Starting phenix.real_space_refine on Thu Feb 22 19:49:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/02_2024/7yyo_14385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/02_2024/7yyo_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_14385/02_2024/7yyo_14385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/02_2024/7yyo_14385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/02_2024/7yyo_14385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yyo_14385/02_2024/7yyo_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 18.39, per 1000 atoms: 0.52 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: 12.67 Conformation dependent library (CDL) restraints added in 6.2 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: 7.30 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: 13.46 Time building geometry restraints manager: 13.83 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: 0.800 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: 0.020 Extract box with map and model: 5.700 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 92.230 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.340 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: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.850 ------------------------------------------------------------------------------- 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 : 4.584 Fit side-chains REVERT: A 434 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7129 (ttm-80) REVERT: B 63 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (mttp) REVERT: E 44 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4811 (tp30) REVERT: E 134 MET cc_start: 0.7454 (mmm) cc_final: 0.7007 (tpp) REVERT: G 434 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6867 (ttm-80) REVERT: H 63 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7479 (mttp) REVERT: I 134 MET cc_start: 0.7816 (mmm) cc_final: 0.7377 (tpp) REVERT: K 35 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8138 (p) REVERT: K 87 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: K 322 THR cc_start: 0.6989 (t) cc_final: 0.6663 (m) REVERT: K 434 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7002 (ttm-80) REVERT: L 63 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7439 (mmtp) REVERT: M 423 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (tmm160) REVERT: M 434 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7171 (ttm110) REVERT: N 63 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7010 (mttp) REVERT: O 231 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: O 294 ASP cc_start: 0.7144 (m-30) cc_final: 0.6899 (t0) outliers start: 466 outliers final: 55 residues processed: 814 average time/residue: 1.5805 time to fit residues: 1515.6094 Evaluate side-chains 412 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 344 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 238 THR Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 434 ARG Chi-restraints excluded: chain L residue 63 LYS Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 385 ILE Chi-restraints excluded: chain M residue 394 PHE Chi-restraints excluded: chain M residue 423 ARG Chi-restraints excluded: chain M residue 434 ARG Chi-restraints excluded: chain N residue 63 LYS Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 231 TYR Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 394 PHE Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 102 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.7980 chunk 327 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 338 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 401 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 G 378 HIS 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 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 K 378 HIS K 393 GLN K 401 HIS K 412 ASN L 11 GLN L 48 HIS L 101 GLN M 145 ASN M 155 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 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 296 HIS O 393 GLN O 401 HIS O 412 ASN P 33 GLN P 48 HIS P 101 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36064 Z= 0.220 Angle : 0.634 7.592 48936 Z= 0.329 Chirality : 0.045 0.314 5136 Planarity : 0.005 0.045 6368 Dihedral : 10.580 173.515 5032 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 3.63 % Allowed : 23.10 % Favored : 73.27 % 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: -2.29 (0.11), residues: 4392 helix: -1.78 (0.11), residues: 1680 sheet: -0.37 (0.21), residues: 560 loop : -1.54 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 206 HIS 0.012 0.002 HIS E 401 PHE 0.018 0.002 PHE E 356 TYR 0.018 0.002 TYR C 231 ARG 0.009 0.001 ARG M 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 541 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 409 time to evaluate : 3.888 Fit side-chains REVERT: A 83 PRO cc_start: 0.8033 (Cg_endo) cc_final: 0.7748 (Cg_exo) REVERT: A 138 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8524 (mmmt) REVERT: C 138 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8479 (mmmt) REVERT: E 134 MET cc_start: 0.7779 (mmm) cc_final: 0.7314 (tpp) REVERT: G 438 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6368 (mpt) REVERT: H 26 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8074 (p) REVERT: I 134 MET cc_start: 0.7875 (mmm) cc_final: 0.7559 (tpp) REVERT: I 194 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: I 211 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7534 (tm-30) REVERT: K 35 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8666 (p) REVERT: K 438 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6174 (mpt) REVERT: M 423 ARG cc_start: 0.7769 (tmm-80) cc_final: 0.7501 (ttp-170) REVERT: M 438 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6328 (mpt) REVERT: O 87 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6793 (tm-30) REVERT: O 295 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7294 (ttp-110) outliers start: 132 outliers final: 26 residues processed: 517 average time/residue: 1.5827 time to fit residues: 969.3747 Evaluate side-chains 363 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 328 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 438 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 295 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain P residue 45 LEU 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: 0.9980 chunk 326 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 424 optimal weight: 0.0270 chunk 350 optimal weight: 0.6980 chunk 389 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 315 optimal weight: 0.9980 overall best weight: 1.3440 ------------------------------------------------------------------------------- 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** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN 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 412 ASN 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 286 HIS H 11 GLN ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 ASN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 412 ASN J 11 GLN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 286 HIS K 354 ASN L 11 GLN M 286 HIS M 354 ASN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 HIS P 11 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 36064 Z= 0.181 Angle : 0.558 5.813 48936 Z= 0.287 Chirality : 0.042 0.236 5136 Planarity : 0.004 0.044 6368 Dihedral : 9.735 169.813 4906 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.83 % Rotamer: Outliers : 3.63 % Allowed : 22.52 % Favored : 73.84 % 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: -1.21 (0.12), residues: 4392 helix: -0.58 (0.12), residues: 1648 sheet: 0.19 (0.21), residues: 600 loop : -1.21 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 206 HIS 0.004 0.001 HIS O 375 PHE 0.015 0.002 PHE G 337 TYR 0.014 0.001 TYR I 231 ARG 0.009 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 520 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 388 time to evaluate : 4.079 Fit side-chains REVERT: A 295 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7687 (ttp-170) REVERT: E 35 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7748 (t) REVERT: E 37 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7071 (mm110) REVERT: E 134 MET cc_start: 0.8115 (mmm) cc_final: 0.7691 (tpp) REVERT: E 194 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: E 258 MET cc_start: 0.8899 (ttt) cc_final: 0.8644 (ttm) REVERT: F 30 ILE cc_start: 0.8665 (mm) cc_final: 0.8450 (mt) REVERT: H 26 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8128 (p) REVERT: I 134 MET cc_start: 0.8123 (mmm) cc_final: 0.7772 (tpp) REVERT: I 379 MET cc_start: 0.9055 (mmt) cc_final: 0.8823 (tpp) REVERT: K 35 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8616 (p) REVERT: K 120 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7739 (mptt) REVERT: O 87 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6701 (tm-30) REVERT: O 294 ASP cc_start: 0.7422 (m-30) cc_final: 0.7127 (t0) outliers start: 132 outliers final: 40 residues processed: 464 average time/residue: 1.5309 time to fit residues: 846.1288 Evaluate side-chains 376 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 329 time to evaluate : 4.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 0.0010 chunk 295 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 394 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 373 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 1.7390 ------------------------------------------------------------------------------- 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** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN I 286 HIS ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN M 155 ASN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN O 393 GLN P 11 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36064 Z= 0.207 Angle : 0.571 7.075 48936 Z= 0.292 Chirality : 0.043 0.159 5136 Planarity : 0.004 0.039 6368 Dihedral : 9.669 168.754 4906 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.21 % Favored : 96.61 % Rotamer: Outliers : 3.33 % Allowed : 22.71 % Favored : 73.95 % 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: -0.81 (0.12), residues: 4392 helix: -0.23 (0.12), residues: 1688 sheet: 0.32 (0.22), residues: 568 loop : -0.95 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 206 HIS 0.005 0.001 HIS C 296 PHE 0.016 0.002 PHE M 337 TYR 0.014 0.001 TYR I 231 ARG 0.010 0.000 ARG I 331 *********************** REFINEMENT MACRO_CYCLE 4 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 474 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 353 time to evaluate : 4.342 