 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ASP 202": "OD1" <-> "OD2" Residue "D4 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ASP 348": "OD1" <-> "OD2" Residue "D4 ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D4 ASP 380": "OD1" <-> "OD2" Residue "D4 TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D4 ASP 409": "OD1" <-> "OD2" Residue "D4 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 ASP 38": "OD1" <-> "OD2" Residue "D5 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 GLU 60": "OE1" <-> "OE2" Residue "D5 ASP 80": "OD1" <-> "OD2" Residue "D5 GLU 92": "OE1" <-> "OE2" Residue "D5 ASP 94": "OD1" <-> "OD2" Residue "D5 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 ASP 108": "OD1" <-> "OD2" Residue "D5 GLU 110": "OE1" <-> "OE2" Residue "D5 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 GLU 117": "OE1" <-> "OE2" Residue "D5 ASP 126": "OD1" <-> "OD2" Residue "D5 ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ASP 195": "OD1" <-> "OD2" Residue "D5 ASP 202": "OD1" <-> "OD2" Residue "D5 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 GLU 321": "OE1" <-> "OE2" Residue "D5 GLU 341": "OE1" <-> "OE2" Residue "D5 ASP 348": "OD1" <-> "OD2" Residue "D5 ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 ASP 409": "OD1" <-> "OD2" Residue "D5 ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 GLU 434": "OE1" <-> "OE2" Residue "D5 ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D5 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 GLU 479": "OE1" <-> "OE2" Residue "D5 TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D5 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ASP 38": "OD1" <-> "OD2" Residue "D6 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 ASP 80": "OD1" <-> "OD2" Residue "D6 GLU 92": "OE1" <-> "OE2" Residue "D6 ASP 94": "OD1" <-> "OD2" Residue "D6 ASP 97": "OD1" <-> "OD2" Residue "D6 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 GLU 117": "OE1" <-> "OE2" Residue "D6 PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ASP 135": "OD1" <-> "OD2" Residue "D6 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 ASP 202": "OD1" <-> "OD2" Residue "D6 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D6 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 ASP 348": "OD1" <-> "OD2" Residue "D6 ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D6 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ASP 38": "OD1" <-> "OD2" Residue "D7 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 GLU 60": "OE1" <-> "OE2" Residue "D7 ASP 80": "OD1" <-> "OD2" Residue "D7 GLU 92": "OE1" <-> "OE2" Residue "D7 ASP 94": "OD1" <-> "OD2" Residue "D7 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ASP 108": "OD1" <-> "OD2" Residue "D7 GLU 110": "OE1" <-> "OE2" Residue "D7 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 GLU 117": "OE1" <-> "OE2" Residue "D7 ASP 126": "OD1" <-> "OD2" Residue "D7 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ASP 195": "OD1" <-> "OD2" Residue "D7 ASP 202": "OD1" <-> "OD2" Residue "D7 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 ASP 409": "OD1" <-> "OD2" Residue "D7 ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 GLU 434": "OE1" <-> "OE2" Residue "D7 ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 GLU 476": "OE1" <-> "OE2" Residue "D7 GLU 479": "OE1" <-> "OE2" Residue "D7 TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ARG 501": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D7 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D7 ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ASP 38": "OD1" <-> "OD2" Residue "D8 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ASP 80": "OD1" <-> "OD2" Residue "D8 GLU 92": "OE1" <-> "OE2" Residue "D8 ASP 94": "OD1" <-> "OD2" Residue "D8 ASP 97": "OD1" <-> "OD2" Residue "D8 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 GLU 117": "OE1" <-> "OE2" Residue "D8 PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ASP 135": "OD1" <-> "OD2" Residue "D8 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ASP 202": "OD1" <-> "OD2" Residue "D8 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 ASP 348": "OD1" <-> "OD2" Residue "D8 TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D8 ASP 409": "OD1" <-> "OD2" Residue "D8 ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D8 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 ASP 38": "OD1" <-> "OD2" Residue "D9 ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 GLU 60": "OE1" <-> "OE2" Residue "D9 ASP 80": "OD1" <-> "OD2" Residue "D9 GLU 92": "OE1" <-> "OE2" Residue "D9 ASP 94": "OD1" <-> "OD2" Residue "D9 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 ASP 108": "OD1" <-> "OD2" Residue "D9 GLU 110": "OE1" <-> "OE2" Residue "D9 ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 GLU 117": "OE1" <-> "OE2" Residue "D9 ASP 126": "OD1" <-> "OD2" Residue "D9 ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 ASP 195": "OD1" <-> "OD2" Residue "D9 ASP 202": "OD1" <-> "OD2" Residue "D9 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 GLU 321": "OE1" <-> "OE2" Residue "D9 ASP 348": "OD1" <-> "OD2" Residue "D9 ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 ASP 380": "OD1" <-> "OD2" Residue "D9 ASP 409": "OD1" <-> "OD2" Residue "D9 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 GLU 434": "OE1" <-> "OE2" Residue "D9 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 GLU 479": "OE1" <-> "OE2" Residue "D9 TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 ARG 501": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D9 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D9 ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ASP 38": "OD1" <-> "OD2" Residue "DA ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ASP 80": "OD1" <-> "OD2" Residue "DA GLU 92": "OE1" <-> "OE2" Residue "DA ASP 94": "OD1" <-> "OD2" Residue "DA ASP 97": "OD1" <-> "OD2" Residue "DA PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DA ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA GLU 117": "OE1" <-> "OE2" Residue "DA ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ASP 135": "OD1" <-> "OD2" Residue "DA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DA ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ASP 202": "OD1" <-> "OD2" Residue "DA PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DA ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DA TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DA ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ASP 348": "OD1" <-> "OD2" Residue "DA ASP 380": "OD1" <-> "OD2" Residue "DA ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DA TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ASP 38": "OD1" <-> "OD2" Residue "DB ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB GLU 60": "OE1" <-> "OE2" Residue "DB ASP 80": "OD1" <-> "OD2" Residue "DB GLU 92": "OE1" <-> "OE2" Residue "DB ASP 94": "OD1" <-> "OD2" Residue "DB PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ASP 108": "OD1" <-> "OD2" Residue "DB GLU 110": "OE1" <-> "OE2" Residue "DB ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB GLU 117": "OE1" <-> "OE2" Residue "DB ASP 126": "OD1" <-> "OD2" Residue "DB ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ASP 195": "OD1" <-> "OD2" Residue "DB ASP 202": "OD1" <-> "OD2" Residue "DB PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB ASP 348": "OD1" <-> "OD2" Residue "DB ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB ASP 380": "OD1" <-> "OD2" Residue "DB ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DB ASP 409": "OD1" <-> "OD2" Residue "DB TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB GLU 434": "OE1" <-> "OE2" Residue "DB PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB GLU 479": "OE1" <-> "OE2" Residue "DB TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DB TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC ASP 38": "OD1" <-> "OD2" Residue "DC ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ASP 80": "OD1" <-> "OD2" Residue "DC GLU 92": "OE1" <-> "OE2" Residue "DC ASP 94": "OD1" <-> "OD2" Residue "DC ASP 97": "OD1" <-> "OD2" Residue "DC PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ASP 135": "OD1" <-> "OD2" Residue "DC ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ASP 202": "OD1" <-> "OD2" Residue "DC PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC ASP 348": "OD1" <-> "OD2" Residue "DC ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "DC ASP 409": "OD1" <-> "OD2" Residue "DC ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "DC TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 126727 Number of models: 1 Model: "" Number of chains: 24 Chain: "B1" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1147 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B2" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1147 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B3" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1147 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B4" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1147 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B5" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1147 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B6" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1147 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "C1" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6335 Classifications: {'peptide': 406} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 1 Chain: "C2" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6335 Classifications: {'peptide': 406} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 1 Chain: "C3" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6335 Classifications: {'peptide': 406} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 1 Chain: "C4" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6335 Classifications: {'peptide': 406} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 1 Chain: "C5" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6335 Classifications: {'peptide': 406} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 1 Chain: "C6" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6335 Classifications: {'peptide': 406} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 1 Chain: "D1" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7458 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 25, 'TRANS': 459} Chain: "D2" Number of atoms: 6155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6155 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "D3" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7459 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 25, 'TRANS': 459} Chain: "D4" Number of atoms: 6308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6308 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain breaks: 1 Chain: "D5" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7459 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 25, 'TRANS': 459} Chain: "D6" Number of atoms: 6155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6155 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "D7" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7459 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 25, 'TRANS': 459} Chain: "D8" Number of atoms: 6154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6154 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "D9" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7459 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 25, 'TRANS': 459} Chain: "DA" Number of atoms: 6156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6156 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Chain: "DB" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7459 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 25, 'TRANS': 459} Chain: "DC" Number of atoms: 6154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6154 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 1 Time building chain proxies: 38.60, per 1000 atoms: 0.30 Number of scatterers: 126727 At special positions: 0 Unit cell: (248.6, 222.2, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 408 16.00 O 10967 8.00 N 10825 7.00 C 40130 6.00 H 64397 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 73.63 Conformation dependent library (CDL) restraints added in 9.5 seconds 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15198 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 37 sheets defined 65.