Starting phenix.real_space_refine on Sat Dec 16 13:31:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/12_2023/7yyo_14385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/12_2023/7yyo_14385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/12_2023/7yyo_14385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/12_2023/7yyo_14385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/12_2023/7yyo_14385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/12_2023/7yyo_14385_updated.pdb" } resolution = 2.87 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= 0.020 sd= 0.188 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 192 5.16 5 C 22328 2.51 5 N 6040 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 20": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E ARG 209": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 260": "OD1" <-> "OD2" Residue "E ARG 277": "NH1" <-> "NH2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 359": "OD1" <-> "OD2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E GLU 452": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 20": "OD1" <-> "OD2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G ARG 209": "NH1" <-> "NH2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 260": "OD1" <-> "OD2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 359": "OD1" <-> "OD2" Residue "G ASP 389": "OD1" <-> "OD2" Residue "G PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 417": "OE1" <-> "OE2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G GLU 439": "OE1" <-> "OE2" Residue "G GLU 446": "OE1" <-> "OE2" Residue "G GLU 452": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 20": "OD1" <-> "OD2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 98": "OD1" <-> "OD2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I ASP 195": "OD1" <-> "OD2" Residue "I ARG 209": "NH1" <-> "NH2" Residue "I GLU 223": "OE1" <-> "OE2" Residue "I TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 260": "OD1" <-> "OD2" Residue "I ARG 277": "NH1" <-> "NH2" Residue "I ASP 294": "OD1" <-> "OD2" Residue "I GLU 343": "OE1" <-> "OE2" Residue "I PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 359": "OD1" <-> "OD2" Residue "I ASP 389": "OD1" <-> "OD2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 417": "OE1" <-> "OE2" Residue "I ARG 434": "NH1" <-> "NH2" Residue "I GLU 439": "OE1" <-> "OE2" Residue "I GLU 446": "OE1" <-> "OE2" Residue "I GLU 452": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J ARG 92": "NH1" <-> "NH2" Residue "J TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "K TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 20": "OD1" <-> "OD2" Residue "K ASP 25": "OD1" <-> "OD2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 52": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 81": "OD1" <-> "OD2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 98": "OD1" <-> "OD2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K ASP 195": "OD1" <-> "OD2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K GLU 223": "OE1" <-> "OE2" Residue "K TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 260": "OD1" <-> "OD2" Residue "K ARG 277": "NH1" <-> "NH2" Residue "K ASP 294": "OD1" <-> "OD2" Residue "K GLU 343": "OE1" <-> "OE2" Residue "K PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 359": "OD1" <-> "OD2" Residue "K ASP 389": "OD1" <-> "OD2" Residue "K PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 417": "OE1" <-> "OE2" Residue "K ARG 434": "NH1" <-> "NH2" Residue "K GLU 439": "OE1" <-> "OE2" Residue "K GLU 446": "OE1" <-> "OE2" Residue "K GLU 452": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L ARG 113": "NH1" <-> "NH2" Residue "M TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 20": "OD1" <-> "OD2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 81": "OD1" <-> "OD2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 98": "OD1" <-> "OD2" Residue "M GLU 101": "OE1" <-> "OE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 153": "NH1" <-> "NH2" Residue "M TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M ASP 195": "OD1" <-> "OD2" Residue "M ARG 209": "NH1" <-> "NH2" Residue "M GLU 223": "OE1" <-> "OE2" Residue "M TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 260": "OD1" <-> "OD2" Residue "M ARG 277": "NH1" <-> "NH2" Residue "M ASP 294": "OD1" <-> "OD2" Residue "M GLU 343": "OE1" <-> "OE2" Residue "M PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 359": "OD1" <-> "OD2" Residue "M ASP 389": "OD1" <-> "OD2" Residue "M PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 417": "OE1" <-> "OE2" Residue "M ARG 434": "NH1" <-> "NH2" Residue "M GLU 439": "OE1" <-> "OE2" Residue "M GLU 446": "OE1" <-> "OE2" Residue "M GLU 452": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 69": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 88": "OD1" <-> "OD2" Residue "N ARG 92": "NH1" <-> "NH2" Residue "N TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 20": "OD1" <-> "OD2" Residue "O ASP 25": "OD1" <-> "OD2" Residue "O PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 52": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 81": "OD1" <-> "OD2" Residue "O GLU 87": "OE1" <-> "OE2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 98": "OD1" <-> "OD2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "O TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O ASP 195": "OD1" <-> "OD2" Residue "O ARG 209": "NH1" <-> "NH2" Residue "O GLU 223": "OE1" <-> "OE2" Residue "O TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 260": "OD1" <-> "OD2" Residue "O ARG 277": "NH1" <-> "NH2" Residue "O ASP 294": "OD1" <-> "OD2" Residue "O GLU 343": "OE1" <-> "OE2" Residue "O PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 359": "OD1" <-> "OD2" Residue "O ASP 389": "OD1" <-> "OD2" Residue "O PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 417": "OE1" <-> "OE2" Residue "O ARG 434": "NH1" <-> "NH2" Residue "O GLU 439": "OE1" <-> "OE2" Residue "O GLU 446": "OE1" <-> "OE2" Residue "O GLU 452": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P ASP 71": "OD1" <-> "OD2" Residue "P GLU 78": "OE1" <-> "OE2" Residue "P GLU 80": "OE1" <-> "OE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 88": "OD1" <-> "OD2" Residue "P ARG 92": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "P ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35136 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "D" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "F" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "K" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "L" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "N" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "O" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.11, per 1000 atoms: 0.46 Number of scatterers: 35136 At special positions: 0 Unit cell: (144.3, 145.41, 129.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 16 15.00 Mg 8 11.99 O 6552 8.00 N 6040 7.00 C 22328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.66 Conformation dependent library (CDL) restraints added in 5.5 seconds 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 32 sheets defined 37.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 134 through 139 removed outlier: 4.341A pdb=" N THR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.636A pdb=" N GLU A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 261 through 264 No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.793A pdb=" N ARG A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 331 through 342 removed outlier: 3.590A pdb=" N PHE A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 removed outlier: 3.720A pdb=" N MET A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Proline residue: A 380 - end of helix removed outlier: 4.148A pdb=" N VAL A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 384 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 386 " --> pdb=" O VAL A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 386' Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 406 through 424 removed outlier: 3.575A pdb=" N VAL A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.503A pdb=" N ILE A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 78 through 85 removed outlier: 3.606A pdb=" N CYS B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 134 through 139 removed outlier: 4.340A pdb=" N THR C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'C' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 224 removed outlier: 3.636A pdb=" N GLU C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 Processing helix chain 'C' and resid 261 through 264 No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.793A pdb=" N ARG C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 331 through 342 removed outlier: 3.591A pdb=" N PHE C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Proline residue: C 380 - end of helix removed outlier: 4.148A pdb=" N VAL C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 384 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 385 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 386 " --> pdb=" O VAL C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 386' Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 406 through 424 removed outlier: 3.575A pdb=" N VAL C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.504A pdb=" N ILE C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 78 through 85 removed outlier: 3.606A pdb=" N CYS D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.341A pdb=" N THR E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'E' and resid 174 through 187 removed outlier: 3.540A pdb=" N GLY E 178 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 224 removed outlier: 3.636A pdb=" N GLU E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 251 Processing helix chain 'E' and resid 261 through 264 No H-bonds generated for 'chain 'E' and resid 261 through 264' Processing helix chain 'E' and resid 266 through 279 removed outlier: 3.793A pdb=" N ARG E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 331 through 342 removed outlier: 3.590A pdb=" N PHE E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET E 379 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Proline residue: E 380 - end of helix removed outlier: 4.148A pdb=" N VAL E 383 " --> pdb=" O PRO E 380 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 384 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE E 385 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE E 386 " --> pdb=" O VAL E 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 376 through 386' Processing helix chain 'E' and resid 396 through 399 No H-bonds generated for 'chain 'E' and resid 396 through 399' Processing helix chain 'E' and resid 406 through 424 removed outlier: 3.575A pdb=" N VAL E 414 " --> pdb=" O ALA E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 437 Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 445 through 453 removed outlier: 3.504A pdb=" N ILE E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 72 through 75 No H-bonds generated for 'chain 'F' and resid 72 through 75' Processing helix chain 'F' and resid 78 through 85 removed outlier: 3.605A pdb=" N CYS F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 52 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 97 through 99 No H-bonds generated for 'chain 'G' and resid 97 through 99' Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 134 through 139 removed outlier: 4.341A pdb=" N THR G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 224 removed outlier: 3.636A pdb=" N GLU G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 251 Processing helix chain 'G' and resid 261 through 264 No H-bonds generated