Fit side-chains REVERT: A 57 THR cc_start: 0.4049 (OUTLIER) cc_final: 0.3755 (p) REVERT: A 295 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7794 (ttp-170) REVERT: C 35 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8169 (t) REVERT: C 57 THR cc_start: 0.3918 (OUTLIER) cc_final: 0.3697 (p) REVERT: E 35 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8098 (t) REVERT: E 37 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7194 (mm110) REVERT: E 134 MET cc_start: 0.8124 (mmm) cc_final: 0.7758 (tpp) REVERT: E 151 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8157 (mtt180) REVERT: E 194 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: F 30 ILE cc_start: 0.8682 (mm) cc_final: 0.8451 (mt) REVERT: G 151 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8130 (mtt180) REVERT: H 29 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: I 134 MET cc_start: 0.8189 (mmm) cc_final: 0.7907 (tpp) REVERT: I 151 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8095 (mtt180) REVERT: I 211 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: I 379 MET cc_start: 0.9060 (mmt) cc_final: 0.8750 (tpp) REVERT: K 35 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8761 (t) REVERT: O 57 THR cc_start: 0.4442 (OUTLIER) cc_final: 0.4040 (p) REVERT: O 294 ASP cc_start: 0.7517 (m-30) cc_final: 0.7199 (t0) REVERT: O 295 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7963 (ttp-170) outliers start: 121 outliers final: 34 residues processed: 424 average time/residue: 1.6818 time to fit residues: 842.5575 Evaluate side-chains 377 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 329 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 295 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 374 optimal weight: 0.0370 chunk 105 optimal weight: 8.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN D 11 GLN D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN G 37 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN H 11 GLN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36064 Z= 0.224 Angle : 0.573 6.867 48936 Z= 0.293 Chirality : 0.043 0.160 5136 Planarity : 0.005 0.045 6368 Dihedral : 9.600 166.508 4906 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 3.85 % Allowed : 22.74 % Favored : 73.40 % 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: -0.55 (0.12), residues: 4392 helix: 0.03 (0.13), residues: 1688 sheet: 0.49 (0.22), residues: 568 loop : -0.86 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 206 HIS 0.005 0.001 HIS A 296 PHE 0.017 0.002 PHE C 394 TYR 0.017 0.001 TYR C 231 ARG 0.011 0.001 ARG G 331 *********************** REFINEMENT MACRO_CYCLE 5 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 476 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 336 time to evaluate : 4.036 Fit side-chains REVERT: A 151 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8033 (mtt180) REVERT: A 194 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: A 281 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8507 (ttp) REVERT: A 438 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6369 (mpt) REVERT: B 29 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: C 151 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8096 (mtt180) REVERT: C 281 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8493 (ttp) REVERT: E 35 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8313 (t) REVERT: E 37 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7285 (mm110) REVERT: E 151 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8154 (mtt180) REVERT: E 194 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: F 29 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: F 30 ILE cc_start: 0.8654 (mm) cc_final: 0.8445 (mt) REVERT: G 87 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6571 (tm-30) REVERT: G 151 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8137 (mtt180) REVERT: G 194 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: I 134 MET cc_start: 0.8074 (mmm) cc_final: 0.7797 (tpp) REVERT: I 151 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8150 (mtt180) REVERT: I 194 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: J 29 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: K 35 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (t) REVERT: K 151 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8090 (mtt180) REVERT: K 281 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8492 (ttp) REVERT: M 151 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8149 (mtt180) REVERT: O 151 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8020 (mtt180) REVERT: O 294 ASP cc_start: 0.7582 (m-30) cc_final: 0.7258 (t0) outliers start: 140 outliers final: 53 residues processed: 430 average time/residue: 1.6581 time to fit residues: 839.6608 Evaluate side-chains 386 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 312 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 11 GLN Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 417 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN J 11 GLN L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 393 GLN N 11 GLN P 11 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 36064 Z= 0.233 Angle : 0.578 7.755 48936 Z= 0.295 Chirality : 0.043 0.163 5136 Planarity : 0.005 0.047 6368 Dihedral : 9.545 163.814 4906 