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'B1' and resid 19 through 40 removed outlier: 3.664A pdb=" N THRB1 24 " --> pdb=" O ARGB1 20 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THRB1 38 " --> pdb=" O ALAB1 34 " (cutoff:3.500A) Processing helix chain 'B1' and resid 47 through 77 removed outlier: 3.725A pdb=" N ARGB1 51 " --> pdb=" O GLUB1 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALB1 56 " --> pdb=" O GLNB1 52 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHEB1 75 " --> pdb=" O LEUB1 71 " (cutoff:3.500A) Processing helix chain 'B2' and resid 19 through 40 removed outlier: 3.590A pdb=" N ARGB2 31 " --> pdb=" O GLNB2 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THRB2 38 " --> pdb=" O ALAB2 34 " (cutoff:3.500A) Processing helix chain 'B2' and resid 47 through 77 removed outlier: 3.766A pdb=" N ARGB2 51 " --> pdb=" O GLUB2 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAB2 55 " --> pdb=" O ARGB2 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VALB2 56 " --> pdb=" O GLNB2 52 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHEB2 75 " --> pdb=" O LEUB2 71 " (cutoff:3.500A) Processing helix chain 'B3' and resid 19 through 40 Processing helix chain 'B3' and resid 47 through 77 removed outlier: 3.825A pdb=" N ARGB3 51 " --> pdb=" O GLUB3 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALB3 56 " --> pdb=" O GLNB3 52 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHEB3 75 " --> pdb=" O LEUB3 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 19 through 40 removed outlier: 3.747A pdb=" N THRB4 38 " --> pdb=" O ALAB4 34 " (cutoff:3.500A) Processing helix chain 'B4' and resid 47 through 77 removed outlier: 3.870A pdb=" N ARGB4 51 " --> pdb=" O GLUB4 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VALB4 56 " --> pdb=" O GLNB4 52 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHEB4 75 " --> pdb=" O LEUB4 71 " (cutoff:3.500A) Processing helix chain 'B5' and resid 19 through 39 removed outlier: 3.645A pdb=" N LEUB5 37 " --> pdb=" O THRB5 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THRB5 38 " --> pdb=" O ALAB5 34 " (cutoff:3.500A) Processing helix chain 'B5' and resid 47 through 77 removed outlier: 4.008A pdb=" N ARGB5 51 " --> pdb=" O GLUB5 47 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VALB5 56 " --> pdb=" O GLNB5 52 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHEB5 75 " --> pdb=" O LEUB5 71 " (cutoff:3.500A) Processing helix chain 'B6' and resid 19 through 39 removed outlier: 3.524A pdb=" N THRB6 24 " --> pdb=" O ARGB6 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUB6 37 " --> pdb=" O THRB6 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THRB6 38 " --> pdb=" O ALAB6 34 " (cutoff:3.500A) Processing helix chain 'B6' and resid 47 through 77 removed outlier: 3.821A pdb=" N ARGB6 51 " --> pdb=" O GLUB6 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VALB6 56 " --> pdb=" O GLNB6 52 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEB6 75 " --> pdb=" O LEUB6 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILEB6 76 " --> pdb=" O LEUB6 72 " (cutoff:3.500A) Processing helix chain 'C1' and resid 36 through 61 removed outlier: 3.934A pdb=" N ILEC1 40 " --> pdb=" O PROC1 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLYC1 51 " --> pdb=" O VALC1 47 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VALC1 57 " --> pdb=" O METC1 53 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHEC1 58 " --> pdb=" O VALC1 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SERC1 60 " --> pdb=" O METC1 56 " (cutoff:3.500A) Processing helix chain 'C1' and resid 70 through 86 removed outlier: 3.765A pdb=" N VALC1 78 " --> pdb=" O LEUC1 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLYC1 79 " --> pdb=" O PHEC1 75 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEC1 80 " --> pdb=" O METC1 76 " (cutoff:3.500A) Processing helix chain 'C1' and resid 87 through 89 No H-bonds generated for 'chain 'C1' and resid 87 through 89' Processing helix chain 'C1' and resid 96 through 133 removed outlier: 3.733A pdb=" N LEUC1 114 " --> pdb=" O METC1 110 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SERC1 121 " --> pdb=" O THRC1 117 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SERC1 124 " --> pdb=" O GLUC1 120 " (cutoff:3.500A) Processing helix chain 'C1' and resid 135 through 137 No H-bonds generated for 'chain 'C1' and resid 135 through 137' Processing helix chain 'C1' and resid 138 through 143 removed outlier: 3.929A pdb=" N ALAC1 142 " --> pdb=" O THRC1 138 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VALC1 143 " --> pdb=" O LEUC1 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 138 through 143' Processing helix chain 'C1' and resid 184 through 188 removed outlier: 3.590A pdb=" N LEUC1 188 " --> pdb=" O ASPC1 185 " (cutoff:3.500A) Processing helix chain 'C1' and resid 189 through 203 Processing helix chain 'C1' and resid 216 through 218 No H-bonds generated for 'chain 'C1' and resid 216 through 218' Processing helix chain 'C1' and resid 226 through 245 Processing helix chain 'C1' and resid 258 through 272 removed outlier: 3.972A pdb=" N ASPC1 263 " --> pdb=" O ASPC1 260 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRPC1 264 " --> pdb=" O GLNC1 261 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRPC1 267 " --> pdb=" O TRPC1 264 " (cutoff:3.500A) Proline residue: C1 269 - end of helix Processing helix chain 'C1' and resid 289 through 297 Processing helix chain 'C1' and resid 297 through 302 Processing helix chain 'C1' and resid 312 through 317 removed outlier: 3.702A pdb=" N ALAC1 316 " --> pdb=" O SERC1 313 " (cutoff:3.500A) Processing helix chain 'C1' and resid 331 through 333 No H-bonds generated for 'chain 'C1' and resid 331 through 333' Processing helix chain 'C1' and resid 334 through 340 Processing helix chain 'C1' and resid 360 through 362 No H-bonds generated for 'chain 'C1' and resid 360 through 362' Processing helix chain 'C1' and resid 400 through 413 removed outlier: 3.787A pdb=" N GLNC1 413 " --> pdb=" O GLNC1 409 " (cutoff:3.500A) Processing helix chain 'C2' and resid 36 through 61 removed outlier: 3.738A pdb=" N ILEC2 40 " --> pdb=" O PROC2 36 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALC2 45 " --> pdb=" O VALC2 41 " (cutoff:3.500A) Processing helix chain 'C2' and resid 66 through 69 Processing helix chain 'C2' and resid 70 through 86 removed outlier: 3.705A pdb=" N ARGC2 86 " --> pdb=" O METC2 82 " (cutoff:3.500A) Processing helix chain 'C2' and resid 96 through 133 removed outlier: 3.794A pdb=" N ALAC2 102 " --> pdb=" O PROC2 98 " (cutoff:3.500A) Processing helix chain 'C2' and resid 135 through 137 No H-bonds generated for 'chain 'C2' and resid 135 through 137' Processing helix chain 'C2' and resid 138 through 143 Processing helix chain 'C2' and resid 189 through 204 removed outlier: 3.508A pdb=" N LYSC2 194 " --> pdb=" O PROC2 190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SERC2 204 " --> pdb=" O GLYC2 200 " (cutoff:3.500A) Processing helix chain 'C2' and resid 216 through 218 No H-bonds generated for 'chain 'C2' and resid 216 through 218' Processing helix chain 'C2' and resid 226 through 245 Processing helix chain 'C2' and resid 258 through 272 removed outlier: 4.309A pdb=" N ASPC2 263 " --> pdb=" O ASPC2 260 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRPC2 264 " --> pdb=" O GLNC2 261 " (cutoff:3.500A) Proline residue: C2 269 - end of helix Processing helix chain 'C2' and resid 289 through 297 removed outlier: 3.540A pdb=" N GLUC2 296 " --> pdb=" O GLUC2 292 " (cutoff:3.500A) Processing helix chain 'C2' and resid 297 through 302 Processing helix chain 'C2' and resid 312 through 317 removed outlier: 3.631A pdb=" N ALAC2 316 " --> pdb=" O SERC2 313 " (cutoff:3.500A) Processing helix chain 'C2' and resid 331 through 333 No H-bonds generated for 'chain 'C2' and resid 331 through 333' Processing helix chain 'C2' and resid 334 through 340 Processing helix chain 'C2' and resid 354 through 359 Processing helix chain 'C2' and resid 360 through 362 No H-bonds generated for 'chain 'C2' and resid 360 through 362' Processing helix chain 'C2' and resid 400 through 413 removed outlier: 3.546A pdb=" N GLNC2 413 " --> pdb=" O GLNC2 409 " (cutoff:3.500A) Processing helix chain 'C3' and resid 36 through 60 removed outlier: 4.024A pdb=" N ILEC3 40 " --> pdb=" O PROC3 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VALC3 57 " --> pdb=" O METC3 53 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHEC3 58 " --> pdb=" O VALC3 54 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SERC3 60 " --> pdb=" O METC3 56 " (cutoff:3.500A) Processing helix chain 'C3' and resid 70 through 88 removed outlier: 3.882A pdb=" N VALC3 78 " --> pdb=" O LEUC3 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLYC3 79 " --> pdb=" O PHEC3 75 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILEC3 80 " --> pdb=" O METC3 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N METC3 81 " --> pdb=" O METC3 77 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARGC3 86 " --> pdb=" O METC3 82 " (cutoff:3.500A) Processing helix chain 'C3' and resid 96 through 133 removed outlier: 3.579A pdb=" N PHEC3 132 " --> pdb=" O ASNC3 128 " (cutoff:3.500A) Processing helix chain 'C3' and resid 135 through 145 removed outlier: 4.330A pdb=" N ALAC3 140 " --> pdb=" O ASNC3 137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALAC3 141 " --> pdb=" O THRC3 138 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLYC3 144 " --> pdb=" O ALAC3 141 " (cutoff:3.500A) Processing helix chain 'C3' and resid 189 through 203 Processing helix chain 'C3' and resid 216 through 218 No H-bonds generated for 'chain 'C3' and resid 216 through 218' Processing helix chain 'C3' and resid 226 through 245 Processing helix chain 'C3' and resid 258 through 272 removed outlier: 4.038A pdb=" N ASPC3 263 " --> pdb=" O ASPC3 260 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TRPC3 264 " --> pdb=" O GLNC3 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRPC3 267 " --> pdb=" O TRPC3 264 " (cutoff:3.500A) Proline residue: C3 269 - end of helix Processing helix chain 'C3' and resid 289 through 297 Processing helix chain 'C3' and resid 297 through 302 Processing helix chain 'C3' and resid 312 through 317 removed outlier: 3.568A pdb=" N ALAC3 316 " --> pdb=" O SERC3 313 " (cutoff:3.500A) Processing helix chain 'C3' and resid 331 through 333 No H-bonds generated for 'chain 'C3' and resid 331 through 333' Processing helix chain 'C3' and resid 334 through 340 removed outlier: 3.571A pdb=" N ALAC3 340 " --> pdb=" O TYRC3 336 " (cutoff:3.500A) Processing helix chain 'C3' and resid 354 through 359 Processing helix chain 'C3' and resid 360 through 362 No H-bonds generated for 'chain 'C3' and resid 360 through 362' Processing helix chain 'C3' and resid 400 through 413 removed outlier: 3.884A pdb=" N GLNC3 413 " --> pdb=" O GLNC3 409 " (cutoff:3.500A) Processing helix chain 'C4' and resid 36 through 60 removed outlier: 5.081A pdb=" N VALC4 42 " --> pdb=" O TRPC4 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALC4 45 " --> pdb=" O VALC4 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLYC4 52 " --> pdb=" O GLYC4 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N METC4 53 " --> pdb=" O LEUC4 49 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VALC4 54 " --> pdb=" O LEUC4 50 " (cutoff:3.500A) Processing helix chain 'C4' and resid 66 through 69 removed outlier: 3.893A pdb=" N GLYC4 69 " --> pdb=" O GLYC4 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C4' and resid 66 through 69' Processing helix chain 'C4' and resid 70 through 84 Processing helix chain 'C4' and resid 96 through 133 removed outlier: 4.026A pdb=" N ALAC4 102 " --> pdb=" O PROC4 98 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N METC4 113 " --> pdb=" O LEUC4 109 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEUC4 114 " --> pdb=" O METC4 110 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALAC4 127 " --> pdb=" O ASPC4 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASNC4 128 " --> pdb=" O SERC4 124 " (cutoff:3.500A) Processing helix chain 'C4' and resid 135 through 137 No H-bonds generated for 'chain 'C4' and resid 135 through 137' Processing helix chain 'C4' and resid 138 through 143 removed outlier: 3.546A pdb=" N ALAC4 142 " --> pdb=" O THRC4 138 " (cutoff:3.500A) Processing helix chain 'C4' and resid 184 through 188 Processing helix chain 'C4' and resid 189 through 203 removed outlier: 3.583A pdb=" N LYSC4 194 " --> pdb=" O PROC4 190 " (cutoff:3.500A) Processing helix chain 'C4' and resid 226 through 245 Processing helix chain 'C4' and resid 262 through 272 Proline residue: C4 269 - end of helix Processing helix chain 'C4' and resid 289 through 297 Processing helix chain 'C4' and resid 297 through 302 Processing helix chain 'C4' and resid 311 through 317 Processing helix chain 'C4' and resid 331 through 333 No H-bonds generated for 'chain 'C4' and resid 331 through 333' Processing helix chain 'C4' and resid 334 through 340 removed outlier: 3.524A pdb=" N ALAC4 340 " --> pdb=" O TYRC4 336 " (cutoff:3.500A) Processing helix chain 'C4' and resid 354 through 359 Processing helix chain 'C4' and resid 360 through 362 No H-bonds generated for 'chain 'C4' and resid 360 through 362' Processing helix chain 'C4' and resid 400 through 413 removed outlier: 3.811A pdb=" N GLNC4 413 " --> pdb=" O GLNC4 409 " (cutoff:3.500A) Processing helix chain 'C5' and resid 36 through 60 removed outlier: 4.265A pdb=" N ILEC5 40 " --> pdb=" O PROC5 36 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VALC5 45 " --> pdb=" O VALC5 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEUC5 50 " --> pdb=" O VALC5 46 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLYC5 51 " --> pdb=" O VALC5 47 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLYC5 52 " --> pdb=" O GLYC5 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VALC5 57 " --> pdb=" O METC5 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHEC5 58 " --> pdb=" O VALC5 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SERC5 60 " --> pdb=" O METC5 56 " (cutoff:3.500A) Processing helix chain 'C5' and resid 70 