for 'chain 'G' and resid 261 through 264' Processing helix chain 'G' and resid 266 through 279 removed outlier: 3.793A pdb=" N ARG G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 278 " --> pdb=" O LYS G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 294 No H-bonds generated for 'chain 'G' and resid 291 through 294' Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 331 through 342 removed outlier: 3.590A pdb=" N PHE G 337 " --> pdb=" O THR G 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 340 " --> pdb=" O GLY G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET G 379 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Proline residue: G 380 - end of helix removed outlier: 4.147A pdb=" N VAL G 383 " --> pdb=" O PRO G 380 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA G 384 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE G 385 " --> pdb=" O LEU G 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE G 386 " --> pdb=" O VAL G 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 376 through 386' Processing helix chain 'G' and resid 396 through 399 No H-bonds generated for 'chain 'G' and resid 396 through 399' Processing helix chain 'G' and resid 406 through 424 removed outlier: 3.576A pdb=" N VAL G 414 " --> pdb=" O ALA G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 437 Processing helix chain 'G' and resid 441 through 443 No H-bonds generated for 'chain 'G' and resid 441 through 443' Processing helix chain 'G' and resid 445 through 453 removed outlier: 3.503A pdb=" N ILE G 449 " --> pdb=" O PRO G 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 39 Processing helix chain 'H' and resid 51 through 53 No H-bonds generated for 'chain 'H' and resid 51 through 53' Processing helix chain 'H' and resid 72 through 75 No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 78 through 85 removed outlier: 3.605A pdb=" N CYS H 82 " --> pdb=" O GLU H 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 97 through 99 No H-bonds generated for 'chain 'I' and resid 97 through 99' Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 134 through 139 removed outlier: 4.341A pdb=" N THR I 139 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'I' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY I 178 " --> pdb=" O GLY I 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY I 187 " --> pdb=" O GLU I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 224 removed outlier: 3.637A pdb=" N GLU I 211 " --> pdb=" O GLN I 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU I 215 " --> pdb=" O GLU I 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN I 222 " --> pdb=" O ALA I 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU I 223 " --> pdb=" O LEU I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 251 Processing helix chain 'I' and resid 261 through 264 No H-bonds generated for 'chain 'I' and resid 261 through 264' Processing helix chain 'I' and resid 266 through 279 removed outlier: 3.793A pdb=" N ARG I 277 " --> pdb=" O SER I 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS I 278 " --> pdb=" O LYS I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 294 No H-bonds generated for 'chain 'I' and resid 291 through 294' Processing helix chain 'I' and resid 303 through 313 Processing helix chain 'I' and resid 331 through 342 removed outlier: 3.589A pdb=" N PHE I 337 " --> pdb=" O THR I 333 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN I 340 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET I 379 " --> pdb=" O VAL I 376 " (cutoff:3.500A) Proline residue: I 380 - end of helix removed outlier: 4.148A pdb=" N VAL I 383 " --> pdb=" O PRO I 380 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA I 384 " --> pdb=" O ALA I 381 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE I 385 " --> pdb=" O LEU I 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE I 386 " --> pdb=" O VAL I 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 376 through 386' Processing helix chain 'I' and resid 396 through 399 No H-bonds generated for 'chain 'I' and resid 396 through 399' Processing helix chain 'I' and resid 406 through 424 removed outlier: 3.575A pdb=" N VAL I 414 " --> pdb=" O ALA I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 437 Processing helix chain 'I' and resid 441 through 443 No H-bonds generated for 'chain 'I' and resid 441 through 443' Processing helix chain 'I' and resid 445 through 453 removed outlier: 3.503A pdb=" N ILE I 449 " --> pdb=" O PRO I 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 39 Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 72 through 75 No H-bonds generated for 'chain 'J' and resid 72 through 75' Processing helix chain 'J' and resid 78 through 85 removed outlier: 3.605A pdb=" N CYS J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 97 through 99 No H-bonds generated for 'chain 'K' and resid 97 through 99' Processing helix chain 'K' and resid 105 through 112 Processing helix chain 'K' and resid 134 through 139 removed outlier: 4.341A pdb=" N THR K 139 " --> pdb=" O ALA K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 154 Processing helix chain 'K' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY K 178 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 224 removed outlier: 3.636A pdb=" N GLU K 211 " --> pdb=" O GLN K 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU K 215 " --> pdb=" O GLU K 211 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN K 222 " --> pdb=" O ALA K 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU K 223 " --> pdb=" O LEU K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 251 Processing helix chain 'K' and resid 261 through 264 No H-bonds generated for 'chain 'K' and resid 261 through 264' Processing helix chain 'K' and resid 266 through 279 removed outlier: 3.792A pdb=" N ARG K 277 " --> pdb=" O SER K 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS K 278 " --> pdb=" O LYS K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 294 No H-bonds generated for 'chain 'K' and resid 291 through 294' Processing helix chain 'K' and resid 303 through 313 Processing helix chain 'K' and resid 331 through 342 removed outlier: 3.590A pdb=" N PHE K 337 " --> pdb=" O THR K 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN K 340 " --> pdb=" O GLY K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET K 379 " --> pdb=" O VAL K 376 " (cutoff:3.500A) Proline residue: K 380 - end of helix removed outlier: 4.148A pdb=" N VAL K 383 " --> pdb=" O PRO K 380 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA K 384 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE K 385 " --> pdb=" O LEU K 382 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE K 386 " --> pdb=" O VAL K 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 376 through 386' Processing helix chain 'K' and resid 396 through 399 No H-bonds generated for 'chain 'K' and resid 396 through 399' Processing helix chain 'K' and resid 406 through 424 removed outlier: 3.576A pdb=" N VAL K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 437 Processing helix chain 'K' and resid 441 through 443 No H-bonds generated for 'chain 'K' and resid 441 through 443' Processing helix chain 'K' and resid 445 through 453 removed outlier: 3.503A pdb=" N ILE K 449 " --> pdb=" O PRO K 445 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU K 452 " --> pdb=" O ALA K 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 39 Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 72 through 75 No H-bonds generated for 'chain 'L' and resid 72 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.606A pdb=" N CYS L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 52 Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 97 through 99 No H-bonds generated for 'chain 'M' and resid 97 through 99' Processing helix chain 'M' and resid 105 through 112 Processing helix chain 'M' and resid 134 through 139 removed outlier: 4.341A pdb=" N THR M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 154 Processing helix chain 'M' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY M 178 " --> pdb=" O GLY M 174 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 187 " --> pdb=" O GLU M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 224 removed outlier: 3.636A pdb=" N GLU M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU M 215 " --> pdb=" O GLU M 211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN M 222 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU M 223 " --> pdb=" O LEU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 251 Processing helix chain 'M' and resid 261 through 264 No H-bonds generated for 'chain 'M' and resid 261 through 264' Processing helix chain 'M' and resid 266 through 279 removed outlier: 3.792A pdb=" N ARG M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 294 No H-bonds generated for 'chain 'M' and resid 291 through 294' Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 331 through 342 removed outlier: 3.590A pdb=" N PHE M 337 " --> pdb=" O THR M 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN M 340 " --> pdb=" O GLY M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET M 379 " --> pdb=" O VAL M 376 " (cutoff:3.500A) Proline residue: M 380 - end of helix removed outlier: 4.149A pdb=" N VAL M 383 " --> pdb=" O PRO M 380 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA M 384 " --> pdb=" O ALA M 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE M 385 " --> pdb=" O LEU M 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE M 386 " --> pdb=" O VAL M 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 376 through 386' Processing helix chain 'M' and resid 396 through 399 No H-bonds generated for 'chain 'M' and resid 396 through 399' Processing helix chain 'M' and resid 406 through 424 removed outlier: 3.576A pdb=" N VAL M 414 " --> pdb=" O ALA M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 437 Processing helix chain 'M' and resid 441 through 443 No H-bonds generated for 'chain 'M' and resid 441 through 443' Processing helix chain 'M' and resid 445 through 453 removed outlier: 3.504A pdb=" N ILE M 449 " --> pdb=" O PRO M 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU M 452 " --> pdb=" O ALA M 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 39 Processing helix chain 'N' and resid 51 through 53 No H-bonds generated for 'chain 'N' and resid 51 through 53' Processing helix chain 'N' and resid 72 through 75 No H-bonds generated for 'chain 'N' and resid 72 through 75' Processing helix chain 'N' and resid 78 through 85 removed outlier: 3.606A pdb=" N CYS N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 52 Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 97 through 99 No H-bonds generated for 'chain 'O' and resid 97 through 99' Processing helix chain 'O' and resid 105 through 112 Processing helix chain 'O' and resid 134 through 139 removed outlier: 4.340A pdb=" N THR O 139 " --> pdb=" O ALA O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 154 Processing helix chain 'O' and resid 174 through 187 removed outlier: 3.541A pdb=" N GLY O 178 " --> pdb=" O GLY O 174 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY O 187 " --> pdb=" O GLU O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 224 removed outlier: 3.637A pdb=" N GLU O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU O 215 " --> pdb=" O GLU O 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN O 222 " --> pdb=" O ALA O 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU O 223 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 251 Processing helix chain 'O' and resid 261 through 264 No H-bonds generated for 'chain 'O' and resid 261 through 264' Processing helix chain 'O' and resid 266 through 279 removed outlier: 3.793A