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.08 % Rotamer: Outliers : 3.88 % Allowed : 23.49 % Favored : 72.63 % 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: -0.38 (0.12), residues: 4392 helix: 0.23 (0.13), residues: 1656 sheet: 0.51 (0.21), residues: 608 loop : -0.81 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 206 HIS 0.005 0.001 HIS M 296 PHE 0.018 0.002 PHE G 337 TYR 0.018 0.001 TYR G 231 ARG 0.013 0.001 ARG G 331 *********************** REFINEMENT MACRO_CYCLE 6 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 468 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 327 time to evaluate : 3.947 Fit side-chains REVERT: A 151 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8088 (mtt180) REVERT: A 194 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 29 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: C 128 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: C 151 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8098 (mtt180) REVERT: E 35 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8403 (t) REVERT: E 37 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7333 (mm110) REVERT: E 151 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8136 (mtt180) REVERT: E 194 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: F 29 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: F 30 ILE cc_start: 0.8644 (mm) cc_final: 0.8435 (mt) REVERT: G 35 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.7956 (t) REVERT: G 87 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6540 (tm-30) REVERT: G 151 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8116 (mtt180) REVERT: G 194 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: H 29 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6896 (mt-10) REVERT: I 134 MET cc_start: 0.8103 (mmm) cc_final: 0.7891 (tpp) REVERT: I 151 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8100 (mtt180) REVERT: I 194 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: J 29 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: K 35 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8767 (t) REVERT: K 128 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: K 151 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8091 (mtt180) REVERT: M 151 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8158 (mtt180) REVERT: O 151 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8079 (mtt180) REVERT: O 294 ASP cc_start: 0.7680 (m-30) cc_final: 0.7232 (t0) outliers start: 141 outliers final: 55 residues processed: 424 average time/residue: 1.6427 time to fit residues: 823.7838 Evaluate side-chains 388 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 312 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 416 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS E 145 ASN F 11 GLN F 89 HIS H 11 GLN H 89 HIS ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 89 HIS L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 89 HIS ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 36064 Z= 0.461 Angle : 0.722 7.780 48936 Z= 0.369 Chirality : 0.050 0.219 5136 Planarity : 0.006 0.052 6368 Dihedral : 9.848 157.453 4906 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.17 % Rotamer: Outliers : 4.02 % Allowed : 23.87 % Favored : 72.11 % 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: -0.76 (0.12), residues: 4392 helix: -0.16 (0.12), residues: 1648 sheet: 0.43 (0.21), residues: 608 loop : -1.00 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 206 HIS 0.008 0.002 HIS C 296 PHE 0.025 0.003 PHE F 110 TYR 0.023 0.002 TYR K 231 ARG 0.011 0.001 ARG I 331 *********************** REFINEMENT MACRO_CYCLE 7 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 461 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 315 time to evaluate : 4.640 Fit side-chains REVERT: A 35 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7882 (m) REVERT: A 42 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7929 (mttm) REVERT: A 87 GLU cc_start: 0.6561 (tm-30) cc_final: 0.6220 (tm-30) REVERT: A 151 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8167 (mtt180) REVERT: B 29 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: C 151 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: E 35 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8651 (t) REVERT: E 37 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7512 (mm110) REVERT: E 151 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8062 (mtt180) REVERT: E 194 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: F 29 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: F 30 ILE cc_start: 0.8662 (mm) cc_final: 0.8414 (mt) REVERT: G 151 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8042 (mtt180) REVERT: H 29 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: I 151 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8142 (mtt180) REVERT: I 194 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: J 29 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: K 35 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8774 (t) REVERT: K 151 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8170 (mtt180) REVERT: M 151 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8205 (mtt180) REVERT: O 151 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8157 (mtt180) REVERT: O 294 ASP cc_start: 