through 89 removed outlier: 3.851A pdb=" N VALC5 78 " --> pdb=" O LEUC5 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLYC5 79 " --> pdb=" O PHEC5 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEC5 80 " --> pdb=" O METC5 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N METC5 81 " --> pdb=" O METC5 77 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLYC5 87 " --> pdb=" O METC5 83 " (cutoff:3.500A) Processing helix chain 'C5' and resid 96 through 133 removed outlier: 3.664A pdb=" N ALAC5 102 " --> pdb=" O PROC5 98 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEUC5 114 " --> pdb=" O METC5 110 " (cutoff:3.500A) Processing helix chain 'C5' and resid 135 through 137 No H-bonds generated for 'chain 'C5' and resid 135 through 137' Processing helix chain 'C5' and resid 138 through 143 removed outlier: 3.753A pdb=" N ALAC5 142 " --> pdb=" O THRC5 138 " (cutoff:3.500A) Processing helix chain 'C5' and resid 184 through 188 Processing helix chain 'C5' and resid 189 through 203 Processing helix chain 'C5' and resid 216 through 218 No H-bonds generated for 'chain 'C5' and resid 216 through 218' Processing helix chain 'C5' and resid 226 through 245 Processing helix chain 'C5' and resid 258 through 272 removed outlier: 3.999A pdb=" N ASPC5 263 " --> pdb=" O ASPC5 260 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRPC5 264 " --> pdb=" O GLNC5 261 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRPC5 267 " --> pdb=" O TRPC5 264 " (cutoff:3.500A) Proline residue: C5 269 - end of helix Processing helix chain 'C5' and resid 289 through 297 Processing helix chain 'C5' and resid 297 through 302 Processing helix chain 'C5' and resid 312 through 317 removed outlier: 3.677A pdb=" N ALAC5 316 " --> pdb=" O SERC5 313 " (cutoff:3.500A) Processing helix chain 'C5' and resid 331 through 333 No H-bonds generated for 'chain 'C5' and resid 331 through 333' Processing helix chain 'C5' and resid 334 through 340 removed outlier: 3.541A pdb=" N ALAC5 340 " --> pdb=" O TYRC5 336 " (cutoff:3.500A) Processing helix chain 'C5' and resid 354 through 359 removed outlier: 3.529A pdb=" N ASPC5 359 " --> pdb=" O SERC5 355 " (cutoff:3.500A) Processing helix chain 'C5' and resid 360 through 362 No H-bonds generated for 'chain 'C5' and resid 360 through 362' Processing helix chain 'C5' and resid 400 through 413 removed outlier: 3.736A pdb=" N GLNC5 413 " --> pdb=" O GLNC5 409 " (cutoff:3.500A) Processing helix chain 'C6' and resid 36 through 61 removed outlier: 3.586A pdb=" N ILEC6 40 " --> pdb=" O PROC6 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALC6 45 " --> pdb=" O VALC6 41 " (cutoff:3.500A) Processing helix chain 'C6' and resid 66 through 69 Processing helix chain 'C6' and resid 70 through 86 removed outlier: 3.749A pdb=" N METC6 83 " --> pdb=" O GLYC6 79 " (cutoff:3.500A) Processing helix chain 'C6' and resid 96 through 133 removed outlier: 3.740A pdb=" N ALAC6 102 " --> pdb=" O PROC6 98 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEUC6 114 " --> pdb=" O METC6 110 " (cutoff:3.500A) Processing helix chain 'C6' and resid 135 through 143 removed outlier: 3.784A pdb=" N LEUC6 139 " --> pdb=" O ALAC6 135 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALAC6 140 " --> pdb=" O PROC6 136 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALAC6 141 " --> pdb=" O ASNC6 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALAC6 142 " --> pdb=" O THRC6 138 " (cutoff:3.500A) Processing helix chain 'C6' and resid 189 through 203 removed outlier: 3.579A pdb=" N LYSC6 194 " --> pdb=" O PROC6 190 " (cutoff:3.500A) Processing helix chain 'C6' and resid 226 through 245 Processing helix chain 'C6' and resid 262 through 272 removed outlier: 3.529A pdb=" N TRPC6 267 " --> pdb=" O TRPC6 264 " (cutoff:3.500A) Proline residue: C6 269 - end of helix Processing helix chain 'C6' and resid 289 through 297 Processing helix chain 'C6' and resid 297 through 302 Processing helix chain 'C6' and resid 311 through 317 removed outlier: 3.685A pdb=" N ALAC6 316 " --> pdb=" O SERC6 313 " (cutoff:3.500A) Processing helix chain 'C6' and resid 331 through 333 No H-bonds generated for 'chain 'C6' and resid 331 through 333' Processing helix chain 'C6' and resid 334 through 340 removed outlier: 3.594A pdb=" N ALAC6 340 " --> pdb=" O TYRC6 336 " (cutoff:3.500A) Processing helix chain 'C6' and resid 360 through 362 No H-bonds generated for 'chain 'C6' and resid 360 through 362' Processing helix chain 'C6' and resid 400 through 413 removed outlier: 3.669A pdb=" N GLNC6 413 " --> pdb=" O GLNC6 409 " (cutoff:3.500A) Processing helix chain 'D1' and resid 28 through 30 No H-bonds generated for 'chain 'D1' and resid 28 through 30' Processing helix chain 'D1' and resid 42 through 62 removed outlier: 3.679A pdb=" N METD1 46 " --> pdb=" O PROD1 42 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASPD1 48 " --> pdb=" O SERD1 44 " (cutoff:3.500A) Proline residue: D1 49 - end of helix Processing helix chain 'D1' and resid 120 through 131 removed outlier: 4.019A pdb=" N LYSD1 129 " --> pdb=" O SERD1 125 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHED1 131 " --> pdb=" O LEUD1 127 " (cutoff:3.500A) Processing helix chain 'D1' and resid 135 through 165 removed outlier: 3.892A pdb=" N GLND1 141 " --> pdb=" O ILED1 137 " (cutoff:3.500A) Processing helix chain 'D1' and resid 168 through 192 removed outlier: 3.968A pdb=" N VALD1 176 " --> pdb=" O ILED1 172 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILED1 177 " --> pdb=" O TYRD1 173 " (cutoff:3.500A) Processing helix chain 'D1' and resid 194 through 218 removed outlier: 3.653A pdb=" N ILED1 209 " --> pdb=" O LEUD1 205 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N METD1 210 " --> pdb=" O METD1 206 " (cutoff:3.500A) Proline residue: D1 211 - end of helix removed outlier: 3.508A pdb=" N ALAD1 216 " --> pdb=" O VALD1 212 " (cutoff:3.500A) Processing helix chain 'D1' and resid 225 through 248 Processing helix chain 'D1' and resid 250 through 274 removed outlier: 3.514A pdb=" N TYRD1 254 " --> pdb=" O ARGD1 250 " (cutoff:3.500A) Processing helix chain 'D1' and resid 277 through 304 removed outlier: 3.622A pdb=" N LEUD1 285 " --> pdb=" O LEUD1 281 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HISD1 294 " --> pdb=" O VALD1 290 " (cutoff:3.500A) Proline residue: D1 297 - end of helix removed outlier: 3.805A pdb=" N ARGD1 301 " --> pdb=" O PROD1 297 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARGD1 302 " --> pdb=" O ALAD1 298 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEUD1 303 " --> pdb=" O LEUD1 299 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALAD1 304 " --> pdb=" O SERD1 300 " (cutoff:3.500A) Processing helix chain 'D1' and resid 312 through 316 Processing helix chain 'D1' and resid 343 through 379 removed outlier: 3.601A pdb=" N ASPD1 348 " --> pdb=" O SERD1 344 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VALD1 349 " --> pdb=" O SERD1 345 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEUD1 350 " --> pdb=" O VALD1 346 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLUD1 354 " --> pdb=" O LEUD1 350 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SERD1 358 " --> pdb=" O GLUD1 354 " (cutoff:3.500A) Processing helix chain 'D1' and resid 386 through 404 removed outlier: 4.001A pdb=" N LEUD1 390 " --> pdb=" O ARGD1 386 " (cutoff:3.500A) Processing helix chain 'D1' and resid 405 through 407 No H-bonds generated for 'chain 'D1' and resid 405 through 407' Processing helix chain 'D1' and resid 409 through 434 removed outlier: 3.576A pdb=" N ILED1 423 " --> pdb=" O THRD1 419 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALAD1 424 " --> pdb=" O ALAD1 420 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLUD1 434 " --> pdb=" O ARGD1 430 " (cutoff:3.500A) Processing helix chain 'D1' and resid 437 through 462 removed outlier: 3.562A pdb=" N VALD1 449 " --> pdb=" O ALAD1 445 " (cutoff:3.500A) Proline residue: D1 452 - end of helix Processing helix chain 'D1' and resid 463 through 465 No H-bonds generated for 'chain 'D1' and resid 463 through 465' Processing helix chain 'D1' and resid 468 through 484 removed outlier: 3.566A pdb=" N GLUD1 476 " --> pdb=" O ARGD1 472 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRPD1 477 " --> pdb=" O LYSD1 473 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILED1 478 " --> pdb=" O PHED1 474 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLUD1 479 " --> pdb=" O VALD1 475 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYRD1 480 " --> pdb=" O GLUD1 476 " (cutoff:3.500A) Processing helix chain 'D1' and resid 485 through 494 removed outlier: 3.642A pdb=" N TRPD1 492 " --> pdb=" O PROD1 488 " (cutoff:3.500A) Processing helix chain 'D1' and resid 495 through 502 Processing helix chain 'D2' and resid 42 through 62 removed outlier: 4.039A pdb=" N METD2 46 " --> pdb=" O PROD2 42 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASPD2 48 " --> pdb=" O SERD2 44 " (cutoff:3.500A) Proline residue: D2 49 - end of helix Processing helix chain 'D2' and resid 118 through 130 removed outlier: 3.761A pdb=" N LYSD2 129 " --> pdb=" O SERD2 125 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARGD2 130 " --> pdb=" O ASPD2 126 " (cutoff:3.500A) Processing helix chain 'D2' and resid 135 through 163 removed outlier: 3.714A pdb=" N GLND2 141 " --> pdb=" O ILED2 137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEUD2 153 " --> pdb=" O THRD2 149 " (cutoff:3.500A) Processing helix chain 'D2' and resid 168 through 192 removed outlier: 3.551A pdb=" N VALD2 176 " --> pdb=" O ILED2 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGD2 191 " --> pdb=" O LEUD2 187 " (cutoff:3.500A) Processing helix chain 'D2' and resid 194 through 218 removed outlier: 3.552A pdb=" N ALAD2 208 " --> pdb=" O METD2 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILED2 209 " --> pdb=" O LEUD2 205 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N METD2 210 " --> pdb=" O METD2 206 " (cutoff:3.500A) Proline residue: D2 211 - end of helix Processing helix chain 'D2' and resid 225 through 248 removed outlier: 4.036A pdb=" N LEUD2 231 " --> pdb=" O PROD2 227 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLYD2 232 " --> pdb=" O GLND2 228 " (cutoff:3.500A) Processing helix chain 'D2' and resid 250 through 274 removed outlier: 3.589A pdb=" N TYRD2 254 " --> pdb=" O ARGD2 250 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 304 removed outlier: 3.583A pdb=" N LEUD2 281 " --> pdb=" O SERD2 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HISD2 294 " --> pdb=" O VALD2 290 " (cutoff:3.500A) Proline residue: D2 297 - end of helix Processing helix chain 'D2' and resid 346 through 379 removed outlier: 3.596A pdb=" N GLND2 352 " --> pdb=" O ASPD2 348 " (cutoff:3.500A) Processing helix chain 'D2' and resid 386 through 405 removed outlier: 3.942A pdb=" N LEUD2 390 " --> pdb=" O ARGD2 386 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARGD2 405 " --> pdb=" O LEUD2 401 " (cutoff:3.500A) Processing helix chain 'D2' and resid 409 through 434 removed outlier: 3.590A pdb=" N ALAD2 420 " --> pdb=" O LEUD2 416 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALD2 421 " --> pdb=" O ALAD2 417 " (cutoff:3.500A) Processing helix chain 'D2' and resid 437 through 461 Proline residue: D2 452 - end of helix removed outlier: 3.793A pdb=" N ALAD2 459 " --> pdb=" O GLYD2 455 " (cutoff:3.500A) Processing helix chain 'D3' and resid 28 through 30 No H-bonds generated for 'chain 'D3' and resid 28 through 30' Processing helix chain 'D3' and resid 42 through 62 removed outlier: 3.640A pdb=" N METD3 46 " --> pdb=" O PROD3 42 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASPD3 48 " --> pdb=" O SERD3 44 " (cutoff:3.500A) Proline residue: D3 49 - end of helix Processing helix chain 'D3' and resid 120 through 131 removed outlier: 3.661A pdb=" N ASPD3 126 " --> pdb=" O ALAD3 122 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYSD3 129 " --> pdb=" O SERD3 125 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHED3 131 " --> pdb=" O LEUD3 127 " (cutoff:3.500A) Processing helix chain 'D3' and resid 135 through 163 Processing helix chain 'D3' and resid 168 through 192 removed outlier: 3.901A pdb=" N VALD3 176 " --> pdb=" O ILED3 172 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILED3 177 " --> pdb=" O TYRD3 173 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N METD3 190 " --> pdb=" O METD3 186 " (cutoff:3.500A) Processing helix chain 'D3' and resid 194 through 219 removed outlier: 3.855A pdb=" N VALD3 200 " --> pdb=" O ALAD3 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILED3 209 " --> pdb=" O LEUD3 205 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N METD3 210 " --> pdb=" O METD3 206 " (cutoff:3.500A) Proline residue: D3 211 - end of helix Processing helix chain 'D3' and resid 225 through 248 removed outlier: 3.651A pdb=" N ALAD3 229 " --> pdb=" O GLYD3 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VALD3 230 " --> pdb=" O SERD3 226 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEUD3 231 " --> pdb=" O PROD3 227 " (cutoff:3.500A) Processing helix chain 'D3' and resid 250 through 275 removed outlier: 3.599A pdb=" N TYRD3 254 " --> pdb=" O ARGD3 250 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILED3 257 " --> pdb=" O ILED3 253 " (cutoff:3.500A) Processing helix chain 'D3' and resid 277 through 304 removed outlier: 3.882A pdb=" N HISD3 294 " --> pdb=" O VALD3 290 " (cutoff:3.500A) Proline residue: D3 297 - end of helix Processing helix chain 'D3' and resid 343 through 348 Processing helix chain 'D3' and resid 348 through 379 removed outlier: 4.270A pdb=" N GLUD3 354 " --> pdb=" O LEUD3 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEUD3 367 " --> pdb=" O LEUD3 363 " (cutoff:3.500A) Processing helix chain 'D3' and resid 386 through 404 removed outlier: 3.963A pdb=" N LEUD3 390 " --> pdb=" O ARGD3 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLYD3 404 " --> pdb=" O LEUD3 400 " (cutoff:3.500A) Processing helix chain 'D3' and resid 411 through 434 removed outlier: 3.654A pdb=" N ALAD3 424 " --> pdb=" O ALAD3 420 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYRD3 431 " --> pdb=" O VALD3 427 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALAD3 432 " --> pdb=" O CYSD3 428 " (cutoff:3.500A) Processing helix chain 'D3' and resid 437 through 462 removed outlier: 3.572A pdb=" N VALD3 449 " --> pdb=" O ALAD3 445 " (cutoff:3.500A) Proline residue: D3 452 - end of helix Processing helix chain 'D3' and resid 463 through 465 No H-bonds generated for 'chain 'D3' and resid 463 through 465' Processing helix chain 'D3' and resid 468 through 484 removed outlier: 3.540A pdb=" N PHED3 474 " --> pdb=" O LEUD3 470 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLUD3 476 " --> pdb=" O ARGD3 472 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRPD3 477 " --> pdb=" O LYSD3 473 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLUD3 479 " --> pdb=" O VALD3 475 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYRD3 480 " --> pdb=" O GLUD3 476 " (cutoff:3.500A) Processing helix chain 'D3' and resid 485 through 494 removed outlier: 3.666A pdb=" N TRPD3 492 " --> pdb=" O PROD3 488 " (cutoff:3.500A) Processing helix chain 'D3' and resid 495 through 502 removed outlier: 3.577A pdb=" N ALAD3 499 " --> pdb=" O ASND3 495 " (cutoff:3.500A) Processing helix chain 'D4' and resid 42 through 45 Processing helix chain 'D4' and resid 46 through 62 Processing helix chain 'D4' and resid 118 through 131 removed outlier: 3.703A pdb=" N LYSD4 129 " --> pdb=" O SERD4 125 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARGD4 130 " --> pdb=" O ASPD4 126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHED4 131 " --> pdb=" O LEUD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 135 through 163 removed outlier: 3.550A pdb=" N VALD4 140 " --> pdb=" O PROD4 136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLND4 141 " --> pdb=" O ILED4 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRPD4 163 " --> pdb=" O GLYD4 159 " (cutoff:3.500A) Processing helix chain 'D4' and resid 168 through 192 removed outlier: 3.702A pdb=" N VALD4 176 " --> pdb=" O ILED4 172 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILED4 177 " --> pdb=" O TYRD4 173 " (cutoff:3.500A) Processing helix chain 'D4' and resid 194 through 207 Processing helix chain 'D4' and resid 208 through 218 Processing helix chain 'D4' and resid 225 through 248 removed outlier: 3.507A pdb=" N VALD4 230 " --> pdb=" O SERD4 226 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEUD4 231 " --> pdb=" O PROD4 227 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLYD4 234 " --> pdb=" O VALD4 230 " (cutoff:3.500A) Processing helix chain 'D4' and resid 250 through 274 Processing helix chain 'D4' and resid 277 through 304 removed outlier: 4.496A pdb=" N HISD4 294 " --> pdb=" O VALD4 290 " (cutoff:3.500A) Proline residue: D4 297 - end of helix Processing helix chain 'D4' and resid 345 through 379 removed outlier: 3.786A pdb=" N VALD4 349 " --> pdb=" O SERD4 345 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VALD4 372 " --> pdb=" O GLYD4 368 " (cutoff:3.500A) Processing helix chain 'D4' and resid 386 through 404 removed outlier: 4.089A pdb=" N LEUD4 390 " --> pdb=" O ARGD4 386 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEUD4 400 " --> pdb=" O THRD4 396 " (cutoff:3.500A) Processing helix chain 'D4' and resid 405 through 407 No H-bonds generated for 'chain 'D4' and resid 405 through 407' Processing helix chain 'D4' and resid 409 through 434 removed outlier: 3.600A pdb=" N ILED4 423 " --> pdb=" O THRD4 419 " (cutoff:3.500A) Processing helix chain 'D4' and resid 437 through 461 Proline residue: D4 452 - end of helix removed outlier: 3.924A pdb=" N GLYD4 455 " --> pdb=" O LEUD4 451 " (cutoff:3.500A) Processing helix chain 'D5' and resid 28 through 30 No H-bonds generated for 'chain 'D5' and resid 28 through 30' Processing helix chain 'D5' and resid 42 through 62 removed outlier: 3.735A pdb=" N METD5 46 " --> pdb=" O PROD5 42 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASPD5 48 " --> pdb=" O SERD5 44 " (cutoff:3.500A) Proline residue: D5 49 - end of helix Processing helix chain 'D5' and resid 120 through 131 Processing helix chain 'D5' and resid 135 through 163 removed outlier: 3.871A pdb=" N GLND5 141 " --> pdb=" O ILED5 137 " (cutoff:3.500A) Processing helix chain 'D5' and resid 168 through 192 removed outlier: 4.231A pdb=" N VALD5 176 " --> pdb=" O ILED5 172 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILED5 177 " --> pdb=" O TYRD5 173 " (cutoff:3.500A) Processing helix chain 'D5' and resid 194 through 218 removed outlier: 3.568A pdb=" N ILED5 209 " --> pdb=" O LEUD5 205 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N METD5 210 " --> pdb=" O METD5 206 " (cutoff:3.500A) Proline residue: D5 211 - end of helix Processing helix chain 'D5' and resid 225 through 248 Processing helix chain 'D5' and resid 250 through 274 removed outlier: 3.584A pdb=" N TYRD5 254 " --> pdb=" O ARGD5 250 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILED5 257 " --> pdb=" O ILED5 253 " (cutoff:3.500A) Processing helix chain 'D5' and resid 277 through 304 removed outlier: 3.613A pdb=" N HISD5 294 " --> pdb=" O VALD5 290 " (cutoff:3.500A) Proline residue: D5 297 - end of helix removed outlier: 3.740A pdb=" N ARGD5 301 " --> pdb=" O PROD5 297 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARGD5 302 " --> pdb=" O ALAD5 298 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALAD5 304 " --> pdb=" O SERD5 300 " (cutoff:3.500A) Processing helix chain 'D5' and resid 312 through 316 Processing helix chain 'D5' and resid 344 through 379 removed outlier: 3.995A pdb=" N ASPD5 348 " --> pdb=" O SERD5 344 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VALD5 349 " --> pdb=" O SERD5 345 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEUD5 350 " --> pdb=" O VALD5 346 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEUD5 351 " --> pdb=" O ARGD5 347 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLUD5 354 " --> pdb=" O LEUD5 350 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYSD5 379 " --> pdb=" O METD5 375 " (cutoff:3.500A) Processing helix chain 'D5' and resid 386 through 404 removed outlier: 3.866A pdb=" N LEUD5 390 " --> pdb=" O ARGD5 386 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUD5 392 " --> pdb=" O LEUD5 388 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALAD5 393 " --> pdb=" O PROD5 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYD5 394 " --> pdb=" O LEUD5 390 " (cutoff:3.500A) Processing helix chain 'D5' and resid 405 through 407 No H-bonds generated for 'chain 'D5' and resid 405 through 407' Processing helix chain 'D5' and resid 409 through 434 removed outlier: 3.584A pdb=" N ILED5 423 " --> pdb=" O THRD5 419 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALAD5 424 " --> pdb=" O ALAD5 420 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLUD5 434 " --> pdb=" O ARGD5 430 " (cutoff:3.500A) Processing helix chain 'D5' and resid 437 through 462 removed outlier: 3.573A pdb=" N ALAD5 446 " --> pdb=" O SERD5 442 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VALD5 449 " --> pdb=" O ALAD5 445 " (cutoff:3.500A) Proline residue: D5 452 - end of helix removed outlier: 3.622A pdb=" N GLYD5 455 " --> pdb=" O LEUD5 451 " (cutoff:3.500A) Processing helix chain 'D5' and resid 463 through 465 No H-bonds generated for 'chain 'D5' and resid 463 through 465' Processing helix chain 'D5' and resid 468 through 484 removed outlier: 3.500A pdb=" N GLUD5 476 " --> pdb=" O ARGD5 472 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRPD5 477 " --> pdb=" O LYSD5 473 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILED5 478 " --> pdb=" O PHED5 474 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLUD5 479 " --> pdb=" O VALD5 475 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYRD5 480 " --> pdb=" O GLUD5 476 " (cutoff:3.500A) Processing helix chain 'D5' and resid 485 through 494 Processing helix chain 'D5' and resid 495 through 502 Processing helix chain 'D6' and resid 42 through 45 Processing helix chain 'D6' and resid 46 through 62 Processing helix chain 'D6' and resid 118 through 130 removed outlier: 3.677A pdb=" N LYSD6 129 " --> pdb=" O SERD6 125 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARGD6 130 " --> pdb=" O ASPD6 126 " (cutoff:3.500A) Processing helix chain 'D6' and resid 135 through 162 removed outlier: 3.548A pdb=" N VALD6 140 " --> pdb=" O PROD6 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLND6 141 " --> pdb=" O ILED6 137 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARGD6 162 " --> pdb=" O LEUD6 158 " (cutoff:3.500A) Processing helix chain 'D6' and resid 168 through 192 removed outlier: 3.539A pdb=" N ILED6 177 " --> pdb=" O TYRD6 173 " (cutoff:3.500A) Processing helix chain 'D6' and resid 194 through 218 removed outlier: 3.715A pdb=" N ILED6 209 " --> pdb=" O LEUD6 205 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N METD6 210 " --> pdb=" O METD6 206 " (cutoff:3.500A) Proline residue: D6 211 - end of helix Processing helix chain 'D6' and resid 225 through 248 removed outlier: 4.248A pdb=" N LEUD6 231 " --> pdb=" O PROD6 227 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYD6 232 " --> pdb=" O GLND6 228 " (cutoff:3.500A) Processing helix chain 'D6' and resid 250 through 274 Processing helix chain 'D6' and resid 277 through 304 removed outlier: 3.514A pdb=" N HISD6 294 " --> pdb=" O VALD6 290 " (cutoff:3.500A) Proline residue: D6 297 - end of helix Processing helix chain 'D6' and resid 346 through 379 removed outlier: 3.678A pdb=" N LEUD6 350 " --> pdb=" O VALD6 346 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLND6 352 " --> pdb=" O ASPD6 348 " (cutoff:3.500A) Processing helix chain 'D6' and resid 387 through 404 Processing helix chain 'D6' and resid 405 through 407 No H-bonds generated for 'chain 'D6' and resid 405 through 407' Processing helix chain 'D6' and resid 409 through 434 removed outlier: 3.508A pdb=" N VALD6 421 " --> pdb=" O ALAD6 417 " (cutoff:3.500A) Processing helix chain 'D6' and resid 437 through 461 Proline residue: D6 452 - end of helix removed outlier: 3.569A pdb=" N GLYD6 455 " --> pdb=" O LEUD6 451 " (cutoff:3.500A) Processing helix chain 'D7' and resid 28 through 30 No H-bonds generated for 'chain 'D7' and resid 28 through 30' Processing helix chain 'D7' and resid 42 through 62 removed outlier: 3.721A pdb=" N METD7 46 " --> pdb=" O PROD7 42 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASPD7 48 " --> pdb=" O SERD7 44 " (cutoff:3.500A) Proline residue: D7 49 - end of helix Processing helix chain 'D7' and resid 120 through 131 removed outlier: 3.603A pdb=" N ASPD7 126 " --> pdb=" O ALAD7 122 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYSD7 129 " --> pdb=" O SERD7 125 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHED7 131 " --> pdb=" O LEUD7 127 " (cutoff:3.500A) Processing helix chain 'D7' and resid 135 through 165 Processing helix chain 'D7' and resid 168 through 192 removed outlier: 3.844A pdb=" N VALD7 176 " --> pdb=" O ILED7 172 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILED7 177 " --> pdb=" O TYRD7 173 " (cutoff:3.500A) Processing helix chain 'D7' and resid 194 through 219 removed outlier: 4.181A pdb=" N VALD7 200 " --> pdb=" O ALAD7 196 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALAD7 201 " --> pdb=" O ASPD7 197 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N METD7 210 " --> pdb=" O METD7 206 " (cutoff:3.500A) Proline residue: D7 211 - end of helix Processing helix chain 'D7' and resid 225 through 248 removed outlier: 3.772A pdb=" N ALAD7 229 " --> pdb=" O GLYD7 225 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VALD7 230 " --> pdb=" O SERD7 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEUD7 231 " --> pdb=" O PROD7 227 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHED7 246 " --> pdb=" O LEUD7 242 " (cutoff:3.500A) Processing helix chain 'D7' and resid 250 through 275 Processing helix chain 'D7' and resid 277 through 304 removed outlier: 3.776A pdb=" N HISD7 294 " --> pdb=" O VALD7 290 " (cutoff:3.500A) Proline residue: D7 297 - end of helix removed outlier: 3.619A pdb=" N ARGD7 302 " --> pdb=" O ALAD7 298 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUD7 303 " --> pdb=" O LEUD7 299 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALAD7 304 " --> pdb=" O SERD7 300 " (cutoff:3.500A) Processing helix chain 'D7' and resid 343 through 348 Processing helix chain 'D7' and resid 348 through 379 removed outlier: 4.154A pdb=" N GLUD7 354 " --> pdb=" O LEUD7 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VALD7 372 " --> pdb=" O GLYD7 368 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SERD7 377 " --> pdb=" O VALD7 373 " (cutoff:3.500A) Processing helix chain 'D7' and resid 386 through 404 removed outlier: 4.217A pdb=" N LEUD7 390 " --> pdb=" O ARGD7 386 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUD7 392 " --> pdb=" O LEUD7 388 " (cutoff:3.500A) Processing helix chain 'D7' and resid 405 through 407 No H-bonds generated for 'chain 'D7' and resid 405 through 407' Processing helix chain 'D7' and resid 409 through 434 removed outlier: 3.690A pdb=" N ILED7 423 " --> pdb=" O THRD7 419 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALAD7 424 " --> pdb=" O ALAD7 420 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLUD7 434 " --> pdb=" O ARGD7 430 " (cutoff:3.500A) Processing helix chain 'D7' and resid 437 through 462 Proline residue: D7 452 - end of helix Processing helix chain 'D7' and resid 463 through 465 No H-bonds generated for 'chain 'D7' and resid 463 through 465' Processing helix chain 'D7' and resid 468 through 484 removed outlier: 3.635A pdb=" N GLUD7 476 " --> pdb=" O ARGD7 472 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRPD7 477 " --> pdb=" O LYSD7 473 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLUD7 479 " --> pdb=" O VALD7 475 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYRD7 480 " --> pdb=" O GLUD7 476 " (cutoff:3.500A) Processing helix chain 'D7' and resid 485 through 494 Processing helix chain 'D7' and resid 495 through 502 removed outlier: 3.538A pdb=" N ALAD7 499 " --> pdb=" O ASND7 495 " (cutoff:3.500A) Processing helix chain 'D8' and resid 42 through 62 removed outlier: 3.992A pdb=" N METD8 46 " --> pdb=" O PROD8 42 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASPD8 48 " --> pdb=" O SERD8 44 " (cutoff:3.500A) Proline residue: D8 49 - end of helix Processing helix chain 'D8' and resid 118 through 131 removed outlier: 3.525A pdb=" N ALAD8 124 " --> pdb=" O SERD8 120 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYSD8 129 " --> pdb=" O SERD8 125 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARGD8 130 " --> pdb=" O ASPD8 126 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHED8 131 " --> pdb=" O LEUD8 127 " (cutoff:3.500A) Processing helix chain 'D8' and resid 135 through 163 removed outlier: 3.946A pdb=" N GLND8 141 " --> pdb=" O ILED8 137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLYD8 156 " --> pdb=" O VALD8 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARGD8 162 " --> pdb=" O LEUD8 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRPD8 163 " --> pdb=" O GLYD8 159 " (cutoff:3.500A) Processing helix chain 'D8' and resid 168 through 192 removed outlier: 3.895A pdb=" N VALD8 176 " --> pdb=" O ILED8 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILED8 177 " --> pdb=" O TYRD8 173 " (cutoff:3.500A) Processing helix chain 'D8' and resid 194 through 207 Processing helix chain 'D8' and resid 208 through 218 Processing helix chain 'D8' and resid 225 through 248 removed outlier: 3.819A pdb=" N LEUD8 231 " --> pdb=" O PROD8 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLYD8 234 " --> pdb=" O VALD8 230 " (cutoff:3.500A) Processing helix chain 'D8' and resid 250 through 274 Processing helix chain 'D8' and resid 277 through 304 removed outlier: 4.354A pdb=" N HISD8 294 " --> pdb=" O VALD8 290 " (cutoff:3.500A) Proline residue: D8 297 - end of helix Processing helix chain 'D8' and resid 345 through 379 removed outlier: 3.723A pdb=" N VALD8 349 " --> pdb=" O SERD8 345 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VALD8 373 " --> pdb=" O VALD8 369 " (cutoff:3.500A) Processing helix chain 'D8' and resid 386 through 404 removed outlier: 3.794A pdb=" N LEUD8 390 " --> pdb=" O ARGD8 386 " (cutoff:3.500A) Processing helix chain 'D8' and resid 405 through 407 No H-bonds generated for 'chain 'D8' and resid 405 through 407' Processing helix chain 'D8' and resid 409 through 434 removed outlier: 3.514A pdb=" N VALD8 421 " --> pdb=" O ALAD8 417 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYRD8 431 " --> pdb=" O VALD8 427 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALAD8 432 " --> pdb=" O CYSD8 428 " (cutoff:3.500A) Processing helix chain 'D8' and resid 437 through 461 Proline residue: D8 452 - end of helix removed outlier: 3.541A pdb=" N GLYD8 455 " --> pdb=" O LEUD8 451 " (cutoff:3.500A) Processing helix chain 'D9' and resid 28 through 30 No H-bonds generated for 'chain 'D9' and resid 28 through 30' Processing helix chain 'D9' and resid 42 through 62 removed outlier: 3.701A pdb=" N METD9 46 " --> pdb=" O PROD9 42 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASPD9 48 " --> pdb=" O SERD9 44 " (cutoff:3.500A) Proline residue: D9 49 - end of helix Processing helix chain 'D9' and resid 120 through 131 Processing helix chain 'D9' and resid 135 through 163 removed outlier: 3.883A pdb=" N GLND9 141 " --> pdb=" O ILED9 137 " (cutoff:3.500A) Processing helix chain 'D9' and resid 168 through 192 removed outlier: 4.051A pdb=" N VALD9 176 " --> pdb=" O ILED9 172 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILED9 177 " --> pdb=" O TYRD9 173 " (cutoff:3.500A) Processing helix chain 'D9' and resid 194 through 218 removed outlier: 3.595A pdb=" N ILED9 209 " --> pdb=" O LEUD9 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N METD9 210 " --> pdb=" O METD9 206 " (cutoff:3.500A) Proline residue: D9 211 - end of helix Processing helix chain 'D9' and resid 225 through 248 Processing helix chain 'D9' and resid 250 through 274 removed outlier: 3.523A pdb=" N TYRD9 254 " --> pdb=" O ARGD9 250 " (cutoff:3.500A) Processing helix chain 'D9' and resid 277 through 304 removed outlier: 4.001A pdb=" N HISD9 294 " --> pdb=" O VALD9 290 " (cutoff:3.500A) Proline residue: D9 297 - end of helix removed outlier: 3.789A pdb=" N ARGD9 301 " --> pdb=" O PROD9 297 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALAD9 304 " --> pdb=" O SERD9 300 " (cutoff:3.500A) Processing helix chain 'D9' and resid 312 through 316 Processing helix chain 'D9' and resid 343 through 379 removed outlier: 3.577A pdb=" N ASPD9 348 " --> pdb=" O SERD9 344 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VALD9 349 " --> pdb=" O SERD9 345 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEUD9 350 " --> pdb=" O VALD9 346 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEUD9 351 " --> pdb=" O ARGD9 347 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLUD9 354 " --> pdb=" O LEUD9 350 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERD9 377 " --> pdb=" O VALD9 373 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYSD9 379 " --> pdb=" O METD9 375 " (cutoff:3.500A) Processing helix chain 'D9' and resid 386 through 404 removed outlier: 3.862A pdb=" N LEUD9 390 " --> pdb=" O ARGD9 386 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALAD9 393 " --> pdb=" O PROD9 389 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLYD9 394 " --> pdb=" O LEUD9 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHED9 395 " --> pdb=" O ILED9 391 " (cutoff:3.500A) Processing helix chain 'D9' and resid 405 through 407 No H-bonds generated for 'chain 'D9' and resid 405 through 407' Processing helix chain 'D9' and resid 409 through 434 removed outlier: 3.720A pdb=" N ALAD9 424 " --> pdb=" O ALAD9 420 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLUD9 434 " --> pdb=" O ARGD9 430 " (cutoff:3.500A) Processing helix chain 'D9' and resid 437 through 462 removed outlier: 3.595A pdb=" N ALAD9 446 " --> pdb=" O SERD9 442 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VALD9 449 " --> pdb=" O ALAD9 445 " (cutoff:3.500A) Proline residue: D9 452 - end of helix Processing helix chain 'D9' and resid 463 through 465 No H-bonds generated for 'chain 'D9' and resid 463 through 465' Processing helix chain 'D9' and resid 468 through 484 removed outlier: 3.569A pdb=" N TRPD9 477 " --> pdb=" O LYSD9 473 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILED9 478 " --> pdb=" O PHED9 474 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLUD9 479 " --> pdb=" O VALD9 475 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYRD9 480 " --> pdb=" O GLUD9 476 " (cutoff:3.500A) Processing helix chain 'D9' and resid 485 through 494 Processing helix chain 'D9' and resid 495 through 502 Processing helix chain 'DA' and resid 42 through 45 Processing helix chain 'DA' and resid 46 through 62 Processing helix chain 'DA' and resid 118 through 131 removed outlier: 3.757A pdb=" N LYSDA 129 " --> pdb=" O SERDA 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARGDA 130 " --> pdb=" O ASPDA 126 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHEDA 131 " --> pdb=" O LEUDA 127 " (cutoff:3.500A) Processing helix chain 'DA' and resid 135 through 162 removed outlier: 3.958A pdb=" N GLNDA 141 " --> pdb=" O ILEDA 137 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARGDA 162 " --> pdb=" O LEUDA 158 " (cutoff:3.500A) Processing helix chain 'DA' and resid 168 through 192 removed outlier: 3.703A pdb=" N VALDA 176 " --> pdb=" O ILEDA 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILEDA 177 " --> pdb=" O TYRDA 173 " (cutoff:3.500A) Processing helix chain 'DA' and resid 194 through 218 removed outlier: 3.618A pdb=" N ILEDA 209 " --> pdb=" O LEUDA 205 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N METDA 210 " --> pdb=" O METDA 206 " (cutoff:3.500A) Proline residue: DA 211 - end of helix Processing helix chain 'DA' and resid 225 through 248 removed outlier: 3.535A pdb=" N ALADA 229 " --> pdb=" O GLYDA 225 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VALDA 230 " --> pdb=" O SERDA 226 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEUDA 231 " --> pdb=" O PRODA 227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLYDA 232 " --> pdb=" O GLNDA 228 " (cutoff:3.500A) Processing helix chain 'DA' and resid 250 through 274 Processing helix chain 'DA' and resid 277 through 304 removed outlier: 3.590A pdb=" N LEUDA 281 " --> pdb=" O SERDA 277 " (cutoff:3.500A) Proline residue: DA 297 - end of helix Processing helix chain 'DA' and resid 346 through 379 removed outlier: 3.556A pdb=" N LEUDA 350 " --> pdb=" O VALDA 346 " (cutoff:3.500A) Processing helix chain 'DA' and resid 386 through 404 removed outlier: 3.987A pdb=" N LEUDA 390 " --> pdb=" O ARGDA 386 " (cutoff:3.500A) Processing helix chain 'DA' and resid 405 through 407 No H-bonds generated for 'chain 'DA' and resid 405 through 407' Processing helix chain 'DA' and resid 409 through 434 Processing helix chain 'DA' and resid 437 through 461 Proline residue: DA 452 - end of helix Processing helix chain 'DB' and resid 28 through 30 No H-bonds generated for 'chain 'DB' and resid 28 through 30' Processing helix chain 'DB' and resid 42 through 62 removed outlier: 3.651A pdb=" N METDB 46 " --> pdb=" O PRODB 42 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASPDB 48 " --> pdb=" O SERDB 44 " (cutoff:3.500A) Proline residue: DB 49 - end of helix Processing helix chain 'DB' and resid 120 through 131 removed outlier: 3.660A pdb=" N ASPDB 126 " --> pdb=" O ALADB 122 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SERDB 128 " --> pdb=" O ALADB 124 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYSDB 129 " --> pdb=" O SERDB 125 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHEDB 131 " --> pdb=" O LEUDB 127 " (cutoff:3.500A) Processing helix chain 'DB' and resid 135 through 163 Processing helix chain 'DB' and resid 168 through 192 removed outlier: 3.970A pdb=" N VALDB 176 " --> pdb=" O ILEDB 172 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILEDB 177 " --> pdb=" O TYRDB 173 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N METDB 190 " --> pdb=" O METDB 186 " (cutoff:3.500A) Processing helix chain 'DB' and resid 194 through 219 removed outlier: 3.603A pdb=" N VALDB 200 " --> pdb=" O ALADB 196 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILEDB 209 " --> pdb=" O LEUDB 205 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N METDB 210 " --> pdb=" O METDB 206 " (cutoff:3.500A) Proline residue: DB 211 - end of helix removed outlier: 3.598A pdb=" N ALADB 219 " --> pdb=" O ALADB 215 " (cutoff:3.500A) Processing helix chain 'DB' and resid 225 through 248 removed outlier: 3.919A pdb=" N LEUDB 231 " --> pdb=" O PRODB 227 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGDB 245 " --> pdb=" O ALADB 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHEDB 246 " --> pdb=" O LEUDB 242 " (cutoff:3.500A) Processing helix chain 'DB' and resid 250 through 275 removed outlier: 3.503A pdb=" N ILEDB 257 " --> pdb=" O ILEDB 253 " (cutoff:3.500A) Processing helix chain 'DB' and resid 277 through 304 removed outlier: 3.910A pdb=" N HISDB 294 " --> pdb=" O VALDB 290 " (cutoff:3.500A) Proline residue: DB 297 - end of helix removed outlier: 3.514A pdb=" N ARGDB 301 " --> pdb=" O PRODB 297 " (cutoff:3.500A) Processing helix chain 'DB' and resid 343 through 348 Processing helix chain 'DB' and resid 348 through 379 removed outlier: 4.350A pdb=" N GLUDB 354 " --> pdb=" O LEUDB 350 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGDB 355 " --> pdb=" O LEUDB 351 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUDB 367 " --> pdb=" O LEUDB 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SERDB 377 " --> pdb=" O VALDB 373 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYSDB 379 " --> pdb=" O METDB 375 " (cutoff:3.500A) Processing helix chain 'DB' and resid 386 through 404 removed outlier: 3.894A pdb=" N LEUDB 390 " --> pdb=" O ARGDB 386 " (cutoff:3.500A) Processing helix chain 'DB' and resid 405 through 407 No H-bonds generated for 'chain 'DB' and resid 405 through 407' Processing helix chain 'DB' and resid 409 through 431 removed outlier: 3.623A pdb=" N LEUDB 416 " --> pdb=" O GLNDB 412 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILEDB 423 " --> pdb=" O THRDB 419 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALADB 424 " --> pdb=" O ALADB 420 " (cutoff:3.500A) Processing helix chain 'DB' and resid 437 through 462 removed outlier: 3.597A pdb=" N VALDB 449 " --> pdb=" O ALADB 445 " (cutoff:3.500A) Proline residue: DB 452 - end of helix Processing helix chain 'DB' and resid 463 through 465 No H-bonds generated for 'chain 'DB' and resid 463 through 465' Processing helix chain 'DB' and resid 468 through 484 removed outlier: 3.576A pdb=" N GLUDB 476 " --> pdb=" O ARGDB 472 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRPDB 477 " --> pdb=" O LYSDB 473 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILEDB 478 " --> pdb=" O PHEDB 474 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLUDB 479 " --> pdb=" O VALDB 475 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYRDB 480 " --> pdb=" O GLUDB 476 " (cutoff:3.500A) Processing helix chain 'DB' and resid 485 through 494 Processing helix chain 'DB' and resid 495 through 502 Processing helix chain 'DC' and resid 42 through 45 Processing helix chain 'DC' and resid 46 through 62 Processing helix chain 'DC' and resid 118 through 131 removed outlier: 3.798A pdb=" N LYSDC 129 " --> pdb=" O SERDC 125 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARGDC 130 " --> pdb=" O ASPDC 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHEDC 131 " --> pdb=" O LEUDC 127 " (cutoff:3.500A) Processing helix chain 'DC' and resid 135 through 163 removed outlier: 3.604A pdb=" N VALDC 140 " --> pdb=" O PRODC 136 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLNDC 141 " --> pdb=" O ILEDC 137 " (cutoff:3.500A) Processing helix chain 'DC' and resid 168 through 192 removed outlier: 3.567A pdb=" N VALDC 176 " --> pdb=" O ILEDC 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEUDC 187 " --> pdb=" O ALADC 183 " (cutoff:3.500A) Processing helix chain 'DC' and resid 194 through 207 removed outlier: 3.506A pdb=" N SERDC 207 " --> pdb=" O ILEDC 203 " (cutoff:3.500A) Processing helix chain 'DC' and resid 208 through 218 Processing helix chain 'DC' and resid 225 through 248 removed outlier: 3.515A pdb=" N VALDC 230 " --> pdb=" O SERDC 226 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEUDC 231 " --> pdb=" O PRODC 227 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLYDC 234 " --> pdb=" O VALDC 230 " (cutoff:3.500A) Processing helix chain 'DC' and resid 250 through 274 removed outlier: 3.553A pdb=" N TYRDC 254 " --> pdb=" O ARGDC 250 " (cutoff:3.500A) Processing helix chain 'DC' and resid 277 through 304 removed outlier: 3.513A pdb=" N LEUDC 281 " --> pdb=" O SERDC 277 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HISDC 294 " --> pdb=" O VALDC 290 " (cutoff:3.500A) Proline residue: DC 297 - end of helix removed outlier: 3.632A pdb=" N ALADC 304 " --> pdb=" O SERDC 300 " (cutoff:3.500A) Processing helix chain 'DC' and resid 345 through 379 Processing helix chain 'DC' and resid 386 through 404 removed outlier: 4.122A pdb=" N LEUDC 390 " --> pdb=" O ARGDC 386 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHEDC 399 " --> pdb=" O PHEDC 395 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEUDC 400 " --> pdb=" O THRDC 396 " (cutoff:3.500A) Processing helix chain 'DC' and resid 405 through 407 No H-bonds generated for 'chain 'DC' and resid 405 through 407' Processing helix chain 'DC' and resid 409 through 434 removed outlier: 3.568A pdb=" N ALADC 420 " --> pdb=" O LEUDC 416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALDC 421 " --> pdb=" O ALADC 417 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILEDC 423 " --> pdb=" O THRDC 419 " (cutoff:3.500A) Processing helix chain 'DC' and resid 437 through 461 Proline residue: DC 452 - end of helix removed outlier: 3.549A pdb=" N GLYDC 455 " --> pdb=" O LEUDC 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C1' and resid 3 through 4 removed outlier: 6.004A pdb=" N ARGC1 3 " --> pdb=" O ARGC1 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C1' and resid 19 through 22 removed outlier: 6.934A pdb=" N GLUC1 19 " --> pdb=" O THRC1 175 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLYC1 177 " --> pdb=" O GLUC1 19 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILEC1 21 " --> pdb=" O GLYC1 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C1' and resid 206 through 214 removed outlier: 5.657A pdb=" N TYRC1 207 " --> pdb=" O THRC1 170 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THRC1 170 " --> pdb=" O TYRC1 207 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLYC1 166 " --> pdb=" O LYSC1 211 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VALC1 213 " --> pdb=" O ARGC1 164 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARGC1 164 " --> pdb=" O VALC1 213 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N METC1 169 " --> pdb=" O PHEC1 393 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N PHEC1 393 " --> pdb=" O METC1 169 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHEC1 392 " --> pdb=" O ALAC1 375 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALAC1 375 " --> pdb=" O PHEC1 392 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEUC1 365 " --> pdb=" O TRPC1 220 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALAC1 222 " --> pdb=" O LEUC1 365 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHEC1 367 " --> pdb=" O ALAC1 222 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VALC1 224 " --> pdb=" O PHEC1 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASPC1 350 " --> pdb=" O TYRC1 221 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYRC1 287 " --> pdb=" O METC1 252 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VALC1 254 " --> pdb=" O TYRC1 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C2' and resid 3 through 4 removed outlier: 6.149A pdb=" N ARGC2 3 " --> pdb=" O ARGC2 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C2' and resid 19 through 22 removed outlier: 6.700A pdb=" N GLUC2 19 " --> pdb=" O THRC2 175 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLYC2 177 " --> pdb=" O GLUC2 19 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILEC2 21 " --> pdb=" O GLYC2 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C2' and resid 206 through 214 removed outlier: 5.346A pdb=" N TYRC2 207 " --> pdb=" O THRC2 170 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THRC2 170 " --> pdb=" O TYRC2 207 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLYC2 166 " --> pdb=" O LYSC2 211 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VALC2 213 " --> pdb=" O ARGC2 164 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARGC2 164 " --> pdb=" O VALC2 213 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N METC2 169 " --> pdb=" O PHEC2 393 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHEC2 393 " --> pdb=" O METC2 169 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILEC2 373 " --> pdb=" O PHEC2 393 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALAC2 222 " --> pdb=" O LEUC2 365 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHEC2 367 " --> pdb=" O ALAC2 222 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VALC2 224 " --> pdb=" O PHEC2 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C2' and resid 286 through 287 removed outlier: 8.934A pdb=" N TYRC2 287 " --> pdb=" O METC2 252 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VALC2 254 " --> pdb=" O TYRC2 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C3' and resid 3 through 4 removed outlier: 6.152A pdb=" N ARGC3 3 " --> pdb=" O ARGC3 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C3' and resid 19 through 22 removed outlier: 7.088A pdb=" N GLUC3 19 " --> pdb=" O THRC3 175 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLYC3 177 " --> pdb=" O GLUC3 19 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILEC3 21 " --> pdb=" O GLYC3 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C3' and resid 206 through 214 removed outlier: 5.806A pdb=" N TYRC3 207 " --> pdb=" O THRC3 170 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THRC3 170 " --> pdb=" O TYRC3 207 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLYC3 166 " --> pdb=" O LYSC3 211 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VALC3 213 " --> pdb=" O ARGC3 164 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARGC3 164 " --> pdb=" O VALC3 213 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VALC3 167 " --> pdb=" O LEUC3 395 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N METC3 169 " --> pdb=" O PHEC3 393 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHEC3 393 " --> pdb=" O METC3 169 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHEC3 392 " --> pdb=" O ALAC3 375 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALAC3 375 " --> pdb=" O PHEC3 392 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEUC3 365 " --> pdb=" O TRPC3 220 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALAC3 222 " --> pdb=" O LEUC3 365 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHEC3 367 " --> pdb=" O ALAC3 222 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VALC3 224 " --> pdb=" O PHEC3 367 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASPC3 350 " --> pdb=" O TYRC3 221 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLNC3 251 " --> pdb=" O VALC3 324 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILEC3 326 " --> pdb=" O GLNC3 251 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILEC3 253 " --> pdb=" O ILEC3 326 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASPC3 328 " --> pdb=" O ILEC3 253 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VALC3 255 " --> pdb=" O ASPC3 328 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N TYRC3 287 " --> pdb=" O METC3 252 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VALC3 254 " --> pdb=" O TYRC3 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C4' and resid 3 through 4 removed outlier: 6.234A pdb=" N ARGC4 3 " --> pdb=" O ARGC4 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C4' and resid 19 through 22 removed outlier: 7.004A pdb=" N GLUC4 19 " --> pdb=" O THRC4 175 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLYC4 177 " --> pdb=" O GLUC4 19 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILEC4 21 " --> pdb=" O GLYC4 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C4' and resid 206 through 214 removed outlier: 5.523A pdb=" N TYRC4 207 " --> pdb=" O THRC4 170 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THRC4 170 " --> pdb=" O TYRC4 207 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLYC4 166 " --> pdb=" O LYSC4 211 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VALC4 213 " --> pdb=" O ARGC4 164 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARGC4 164 " --> pdb=" O VALC4 213 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VALC4 167 " --> pdb=" O LEUC4 395 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N METC4 169 " --> pdb=" O PHEC4 393 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHEC4 393 " --> pdb=" O METC4 169 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILEC4 373 " --> pdb=" O PHEC4 393 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEUC4 365 " --> pdb=" O TRPC4 220 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALAC4 222 " --> pdb=" O LEUC4 365 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHEC4 367 " --> pdb=" O ALAC4 222 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VALC4 224 " --> pdb=" O PHEC4 367 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASPC4 350 " --> pdb=" O TYRC4 221 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYRC4 287 " --> pdb=" O METC4 252 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VALC4 254 " --> pdb=" O TYRC4 287 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C5' and resid 3 through 4 removed outlier: 6.027A pdb=" N ARGC5 3 " --> pdb=" O ARGC5 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C5' and resid 19 through 22 removed outlier: 7.057A pdb=" N GLUC5 19 " --> pdb=" O THRC5 175 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLYC5 177 " --> pdb=" O GLUC5 19 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILEC5 21 " --> pdb=" O GLYC5 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C5' and resid 206 through 214 removed outlier: 5.657A pdb=" N TYRC5 207 " --> pdb=" O THRC5 170 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THRC5 170 " --> pdb=" O TYRC5 207 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLYC5 166 " --> pdb=" O LYSC5 211 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VALC5 213 " --> pdb=" O ARGC5 164 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARGC5 164 " --> pdb=" O VALC5 213 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N METC5 169 " --> pdb=" O PHEC5 393 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHEC5 393 " --> pdb=" O METC5 169 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHEC5 392 " --> pdb=" O ALAC5 375 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALAC5 375 " --> pdb=" O PHEC5 392 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEUC5 365 " --> pdb=" O TRPC5 220 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALAC5 222 " --> pdb=" O LEUC5 365 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHEC5 367 " --> pdb=" O ALAC5 222 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VALC5 224 " --> pdb=" O PHEC5 367 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N TYRC5 287 " --> pdb=" O METC5 252 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VALC5 254 " --> pdb=" O TYRC5 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C6' and resid 3 through 4 removed outlier: 6.032A pdb=" N ARGC6 3 " --> pdb=" O ARGC6 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C6' and resid 19 through 22 removed outlier: 6.610A pdb=" N GLUC6 19 " --> pdb=" O THRC6 175 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLYC6 177 " --> pdb=" O GLUC6 19 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILEC6 21 " --> pdb=" O GLYC6 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C6' and resid 206 through 214 removed outlier: 7.422A pdb=" N TYRC6 207 " --> pdb=" O METC6 169 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N METC6 169 " --> pdb=" O TYRC6 207 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEUC6 209 " --> pdb=" O VALC6 167 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VALC6 167 " --> pdb=" O LEUC6 209 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYSC6 211 " --> pdb=" O VALC6 165 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N METC6 169 " --> pdb=" O PHEC6 393 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHEC6 393 " --> pdb=" O METC6 169 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHEC6 392 " --> pdb=" O ALAC6 375 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALAC6 375 " --> pdb=" O PHEC6 392 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEUC6 365 " --> pdb=" O TRPC6 220 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALAC6 222 " --> pdb=" O LEUC6 365 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHEC6 367 " --> pdb=" O ALAC6 222 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VALC6 224 " --> pdb=" O PHEC6 367 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASPC6 350 " --> pdb=" O TYRC6 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D1' and resid 32 through 38 removed outlier: 3.661A pdb=" N ILED1 103 " --> pdb=" O METD1 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D1' and resid 116 through 118 removed outlier: 8.552A pdb=" N LEUD2 101 " --> pdb=" O VALD2 22 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLYD2 24 " --> pdb=" O LEUD2 101 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILED2 103 " --> pdb=" O GLYD2 24 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N METD2 26 " --> pdb=" O ILED2 103 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N PHED2 105 " --> pdb=" O METD2 26 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D1' and resid 328 through 330 removed outlier: 6.663A pdb=" N THRD1 328 " --> pdb=" O GLUD1 341 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D3' and resid 32 through 38 removed outlier: 3.553A pdb=" N ILED3 103 " --> pdb=" O METD3 26 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D3' and resid 116 through 118 Processing sheet with id=AC7, first strand: chain 'D3' and resid 328 through 330 removed outlier: 6.702A pdb=" N THRD3 328 " --> pdb=" O GLUD3 341 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D5' and resid 32 through 38 removed outlier: 3.622A pdb=" N ILED5 103 " --> pdb=" O METD5 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D5' and resid 116 through 118 Processing sheet with id=AD1, first strand: chain 'D5' and resid 327 through 330 removed outlier: 6.370A pdb=" N THRD5 328 " --> pdb=" O GLUD5 341 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D7' and resid 32 through 38 removed outlier: 8.381A pdb=" N LEUD7 101 " --> pdb=" O VALD7 22 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLYD7 24 " --> pdb=" O LEUD7 101 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILED7 103 " --> pdb=" O GLYD7 24 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N METD7 26 " --> pdb=" O ILED7 103 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N PHED7 105 " --> pdb=" O METD7 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D7' and resid 116 through 118 removed outlier: 8.368A pdb=" N LEUD8 101 " --> pdb=" O VALD8 22 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLYD8 24 " --> pdb=" O LEUD8 101 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILED8 103 " --> pdb=" O GLYD8 24 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N METD8 26 " --> pdb=" O ILED8 103 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHED8 105 " --> pdb=" O METD8 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D7' and resid 329 through 330 Processing sheet with id=AD5, first strand: chain 'D9' and resid 32 through 38 removed outlier: 4.272A pdb=" N ASPD9 99 " --> pdb=" O VALD9 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILED9 103 " --> pdb=" O METD9 26 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D9' and resid 116 through 118 removed outlier: 8.487A pdb=" N LEUDA 101 " --> pdb=" O VALDA 22 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLYDA 24 " --> pdb=" O LEUDA 101 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILEDA 103 " --> pdb=" O GLYDA 24 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N METDA 26 " --> pdb=" O ILEDA 103 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N PHEDA 105 " --> pdb=" O METDA 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D9' and resid 328 through 330 removed outlier: 6.465A pdb=" N THRD9 328 " --> pdb=" O GLUD9 341 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'DB' and resid 32 through 38 Processing sheet with id=AD9, first strand: chain 'DB' and resid 116 through 118 Processing sheet with id=AE1, first strand: chain 'DB' and resid 328 through 330 removed outlier: 6.685A pdb=" N THRDB 328 " --> pdb=" O GLUDB 341 " (cutoff:3.500A) 3911 hydrogen bonds defined for protein. 11496 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: 43.05 Time building geometry restraints manager: 78.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 64319 1.03 - 1.23: 199 1.23 - 1.43: 25499 1.43 - 1.62: 37313 1.62 - 1.82: 738 Bond restraints: 128068 Sorted by residual: bond pdb=" N METC4 1 " pdb=" H1 METC4 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" N METC2 1 " pdb=" H1 METC2 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N METC6 1 " pdb=" H1 METC6 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N METC3 1 " pdb=" H1 METC3 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N METC5 1 " pdb=" H1 METC5 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 128063 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.73: 3 85.73 - 97.91: 1 97.91 - 110.09: 121698 110.09 - 122.27: 92200 122.27 - 134.45: 18473 Bond angle restraints: 232375 Sorted by residual: angle pdb=" N ILEDC 119 " pdb=" CA ILEDC 119 " pdb=" HA ILEDC 119 " ideal model delta sigma weight residual 110.00 74.29 35.71 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ILEDC 119 " pdb=" CA ILEDC 119 " pdb=" HA ILEDC 119 " ideal model delta sigma weight residual 109.00 73.55 35.45 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB ILEDC 119 " pdb=" CA ILEDC 119 " pdb=" HA ILEDC 119 " ideal model delta sigma weight residual 109.00 78.16 30.84 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C GLYC3 34 " pdb=" N LYSC3 35 " pdb=" CA LYSC3 35 " ideal model delta sigma weight residual 120.49 128.37 -7.88 1.42e+00 4.96e-01 3.08e+01 angle pdb=" C METC3 88 " pdb=" N GLYC3 89 " pdb=" CA GLYC3 89 " ideal model delta sigma weight residual 120.44 126.39 -5.95 1.09e+00 8.42e-01 2.98e+01 ... (remaining 232370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 53896 17.91 - 35.82: 2579 35.82 - 53.74: 560 53.74 - 71.65: 1231 71.65 - 89.56: 89 Dihedral angle restraints: 58355 sinusoidal: 31313 harmonic: 27042 Sorted by residual: dihedral pdb=" C ILEDC 119 " pdb=" N ILEDC 119 " pdb=" CA ILEDC 119 " pdb=" CB ILEDC 119 " ideal model delta harmonic sigma weight residual -122.00 -131.58 9.58 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C TRPD5 411 " pdb=" N TRPD5 411 " pdb=" CA TRPD5 411 " pdb=" CB TRPD5 411 " ideal model delta harmonic sigma weight residual -122.60 -131.40 8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA HISDA 118 " pdb=" C HISDA 118 " pdb=" N ILEDA 119 " pdb=" CA ILEDA 119 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 58352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 8021 0.064 - 0.127: 2061 0.127 - 0.191: 297 0.191 - 0.255: 35 0.255 - 0.318: 8 Chirality restraints: 10422 Sorted by residual: chirality pdb=" CA ILEDC 119 " pdb=" N ILEDC 119 " pdb=" C ILEDC 119 " pdb=" CB ILEDC 119 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA TRPD5 411 " pdb=" N TRPD5 411 " pdb=" C TRPD5 411 " pdb=" CB TRPD5 411 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA TRPD9 411 " pdb=" N TRPD9 411 " pdb=" C TRPD9 411 " pdb=" CB TRPD9 411 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 10419 not shown) Planarity restraints: 18634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HISD8 118 " 0.001 2.00e-02 2.50e+03 3.56e-02 3.16e+01 pdb=" CG HISD8 118 " -0.003 2.00e-02 2.50e+03 pdb=" ND1 HISD8 118 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 HISD8 118 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 HISD8 118 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HISD8 118 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 HISD8 118 " -0.049 2.00e-02 2.50e+03 pdb=" HD2 HISD8 118 " -0.051 2.00e-02 2.50e+03 pdb=" HE1 HISD8 118 " -0.031 2.00e-02 2.50e+03 pdb=" HE2 HISD8 118 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGC3 380 " 0.096 9.50e-02 1.11e+02 4.82e-02 3.03e+01 pdb=" NE ARGC3 380 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARGC3 380 " 0.052 2.00e-02 2.50e+03 pdb=" NH1 ARGC3 380 " -0.082 2.00e-02 2.50e+03 pdb=" NH2 ARGC3 380 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARGC3 380 " 0.014 2.00e-02 2.50e+03 pdb="HH12 ARGC3 380 " 0.041 2.00e-02 2.50e+03 pdb="HH21 ARGC3 380 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARGC3 380 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGC1 3 " 0.178 9.50e-02 1.11e+02 6.83e-02 2.90e+01 pdb=" NE ARGC1 3 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARGC1 3 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARGC1 3 " 0.067 2.00e-02 2.50e+03 pdb=" NH2 ARGC1 3 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARGC1 3 " -0.017 2.00e-02 2.50e+03 pdb="HH12 ARGC1 3 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARGC1 3 " -0.033 2.00e-02 2.50e+03 pdb="HH22 ARGC1 3 " 0.049 2.00e-02 2.50e+03 ... (remaining 18631 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 1685 2.05 - 2.69: 190417 2.69 - 3.33: 350970 3.33 - 3.96: 423251 3.96 - 4.60: 666442 Nonbonded interactions: 1632765 Sorted by model distance: nonbonded pdb=" OE2 GLUD3 341 " pdb=" HE ARGD3 347 " model vdw 1.415 1.850 nonbonded pdb=" OE1 GLUD1 354 " pdb="HH22 ARGD2 130 " model vdw 1.506 1.850 nonbonded pdb=" OE1 GLNC6 180 " pdb="HD21 ASNC6 181 " model vdw 1.512 1.850 nonbonded pdb=" OE1 GLNC4 180 " pdb="HD21 ASNC4 181 " model vdw 1.527 1.850 nonbonded pdb=" O GLYC2 67 " pdb=" HG SERC2 70 " model vdw 1.539 1.850 ... (remaining 1632760 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 'B1' selection = chain 'B2' selection = chain 'B3' selection = chain 'B4' selection = chain 'B5' selection = chain 'B6' } ncs_group { reference = chain 'C1' selection = chain 'C2' selection = chain 'C3' selection = chain 'C4' selection = chain 'C5' selection = chain 'C6' } ncs_group { reference = (chain 'D1' and (resid 19 through 314 or resid 344 through 461)) selection = (chain 'D3' and (resid 19 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 314 or resid 344 through 461)) selection = (chain 'D4' and (resid 19 through 117 or (resid 118 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 119 through 461)) selection = (chain 'D5' and (resid 19 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 314 or resid 344 through 461)) selection = (chain 'D7' and (resid 19 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 314 or resid 344 through 461)) selection = (chain 'D9' and (resid 19 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 314 or resid 344 through 461)) selection = (chain 'DB' and (resid 19 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 314 or resid 344 through 461)) } ncs_group { reference = (chain 'D2' and (resid 18 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 461)) selection = (chain 'D6' and (resid 18 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 461)) selection = chain 'D8' selection = (chain 'DA' and (resid 18 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 295 through 381 or (resid 382 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2 \ )) or resid 383 through 461)) selection = chain 'DC' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 1.410 Extract box with map and model: 17.290 Check model and map are aligned: 1.380 Set scattering table: 0.880 Process input model: 282.710 Find NCS groups from input model: 4.820 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 314.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 0.075 63671 Z= 0.532 Angle : 1.195 11.843 86872 Z= 0.729 Chirality : 0.056 0.318 10422 Planarity : 0.008 0.103 10874 Dihedral : 11.872 89.562 22685 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.83 % Favored : 98.06 % Rotamer: Outliers : 0.37 % Allowed : 1.39 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.08), residues: 8158 helix: -0.22 (0.07), residues: 4629 sheet: -0.63 (0.19), residues: 638 loop : -0.37 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRPC3 267 HIS 0.026 0.004 HISD9 294 PHE 0.039 0.004 PHEC3 75 TYR 0.039 0.008 TYRD1 467 ARG 0.068 0.007 ARGC5 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1304 time to evaluate : 7.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 1324 average time/residue: 1.3615 time to fit residues: 2991.9397 Evaluate side-chains 796 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 784 time to evaluate : 7.188 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 1.5710 time to fit residues: 38.1851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 684 optimal weight: 0.0980 chunk 614 optimal weight: 0.9990 chunk 341 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 414 optimal weight: 0.3980 chunk 328 optimal weight: 3.9990 chunk 635 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 386 optimal weight: 8.9990 chunk 473 optimal weight: 7.9990 chunk 736 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 52 GLN B4 83 ASN C4 92 GLN C6 20 ASN D1 461 HIS D3 461 HIS D5 412 GLN D5 461 HIS D6 165 HIS D7 164 HIS D7 461 HIS D7 464 HIS D9 164 HIS D9 464 HIS DB 32 GLN DB 461 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 63671 Z= 0.212 Angle : 0.657 7.210 86872 Z= 0.361 Chirality : 0.041 0.315 10422 Planarity : 0.005 0.073 10874 Dihedral : 4.255 24.085 8897 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.09), residues: 8158 helix: 1.05 (0.07), residues: 4867 sheet: -0.70 (0.17), residues: 782 loop : -0.15 (0.13), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPB6 73 HIS 0.007 0.001 HISD3 464 PHE 0.038 0.001 PHEC3 293 TYR 0.037 0.002 TYRD7 96 ARG 0.028 0.001 ARGC1 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 951 time to evaluate : 7.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 951 average time/residue: 1.3744 time to fit residues: 2215.7667 Evaluate side-chains 736 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 736 time to evaluate : 7.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 409 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 612 optimal weight: 0.9990 chunk 501 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 737 optimal weight: 20.0000 chunk 797 optimal weight: 8.9990 chunk 657 optimal weight: 9.9990 chunk 731 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 591 optimal weight: 0.5980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 52 GLN ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 197 GLN DA 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63671 Z= 0.206 Angle : 0.584 6.597 86872 Z= 0.322 Chirality : 0.039 0.319 10422 Planarity : 0.004 0.046 10874 Dihedral : 4.241 23.692 8897 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.09), residues: 8158 helix: 1.39 (0.07), residues: 4789 sheet: -0.73 (0.17), residues: 771 loop : -0.10 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPD7 160 HIS 0.012 0.001 HISD3 294 PHE 0.026 0.001 PHED3 399 TYR 0.018 0.001 TYRC1 336 ARG 0.009 0.000 ARGC6 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 832 time to evaluate : 7.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 832 average time/residue: 1.3738 time to fit residues: 1944.4596 Evaluate side-chains 687 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 7.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.9034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 728 optimal weight: 20.0000 chunk 554 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 495 optimal weight: 0.0070 chunk 740 optimal weight: 9.9990 chunk 783 optimal weight: 0.9990 chunk 386 optimal weight: 2.9990 chunk 701 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 52 GLN C1 197 GLN ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 63671 Z= 0.178 Angle : 0.540 8.251 86872 Z= 0.294 Chirality : 0.039 0.309 10422 Planarity : 0.004 0.058 10874 Dihedral : 4.200 23.330 8897 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.09), residues: 8158 helix: 1.63 (0.07), residues: 4781 sheet: -0.58 (0.18), residues: 741 loop : -0.01 (0.13), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPD7 160 HIS 0.006 0.001 HISD3 294 PHE 0.027 0.001 PHED1 399 TYR 0.033 0.001 TYRC5 129 ARG 0.010 0.000 ARGD1 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 811 time to evaluate : 7.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 811 average time/residue: 1.2847 time to fit residues: 1771.4008 Evaluate side-chains 685 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 7.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 652 optimal weight: 3.9990 chunk 444 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 583 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 668 optimal weight: 0.8980 chunk 541 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 400 optimal weight: 0.9990 chunk 703 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 63671 Z= 0.213 Angle : 0.552 9.391 86872 Z= 0.303 Chirality : 0.039 0.313 10422 Planarity : 0.004 0.047 10874 Dihedral : 4.217 22.138 8897 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.09), residues: 8158 helix: 1.59 (0.07), residues: 4805 sheet: -0.70 (0.18), residues: 760 loop : -0.11 (0.13), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPC3 37 HIS 0.010 0.001 HISC3 133 PHE 0.022 0.002 PHED5 399 TYR 0.020 0.001 TYRC4 336 ARG 0.003 0.000 ARGD3 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 780 time to evaluate : 7.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 780 average time/residue: 1.4324 time to fit residues: 1924.5340 Evaluate side-chains 655 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 7.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 263 optimal weight: 1.9990 chunk 705 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 460 optimal weight: 0.6980 chunk 193 optimal weight: 10.0000 chunk 784 optimal weight: 4.9990 chunk 651 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 259 optimal weight: 0.4980 chunk 411 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 63671 Z= 0.150 Angle : 0.508 8.768 86872 Z= 0.272 Chirality : 0.038 0.308 10422 Planarity : 0.004 0.080 10874 Dihedral : 4.065 21.523 8897 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.09), residues: 8158 helix: 1.95 (0.07), residues: 4781 sheet: -0.56 (0.18), residues: 753 loop : 0.01 (0.13), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPC6 220 HIS 0.009 0.001 HISC3 133 PHE 0.031 0.001 PHEC6 75 TYR 0.020 0.001 TYRD1 431 ARG 0.007 0.000 ARGD4 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 780 time to evaluate : 7.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 780 average time/residue: 1.4179 time to fit residues: 1908.3371 Evaluate side-chains 661 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 7.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 756 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 447 optimal weight: 0.4980 chunk 573 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 660 optimal weight: 0.6980 chunk 438 optimal weight: 7.9990 chunk 781 optimal weight: 0.8980 chunk 489 optimal weight: 0.9990 chunk 476 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 141 GLN D9 461 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 63671 Z= 0.145 Angle : 0.502 6.605 86872 Z= 0.266 Chirality : 0.038 0.303 10422 Planarity : 0.004 0.059 10874 Dihedral : 3.962 20.712 8897 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.09), residues: 8158 helix: 2.11 (0.07), residues: 4821 sheet: -0.52 (0.19), residues: 759 loop : 0.08 (0.13), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPC5 220 HIS 0.010 0.001 HISC3 133 PHE 0.035 0.001 PHEDB 233 TYR 0.030 0.001 TYRC2 336 ARG 0.013 0.000 ARGB2 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 789 time to evaluate : 7.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 1.2729 time to fit residues: 1715.5187 Evaluate side-chains 668 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 7.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 483 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 466 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 496 optimal weight: 6.9990 chunk 532 optimal weight: 20.0000 chunk 386 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 614 optimal weight: 0.6980 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 261 GLN ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 63671 Z= 0.174 Angle : 0.515 9.112 86872 Z= 0.277 Chirality : 0.038 0.304 10422 Planarity : 0.004 0.072 10874 Dihedral : 3.976 20.271 8897 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.09), residues: 8158 helix: 2.07 (0.07), residues: 4826 sheet: -0.53 (0.19), residues: 759 loop : -0.04 (0.13), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPC2 38 HIS 0.008 0.001 HISC3 133 PHE 0.016 0.001 PHED1 233 TYR 0.014 0.001 TYRD8 293 ARG 0.011 0.000 ARGDA 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 769 time to evaluate : 7.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 769 average time/residue: 1.2685 time to fit residues: 1667.0627 Evaluate side-chains 652 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 7.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 711 optimal weight: 7.9990 chunk 748 optimal weight: 10.0000 chunk 683 optimal weight: 9.9990 chunk 728 optimal weight: 20.0000 chunk 438 optimal weight: 6.9990 chunk 317 optimal weight: 0.3980 chunk 571 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 658 optimal weight: 4.9990 chunk 688 optimal weight: 9.9990 chunk 725 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 52 GLN ** C2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 251 GLN ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DA 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 63671 Z= 0.255 Angle : 0.579 8.108 86872 Z= 0.318 Chirality : 0.039 0.308 10422 Planarity : 0.005 0.062 10874 Dihedral : 4.170 21.274 8897 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.09), residues: 8158 helix: 1.69 (0.07), residues: 4801 sheet: -0.75 (0.19), residues: 750 loop : -0.22 (0.13), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPB5 40 HIS 0.012 0.002 HISC3 133 PHE 0.017 0.002 PHED9 311 TYR 0.019 0.002 TYRD6 293 ARG 0.010 0.001 ARGDA 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 733 time to evaluate : 7.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 733 average time/residue: 1.2958 time to fit residues: 1615.8752 Evaluate side-chains 625 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 7.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 478 optimal weight: 3.9990 chunk 770 optimal weight: 0.7980 chunk 470 optimal weight: 0.9990 chunk 365 optimal weight: 3.9990 chunk 535 optimal weight: 8.9990 chunk 807 optimal weight: 9.9990 chunk 743 optimal weight: 0.9980 chunk 643 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 496 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D7 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 63671 Z= 0.151 Angle : 0.513 8.606 86872 Z= 0.271 Chirality : 0.038 0.299 10422 Planarity : 0.004 0.088 10874 Dihedral : 4.016 19.974 8897 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.09), residues: 8158 helix: 2.09 (0.07), residues: 4844 sheet: -0.66 (0.18), residues: 771 loop : -0.01 (0.13), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPC4 149 HIS 0.017 0.001 HISD6 164 PHE 0.022 0.001 PHED9 320 TYR 0.012 0.001 TYRC2 336 ARG 0.009 0.000 ARGB4 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16316 Ramachandran restraints generated. 8158 Oldfield, 0 Emsley, 8158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 766 time to evaluate : 6.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 1.2705 time to fit residues: 1671.1667 Evaluate side-chains 650 residues out of total 6560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 7.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 811 random chunks: chunk 511 optimal weight: 0.2980 chunk 685 optimal weight: 9.9990 chunk 197 optimal weight: 0.3980 chunk 593 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 644 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 chunk 661 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.077854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.067494 restraints weight = 1809880.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.069560 restraints weight = 729932.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.070504 restraints weight = 408844.158| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 63671 Z= 0.137 Angle : 0.496 7.536 86872 Z= 0.259 Chirality : 0.038 0.297 10422 Planarity : 0.004 0.060 10874 Dihedral : 3.861 19.474 8897 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.10), residues: 8158 helix: 2.37 (0.07), residues: 4832 sheet: -0.60 (0.19), residues: 728 loop : 0.09 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPC3 149 HIS 0.005 0.001 HISD6 164 PHE 0.019 0.001 PHEC3 75 TYR 0.014 0.001 TYRDA 293 ARG 0.014 0.000 ARGB4 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27532.31 seconds wall clock time: 472 minutes 35.13 seconds (28355.13 seconds total)