pdb=" N ARG O 277 " --> pdb=" O SER O 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS O 278 " --> pdb=" O LYS O 274 " (cutoff:3.500A) Processing helix chain 'O' and resid 291 through 294 No H-bonds generated for 'chain 'O' and resid 291 through 294' Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 331 through 342 removed outlier: 3.590A pdb=" N PHE O 337 " --> pdb=" O THR O 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN O 340 " --> pdb=" O GLY O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 386 removed outlier: 3.719A pdb=" N MET O 379 " --> pdb=" O VAL O 376 " (cutoff:3.500A) Proline residue: O 380 - end of helix removed outlier: 4.148A pdb=" N VAL O 383 " --> pdb=" O PRO O 380 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA O 384 " --> pdb=" O ALA O 381 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE O 385 " --> pdb=" O LEU O 382 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE O 386 " --> pdb=" O VAL O 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 376 through 386' Processing helix chain 'O' and resid 396 through 399 No H-bonds generated for 'chain 'O' and resid 396 through 399' Processing helix chain 'O' and resid 406 through 424 removed outlier: 3.575A pdb=" N VAL O 414 " --> pdb=" O ALA O 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 433 through 437 Processing helix chain 'O' and resid 441 through 443 No H-bonds generated for 'chain 'O' and resid 441 through 443' Processing helix chain 'O' and resid 445 through 453 removed outlier: 3.504A pdb=" N ILE O 449 " --> pdb=" O PRO O 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU O 452 " --> pdb=" O ALA O 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 39 Processing helix chain 'P' and resid 51 through 53 No H-bonds generated for 'chain 'P' and resid 51 through 53' Processing helix chain 'P' and resid 72 through 75 No H-bonds generated for 'chain 'P' and resid 72 through 75' Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.606A pdb=" N CYS P 82 " --> pdb=" O GLU P 78 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 124 through 131 removed outlier: 3.515A pdb=" N HIS A 124 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS A 31 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 130 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 29 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 78 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 94 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS A 76 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 229 through 231 removed outlier: 6.370A pdb=" N ALA A 368 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN A 393 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 370 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 removed outlier: 6.522A pdb=" N LEU A 282 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS A 259 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS A 284 " --> pdb=" O HIS A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE B 46 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 49 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 93 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 108 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY B 95 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS B 106 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS C 124 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS C 31 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE C 130 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 29 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 78 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA C 94 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N CYS C 76 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 231 removed outlier: 6.371A pdb=" N ALA C 368 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN C 393 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C 370 " --> pdb=" O GLN C 393 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 256 through 260 removed outlier: 6.522A pdb=" N LEU C 282 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS C 259 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS C 284 " --> pdb=" O HIS C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE D 46 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 49 " --> pdb=" O HIS D 90 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU D 93 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL D 108 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY D 95 " --> pdb=" O CYS D 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS D 106 " --> pdb=" O GLY D 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS E 124 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS E 31 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE E 130 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU E 29 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 78 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA E 94 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS E 76 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 229 through 231 removed outlier: 6.371A pdb=" N ALA E 368 " --> pdb=" O VAL E 391 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN E 393 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA E 370 " --> pdb=" O GLN E 393 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 256 through 260 removed outlier: 6.523A pdb=" N LEU E 282 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS E 259 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS E 284 " --> pdb=" O HIS E 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE F 46 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL F 49 " --> pdb=" O HIS F 90 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU F 93 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL F 108 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY F 95 " --> pdb=" O CYS F 106 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS F 106 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS G 124 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS G 31 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE G 130 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU G 29 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 78 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA G 94 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N CYS G 76 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 229 through 231 removed outlier: 6.371A pdb=" N ALA G 368 " --> pdb=" O VAL G 391 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN G 393 " --> pdb=" O ALA G 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA G 370 " --> pdb=" O GLN G 393 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 256 through 260 removed outlier: 6.522A pdb=" N LEU G 282 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS G 259 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS G 284 " --> pdb=" O HIS G 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE H 46 " --> pdb=" O TRP H 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL H 49 " --> pdb=" O HIS H 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU H 93 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL H 108 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY H 95 " --> pdb=" O CYS H 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS H 106 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS I 124 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS I 31 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE I 130 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU I 29 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG I 78 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA I 94 " --> pdb=" O CYS I 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS I 76 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 229 through 231 removed outlier: 6.370A pdb=" N ALA I 368 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN I 393 " --> pdb=" O ALA I 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA I 370 " --> pdb=" O GLN I 393 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 256 through 260 removed outlier: 6.523A pdb=" N LEU I 282 " --> pdb=" O ILE I 257 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS I 259 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS I 284 " --> pdb=" O HIS I 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE J 46 " --> pdb=" O TRP J 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL J 49 " --> pdb=" O HIS J 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU J 93 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL J 108 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY J 95 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS J 106 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS K 124 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS K 31 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE K 130 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU K 29 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG K 78 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA K 94 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS K 76 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 229 through 231 removed outlier: 6.371A pdb=" N ALA K 368 " --> pdb=" O VAL K 391 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN K 393 " --> pdb=" O ALA K 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA K 370 " --> pdb=" O GLN K 393 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 256 through 260 removed outlier: 6.523A pdb=" N LEU K 282 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS K 259 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS K 284 " --> pdb=" O HIS K 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE L 46 " --> pdb=" O TRP L 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL L 49 " --> pdb=" O HIS L 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU L 93 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL L 108 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY L 95 " --> pdb=" O CYS L 106 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS L 106 " --> pdb=" O GLY L 95 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS M 124 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS M 31 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE M 130 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU M 29 " --> pdb=" O ILE M 130 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG M 78 " --> pdb=" O PHE M 92 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA M 94 " --> pdb=" O CYS M 76 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N CYS M 76 " --> pdb=" O ALA M 94 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 229 through 231 removed outlier: 6.371A pdb=" N ALA M 368 " --> pdb=" O VAL M 391 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN M 393 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA M 370 " --> pdb=" O GLN M 393 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 256 through 260 removed outlier: 6.523A pdb=" N LEU M 282 " --> pdb=" O ILE M 257 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS M 259 " --> pdb=" O LEU M 282 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS M 284 " --> pdb=" O HIS M 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 60 through 62 removed outlier: 3.987A pdb=" N ILE N 46 " --> pdb=" O TRP N 62 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL N 49 " --> pdb=" O HIS N 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU N 93 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL N 108 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY N 95 " --> pdb=" O CYS N 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS N 106 " --> pdb=" O GLY N 95 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 124 through 131 removed outlier: 3.514A pdb=" N HIS O 124 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS O 31 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE O 130 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU O 29 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG O 78 " --> pdb=" O PHE O 92 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA O 94 " --> pdb=" O CYS O 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS O 76 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 229 through 231 removed outlier: 6.371A pdb=" N ALA O 368 " --> pdb=" O VAL O 391 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN O 393 " --> pdb=" O ALA O 368 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA O 370 " --> pdb=" O GLN O 393 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 256 through 260 removed outlier: 6.522A pdb=" N LEU O 282 " --> pdb=" O ILE O 257 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS O 259 " --> pdb=" O LEU O 282 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N HIS O 284 " --> pdb=" O HIS O 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE P 46 " --> pdb=" O TRP P 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL P 49 " --> pdb=" O HIS P 90 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU P 93 " --> pdb=" O VAL P 108 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL P 108 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY P 95 " --> pdb=" O CYS P 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS P 106 " --> pdb=" O GLY P 95 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3072 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: 10.91 Time building geometry restraints manager: 12.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 35760 1.57 - 1.93: 296 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 8 Bond restraints: 36064 Sorted by residual: bond pdb=" C GLU G 328 " pdb=" N ASP G 330 " ideal model delta sigma weight residual 1.329 2.999 -1.670 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU K 328 " pdb=" N ASP K 330 " ideal model delta sigma weight residual 1.329 2.999 -1.670 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU O 328 " pdb=" N ASP O 330 " ideal model delta sigma weight residual 1.329 2.999 -1.670 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU M 328 " pdb=" N ASP M 330 " ideal model delta sigma weight residual 1.329 2.998 -1.669 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU A 328 " pdb=" N ASP A 330 " ideal model delta sigma weight residual 1.329 2.998 -1.669 1.40e-02 5.10e+03 1.42e+04 ... (remaining 36059 not shown) Histogram of bond angle deviations from ideal: 41.98 - 60.41: 8 60.41 - 78.84: 0 78.84 - 97.27: 0 97.27 - 115.70: 22684 115.70 - 134.13: 26244 Bond angle restraints: 48936 Sorted by residual: angle pdb=" O GLU G 328 " pdb=" C GLU G 328 " pdb=" N ASP G 330 " ideal model delta sigma weight residual 122.59 41.98 80.61 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU A 328 " pdb=" C GLU A 328 " pdb=" N ASP A 330 " ideal model delta sigma weight residual 122.59 42.00 80.59 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU I 328 " pdb=" C GLU I 328 " pdb=" N ASP I 330 " ideal model delta sigma weight residual 122.59 42.00 80.59 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU E 328 " pdb=" C GLU E 328 " pdb=" N ASP E 330 " ideal model delta sigma weight residual 122.59 42.00 80.59 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU C 328 " pdb=" C GLU C 328 " pdb=" N ASP C 330 " ideal model delta sigma weight residual 122.59 42.01 80.58 1.33e+00 5.65e-01 3.67e+03 ... (remaining 48931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 19778 34.74 - 69.48: 1122 69.48 - 104.23: 116 104.23 - 138.97: 4 138.97 - 173.71: 12 Dihedral angle restraints: 21032 sinusoidal: 8424 harmonic: 12608 Sorted by residual: dihedral pdb=" C3 CAP C 501 " pdb=" C CAP C 501 " pdb=" C2 CAP C 501 " pdb=" O6 CAP C 501 " ideal model delta sinusoidal sigma weight residual 81.86 -104.43 -173.71 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP G 501 " pdb=" C CAP G 501 " pdb=" C2 CAP G 501 " pdb=" O6 CAP G 501 " ideal model delta sinusoidal sigma weight residual 81.86 -104.44 -173.70 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP E 501 " pdb=" C CAP E 501 " pdb=" C2 CAP E 501 " pdb=" O6 CAP E 501 " ideal model delta sinusoidal sigma weight residual 81.86 -104.45 -173.69 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 21029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4382 0.073 - 0.146: 728 0.146 - 0.220: 18 0.220 - 0.293: 0 0.293 - 0.366: 8 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CB VAL C 324 " pdb=" CA VAL C 324 " pdb=" CG1 VAL C 324 " pdb=" CG2 VAL C 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL A 324 " pdb=" CA VAL A 324 " pdb=" CG1 VAL A 324 " pdb=" CG2 VAL A 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL O 324 " pdb=" CA VAL O 324 " pdb=" CG1 VAL O 324 " pdb=" CG2 VAL O 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 5133 not shown) Planarity restraints: 6368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 328 " 0.132 2.00e-02 2.50e+03 2.45e-01 6.01e+02 pdb=" C GLU C 328 " -0.367 2.00e-02 2.50e+03 pdb=" O GLU C 328 " 0.291 2.00e-02 2.50e+03 pdb=" N ASP C 330 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 328 " -0.133 2.00e-02 2.50e+03 2.45e-01 6.00e+02 pdb=" C GLU I 328 " 0.367 2.00e-02 2.50e+03 pdb=" O GLU I 328 " -0.291 2.00e-02 2.50e+03 pdb=" N ASP I 330 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 328 " -0.133 2.00e-02 2.50e+03 2.45e-01 6.00e+02 pdb=" C GLU K 328 " 0.367 2.00e-02 2.50e+03 pdb=" O GLU K 328 " -0.291 2.00e-02 2.50e+03 pdb=" N ASP K 330 " 0.057 2.00e-02 2.50e+03 ... (remaining 6365 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 418 2.60 - 3.17: 28591 3.17 - 