0.7686 (m-30) cc_final: 0.7379 (t0) REVERT: P 11 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7916 (tt0) outliers start: 146 outliers final: 67 residues processed: 425 average time/residue: 1.7164 time to fit residues: 863.3422 Evaluate side-chains 392 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 306 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 11 GLN Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 11 GLN Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 283 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN H 11 GLN J 11 GLN K 393 GLN L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 378 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36064 Z= 0.187 Angle : 0.564 9.184 48936 Z= 0.289 Chirality : 0.042 0.139 5136 Planarity : 0.005 0.057 6368 Dihedral : 9.322 154.368 4906 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.82 % Favored : 96.99 % Rotamer: Outliers : 2.84 % Allowed : 24.61 % Favored : 72.55 % 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: -0.21 (0.12), residues: 4392 helix: 0.37 (0.13), residues: 1640 sheet: 0.69 (0.21), residues: 608 loop : -0.74 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 206 HIS 0.004 0.001 HIS O 296 PHE 0.017 0.001 PHE I 337 TYR 0.014 0.001 TYR A 231 ARG 0.016 0.001 ARG G 331 *********************** REFINEMENT MACRO_CYCLE 8 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 407 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 304 time to evaluate : 3.971 Fit side-chains REVERT: A 42 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7901 (mttm) REVERT: A 151 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8083 (mtt180) REVERT: A 281 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8515 (ttp) REVERT: C 151 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8093 (mtt180) REVERT: D 29 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: E 35 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8614 (t) REVERT: E 37 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7414 (mm110) REVERT: E 151 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8130 (mtt180) REVERT: E 194 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: F 29 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: G 87 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6523 (tm-30) REVERT: G 151 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8127 (mtt180) REVERT: I 194 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: I 431 LYS cc_start: 0.7530 (tptt) cc_final: 0.7318 (ttpp) REVERT: J 29 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6914 (mt-10) REVERT: K 35 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (t) REVERT: K 83 PRO cc_start: 0.8361 (Cg_endo) cc_final: 0.8116 (Cg_exo) REVERT: K 151 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8092 (mtt180) REVERT: K 281 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8505 (ttp) REVERT: M 151 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8152 (mtt180) REVERT: O 151 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8096 (mtt180) REVERT: O 294 ASP cc_start: 0.7678 (m-30) cc_final: 0.7387 (t0) outliers start: 103 outliers final: 50 residues processed: 383 average time/residue: 1.6938 time to fit residues: 762.3985 Evaluate side-chains 364 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 297 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 388 optimal weight: 0.2980 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 386 optimal weight: 0.7980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN H 11 GLN J 11 GLN L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 378 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36064 Z= 0.243 Angle : 0.590 9.563 48936 Z= 0.301 Chirality : 0.044 0.172 5136 Planarity : 0.005 0.057 6368 Dihedral : 9.039 154.535 4906 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 2.75 % Allowed : 24.89 % Favored : 72.36 % 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: -0.24 (0.12), residues: 4392 helix: 0.36 (0.13), residues: 1656 sheet: 0.65 (0.21), residues: 608 loop : -0.76 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 206 HIS 0.005 0.001 HIS M 296 PHE 0.018 0.002 PHE G 337 TYR 0.018 0.001 TYR E 231 ARG 0.017 0.001 ARG G 331 *********************** REFINEMENT MACRO_CYCLE 9 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 417 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 317 time to evaluate : 4.092 Fit side-chains REVERT: A 42 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (mttm) REVERT: A 151 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8092 (mtt180) REVERT: C 83 PRO cc_start: 0.8271 (Cg_endo) cc_final: 0.8014 (Cg_exo) REVERT: C 151 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8097 (mtt180) REVERT: D 29 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: E 35 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8602 (t) REVERT: E 37 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7458 (mm110) REVERT: E 151 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8134 (mtt180) REVERT: E 194 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: F 29 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: G 151 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8117 (mtt180) REVERT: I 151 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8109 (mtt180) REVERT: I 194 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: J 29 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: K 35 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8687 (t) REVERT: K 83 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8111 (Cg_exo) REVERT: K 151 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8099 (mtt180) REVERT: M 83 PRO cc_start: 0.8288 (Cg_endo) cc_final: 0.7998 (Cg_exo) REVERT: M 151 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8156 (mtt180) REVERT: N 29 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: O 151 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8081 (mtt180) REVERT: O 294 ASP cc_start: 0.7684 (m-30) cc_final: 0.7383 (t0) REVERT: O 428 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7172 (pm20) outliers start: 100 outliers final: 57 residues processed: 394 average time/residue: 1.7236 time to fit residues: 798.5989 Evaluate side-chains 383 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 308 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 428 GLU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 9.9990 chunk 410 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 396 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 11 GLN H 11 GLN J 11 GLN L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 378 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36064 Z= 0.221 Angle : 0.583 9.981 48936 Z= 0.297 Chirality : 0.043 0.158 5136 Planarity : 0.005 0.054 6368 Dihedral : 8.642 154.712 4906 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.39 % Favored : 96.43 % Rotamer: Outliers : 2.56 % Allowed : 25.00 % Favored : 72.44 % 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: -0.11 (0.12), residues: 4392 helix: 0.50 (0.13), residues: 1656 sheet: 0.72 (0.21), residues: 608 loop : -0.71 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 206 HIS 0.004 0.001 HIS G 296 PHE 0.017 0.001 PHE G 337 TYR 0.020 0.001 TYR G 231 ARG 0.016 0.001 ARG G 331 ********************** REFINEMENT MACRO_CYCLE 10 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 402 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 309 time to evaluate : 3.997 Fit side-chains REVERT: A 42 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7918 (mttm) REVERT: A 151 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8087 (mtt180) REVERT: C 83 PRO cc_start: 0.8257 (Cg_endo) cc_final: 0.7998 (Cg_exo) REVERT: C 151 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8093 (mtt180) REVERT: D 29 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: E 35 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8599 (t) REVERT: E 37 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7444 (mm110) REVERT: E 151 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8158 (mtt180) REVERT: E 194 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: F 29 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: G 151 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8131 (mtt180) REVERT: I 151 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8098 (mtt180) REVERT: I 194 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: J 29 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: K 35 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8701 (t) REVERT: K 83 PRO cc_start: 0.8357 (Cg_endo) cc_final: 0.8124 (Cg_exo) REVERT: K 151 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8092 (mtt180) REVERT: M 83 PRO cc_start: 0.8264 (Cg_endo) cc_final: 0.7959 (Cg_exo) REVERT: M 151 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8151 (mtt180) REVERT: N 29 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: O 151 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8074 (mtt180) REVERT: O 294 ASP cc_start: 0.7692 (m-30) cc_final: 0.7278 (t0) outliers start: 93 outliers final: 62 residues processed: 386 average time/residue: 1.7456 time to fit residues: 797.1677 Evaluate side-chains 385 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 306 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 11 GLN Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 11 GLN Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 8.9990 chunk 365 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 50 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 352 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN J 11 GLN L 11 GLN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 378 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117543 restraints weight = 45337.548| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.57 r_work: 0.3361 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.211 36064 Z= 0.415 Angle : 0.983 59.150 48936 Z= 0.568 Chirality : 0.050 0.786 5136 Planarity : 0.006 0.225 6368 Dihedral : 8.669 154.732 4906 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 2.45 % Allowed : 25.17 % Favored : 72.38 % Cbeta Deviations : 0.15 % 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: -0.12 (0.12), residues: 4392 helix: 0.49 (0.13), residues: 1656 sheet: 0.72 (0.21), residues: 608 loop : -0.73 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 206 HIS 0.004 0.001 HIS M 296 PHE 0.017 0.002 PHE G 337 TYR 0.017 0.001 TYR G 231 ARG 0.013 0.001 ARG I 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13085.59 seconds wall clock time: 234 minutes 26.27 seconds (14066.27 seconds total)