3.75: 52410 3.75 - 4.32: 82169 4.32 - 4.90: 134769 Nonbonded interactions: 298357 Sorted by model distance: nonbonded pdb=" NH1 ARG M 304 " pdb=" O GLY M 353 " model vdw 2.025 2.520 nonbonded pdb=" NH1 ARG A 304 " pdb=" O GLY A 353 " model vdw 2.025 2.520 nonbonded pdb=" NH1 ARG C 304 " pdb=" O GLY C 353 " model vdw 2.025 2.520 nonbonded pdb=" NH1 ARG O 304 " pdb=" O GLY O 353 " model vdw 2.025 2.520 nonbonded pdb=" NH1 ARG K 304 " pdb=" O GLY K 353 " model vdw 2.025 2.520 ... (remaining 298352 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 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.330 Check model and map are aligned: 0.470 Set scattering table: 0.340 Process input model: 81.170 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.310 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: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.026 1.670 36064 Z= 1.947 Angle : 1.415 80.612 48936 Z= 0.971 Chirality : 0.052 0.366 5136 Planarity : 0.011 0.245 6368 Dihedral : 20.684 173.709 13000 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 12.83 % Allowed : 16.63 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.15 % 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: -4.07 (0.10), residues: 4376 helix: -3.75 (0.08), residues: 1680 sheet: -1.23 (0.19), residues: 696 loop : -2.14 (0.11), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 206 HIS 0.020 0.004 HIS E 259 PHE 0.035 0.004 PHE A 92 TYR 0.034 0.003 TYR E 157 ARG 0.020 0.002 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 466 poor density : 454 time to evaluate : 4.017 Fit side-chains outliers start: 466 outliers final: 55 residues processed: 814 average time/residue: 1.6544 time to fit residues: 1590.3814 Evaluate side-chains 398 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 343 time to evaluate : 3.885 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 46 residues processed: 9 average time/residue: 0.9788 time to fit residues: 16.6349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 338 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 155 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 401 HIS A 412 ASN B 33 GLN B 48 HIS B 101 GLN C 37 GLN C 145 ASN C 155 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN C 401 HIS C 412 ASN D 33 GLN D 48 HIS D 101 GLN E 37 GLN E 107 ASN E 375 HIS E 378 HIS E 401 HIS E 412 ASN F 48 HIS F 101 GLN G 37 GLN G 145 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN G 401 HIS G 412 ASN H 11 GLN H 48 HIS H 101 GLN I 107 ASN I 155 ASN I 375 HIS I 378 HIS I 401 HIS ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 48 HIS J 101 GLN K 145 ASN K 155 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 GLN K 401 HIS K 412 ASN L 11 GLN L 48 HIS L 101 GLN M 145 ASN ** M 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 393 GLN M 401 HIS M 412 ASN N 48 HIS N 101 GLN O 145 ASN O 284 HIS ** O 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 401 HIS O 412 ASN P 33 GLN P 48 HIS P 101 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 36064 Z= 0.230 Angle : 0.650 7.620 48936 Z= 0.338 Chirality : 0.046 0.307 5136 Planarity : 0.005 0.045 6368 Dihedral : 10.190 173.343 4904 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 4.82 % Allowed : 22.96 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -2.31 (0.11), residues: 4392 helix: -1.75 (0.11), residues: 1640 sheet: -0.51 (0.20), residues: 608 loop : -1.57 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 206 HIS 0.013 0.002 HIS I 401 PHE 0.017 0.002 PHE E 356 TYR 0.018 0.002 TYR C 231 ARG 0.010 0.001 ARG I 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 400 time to evaluate : 3.916 Fit side-chains outliers start: 175 outliers final: 66 residues processed: 543 average time/residue: 1.5734 time to fit residues: 1018.3520 Evaluate side-chains 400 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 334 time to evaluate : 3.964 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 59 residues processed: 7 average time/residue: 0.9185 time to fit residues: 13.8682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 chunk 350 optimal weight: 0.9980 chunk 389 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN E 286 HIS E 354 ASN F 11 GLN G 155 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 HIS ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN I 286 HIS I 354 ASN I 412 ASN J 11 GLN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 286 HIS K 354 ASN ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN M 155 ASN M 286 HIS M 354 ASN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 HIS ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 36064 Z= 0.318 Angle : 0.664 6.347 48936 Z= 0.342 Chirality : 0.047 0.275 5136 Planarity : 0.005 0.060 6368 Dihedral : 10.081 168.913 4904 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.90 % Rotamer: Outliers : 5.04 % Allowed : 22.05 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -1.64 (0.12), residues: 4392 helix: -1.03 (0.12), residues: 1696 sheet: -0.05 (0.22), residues: 576 loop : -1.36 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 206 HIS 0.006 0.002 HIS O 286 PHE 0.016 0.002 PHE H 110 TYR 0.017 0.002 TYR E 21 ARG 0.010 0.001 ARG I 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 369 time to evaluate : 4.466 Fit side-chains outliers start: 183 outliers final: 86 residues processed: 500 average time/residue: 1.5471 time to fit residues: 926.4631 Evaluate side-chains 421 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 335 time to evaluate : 2.992 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 76 residues processed: 10 average time/residue: 0.8761 time to fit residues: 15.2432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 0.8980 chunk 295 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 394 optimal weight: 5.9990 chunk 417 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: