Starting phenix.real_space_refine on Sat Mar 23 22:03:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/03_2024/7k3w_22658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/03_2024/7k3w_22658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/03_2024/7k3w_22658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/03_2024/7k3w_22658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/03_2024/7k3w_22658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/03_2024/7k3w_22658.pdb" } resolution = 1.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 Zn 270 6.06 5 S 192 5.16 5 Na 112 4.78 5 C 22680 2.51 5 N 6264 2.21 5 O 9568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ASP 126": "OD1" <-> "OD2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 84": "OD1" <-> "OD2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 107": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H ASP 126": "OD1" <-> "OD2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 171": "OD1" <-> "OD2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I ASP 126": "OD1" <-> "OD2" Residue "I PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 150": "OD1" <-> "OD2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 171": "OD1" <-> "OD2" Residue "J ASP 15": "OD1" <-> "OD2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 84": "OD1" <-> "OD2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J ASP 126": "OD1" <-> "OD2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 171": "OD1" <-> "OD2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 84": "OD1" <-> "OD2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K ASP 126": "OD1" <-> "OD2" Residue "K PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "K ASP 150": "OD1" <-> "OD2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 171": "OD1" <-> "OD2" Residue "L ASP 15": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L ASP 150": "OD1" <-> "OD2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L GLU 167": "OE1" <-> "OE2" Residue "L TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 171": "OD1" <-> "OD2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 62": "OE1" <-> "OE2" Residue "M PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ASP 126": "OD1" <-> "OD2" Residue "M PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 150": "OD1" <-> "OD2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "N ASP 15": "OD1" <-> "OD2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 61": "OE1" <-> "OE2" Residue "N GLU 61": "OE1" <-> "OE2" Residue "N GLU 61": "OE1" <-> "OE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N GLU 94": "OE1" <-> "OE2" Residue "N GLU 94": "OE1" <-> "OE2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "N GLU 147": "OE1" <-> "OE2" Residue "N ASP 150": "OD1" <-> "OD2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 171": "OD1" <-> "OD2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O GLU 17": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 171": "OD1" <-> "OD2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 84": "OD1" <-> "OD2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "P PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 171": "OD1" <-> "OD2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 84": "OD1" <-> "OD2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "Q ASP 150": "OD1" <-> "OD2" Residue "Q GLU 162": "OE1" <-> "OE2" Residue "Q GLU 162": "OE1" <-> "OE2" Residue "Q GLU 162": "OE1" <-> "OE2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 171": "OD1" <-> "OD2" Residue "R ASP 15": "OD1" <-> "OD2" Residue "R GLU 17": "OE1" <-> "OE2" Residue "R GLU 27": "OE1" <-> "OE2" Residue "R TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 84": "OD1" <-> "OD2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R GLU 94": "OE1" <-> "OE2" Residue "R GLU 94": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R ASP 126": "OD1" <-> "OD2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 134": "OE1" <-> "OE2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 147": "OE1" <-> "OE2" Residue "R ASP 150": "OD1" <-> "OD2" Residue "R GLU 162": "OE1" <-> "OE2" Residue "R GLU 162": "OE1" <-> "OE2" Residue "R GLU 162": "OE1" <-> "OE2" Residue "R GLU 167": "OE1" <-> "OE2" Residue "R TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 171": "OD1" <-> "OD2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "S PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "S ASP 92": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 107": "OE1" <-> "OE2" Residue "S ASP 126": "OD1" <-> "OD2" Residue "S PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 134": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S ASP 150": "OD1" <-> "OD2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S GLU 167": "OE1" <-> "OE2" Residue "S TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 171": "OD1" <-> "OD2" Residue "T ASP 15": "OD1" <-> "OD2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T GLU 62": "OE1" <-> "OE2" Residue "T PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ASP 126": "OD1" <-> "OD2" Residue "T PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 134": "OE1" <-> "OE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T GLU 147": "OE1" <-> "OE2" Residue "T ASP 150": "OD1" <-> "OD2" Residue "T GLU 162": "OE1" <-> "OE2" Residue "T GLU 162": "OE1" <-> "OE2" Residue "T GLU 162": "OE1" <-> "OE2" Residue "T GLU 167": "OE1" <-> "OE2" Residue "T TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 171": "OD1" <-> "OD2" Residue "U ASP 15": "OD1" <-> "OD2" Residue "U GLU 17": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 84": "OD1" <-> "OD2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U ASP 126": "OD1" <-> "OD2" Residue "U PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U GLU 147": "OE1" <-> "OE2" Residue "U ASP 150": "OD1" <-> "OD2" Residue "U GLU 162": "OE1" <-> "OE2" Residue "U GLU 162": "OE1" <-> "OE2" Residue "U GLU 162": "OE1" <-> "OE2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 171": "OD1" <-> "OD2" Residue "V ASP 15": "OD1" <-> "OD2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 27": "OE1" <-> "OE2" Residue "V TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 84": "OD1" <-> "OD2" Residue "V ASP 92": "OD1" <-> "OD2" Residue "V GLU 94": "OE1" <-> "OE2" Residue "V GLU 94": "OE1" <-> "OE2" Residue "V GLU 107": "OE1" <-> "OE2" Residue "V ASP 126": "OD1" <-> "OD2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "V GLU 147": "OE1" <-> "OE2" Residue "V ASP 150": "OD1" <-> "OD2" Residue "V GLU 162": "OE1" <-> "OE2" Residue "V GLU 162": "OE1" <-> "OE2" Residue "V GLU 162": "OE1" <-> "OE2" Residue "V GLU 167": "OE1" <-> "OE2" Residue "V TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 171": "OD1" <-> "OD2" Residue "W ASP 15": "OD1" <-> "OD2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 84": "OD1" <-> "OD2" Residue "W ASP 92": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 107": "OE1" <-> "OE2" Residue "W ASP 126": "OD1" <-> "OD2" Residue "W PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ASP 150": "OD1" <-> "OD2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "W TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 171": "OD1" <-> "OD2" Residue "X ASP 15": "OD1" <-> "OD2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X GLU 27": "OE1" <-> "OE2" Residue "X TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 84": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 107": "OE1" <-> "OE2" Residue "X ASP 126": "OD1" <-> "OD2" Residue "X PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 147": "OE1" <-> "OE2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X GLU 162": "OE1" <-> "OE2" Residue "X GLU 162": "OE1" <-> "OE2" Residue "X GLU 162": "OE1" <-> "OE2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 171": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39086 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "B" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "C" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "D" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "E" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "F" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "G" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "H" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "I" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "J" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "K" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "L" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "M" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "N" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "O" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "P" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "Q" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "R" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "S" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "T" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "U" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "V" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "W" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "X" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "M" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "Q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "V" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "F" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "G" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "H" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "L" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "M" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "N" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "O" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "P" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "S" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "T" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "U" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "V" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "W" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Time building chain proxies: 60.51, per 1000 atoms: 1.55 Number of scatterers: 39086 At special positions: 0 Unit cell: (136.042, 136.042, 136.042, 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) Zn 270 29.99 S 192 16.00 Na 112 11.00 O 9568 8.00 N 6264 7.00 C 22680 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=0, symmetry=0 Time building additional restraints: 17.77 Conformation dependent library (CDL) restraints added in 21.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 208 " pdb="ZN ZN F 208 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 206 " pdb="ZN ZN G 206 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 207 " pdb="ZN ZN J 207 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 206 " pdb="ZN ZN K 206 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 206 " pdb="ZN ZN M 206 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 207 " pdb="ZN ZN N 207 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 206 " pdb="ZN ZN O 206 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 207 " pdb="ZN ZN P 207 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 211 " pdb="ZN ZN Q 211 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 211 " pdb="ZN ZN R 211 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 209 " pdb="ZN ZN S 209 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 211 " pdb="ZN ZN T 211 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 209 " pdb="ZN ZN U 209 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 211 " pdb="ZN ZN V 211 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 209 " pdb="ZN ZN W 209 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 209 " pdb="ZN ZN X 209 " - pdb=" ND1 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 2688 hydrogen bonds defined for protein. 8064 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: 12.42 Time building geometry restraints manager: 18.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12072 1.34 - 1.46: 7632 1.46 - 1.58: 16752 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 36744 Sorted by residual: bond pdb=" CB PHE L 41 " pdb=" CG PHE L 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE N 41 " pdb=" CG PHE N 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE R 41 " pdb=" CG PHE R 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE F 41 " pdb=" CG PHE F 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE W 41 " pdb=" CG PHE W 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 ... (remaining 36739 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.96: 360 105.96 - 112.95: 19944 112.95 - 119.93: 13584 119.93 - 126.91: 15168 126.91 - 133.89: 408 Bond angle restraints: 49464 Sorted by residual: angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 ... (remaining 49459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 22488 34.88 - 69.77: 432 69.77 - 104.65: 72 104.65 - 139.53: 24 139.53 - 174.42: 96 Dihedral angle restraints: 23112 sinusoidal: 10032 harmonic: 13080 Sorted by residual: dihedral pdb=" CB BGLU V 162 " pdb=" CG BGLU V 162 " pdb=" CD BGLU V 162 " pdb=" OE1BGLU V 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.42 -174.42 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU L 162 " pdb=" CG BGLU L 162 " pdb=" CD BGLU L 162 " pdb=" OE1BGLU L 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.42 -174.42 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU W 162 " pdb=" CG BGLU W 162 " pdb=" CD BGLU W 162 " pdb=" OE1BGLU W 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.42 -174.42 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 23109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2688 0.026 - 0.052: 1656 0.052 - 0.078: 528 0.078 - 0.104: 216 0.104 - 0.130: 216 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA TYR V 39 " pdb=" N TYR V 39 " pdb=" C TYR V 39 " pdb=" CB TYR V 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA TYR G 39 " pdb=" N TYR G 39 " pdb=" C TYR G 39 " pdb=" CB TYR G 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA TYR I 39 " pdb=" N TYR I 39 " pdb=" C TYR I 39 " pdb=" CB TYR I 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 5301 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU C 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU C 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU B 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU B 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU S 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU S 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU S 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER S 95 " -0.011 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 720 2.53 - 3.12: 32688 3.12 - 3.71: 74220 3.71 - 4.31: 111552 4.31 - 4.90: 166356 Nonbonded interactions: 385536 Sorted by model distance: nonbonded pdb=" OE1 GLN O 112 " pdb="NA NA O 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN M 112 " pdb="NA NA M 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN H 112 " pdb="NA NA H 216 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN E 112 " pdb="NA NA E 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN K 112 " pdb="NA NA K 215 " model vdw 1.934 2.470 ... (remaining 385531 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' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'B' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'C' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'E' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'G' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'H' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'I' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'J' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'K' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'L' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'M' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'N' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'O' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'P' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'Q' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'R' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'S' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'T' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'U' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'V' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'W' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'X' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) } 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=0.25 max=1.00 mean=0.95 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: 2.030 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: 0.030 Extract box with map and model: 10.530 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 167.180 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.005 0.027 36744 Z= 0.287 Angle : 0.757 6.786 49464 Z= 0.422 Chirality : 0.042 0.130 5304 Planarity : 0.004 0.033 6408 Dihedral : 20.576 174.417 14376 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.13), residues: 4080 helix: 2.52 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP V 93 HIS 0.008 0.002 HIS M 57 PHE 0.023 0.004 PHE G 41 TYR 0.026 0.004 TYR R 39 ARG 0.003 0.001 ARG O 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.5736 time to fit residues: 781.2043 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.0358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 36744 Z= 0.180 Angle : 0.631 6.785 49464 Z= 0.342 Chirality : 0.038 0.139 5304 Planarity : 0.004 0.031 6408 Dihedral : 4.551 17.902 4560 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.13), residues: 4080 helix: 3.06 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 93 HIS 0.005 0.001 HIS P 57 PHE 0.016 0.003 PHE I 41 TYR 0.021 0.003 TYR U 39 ARG 0.002 0.001 ARG W 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.5314 time to fit residues: 763.1373 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 8.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.0372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 36744 Z= 0.187 Angle : 0.632 6.823 49464 Z= 0.344 Chirality : 0.038 0.141 5304 Planarity : 0.004 0.031 6408 Dihedral : 4.531 17.898 4560 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.13), residues: 4080 helix: 3.11 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.15 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 93 HIS 0.004 0.001 HIS L 57 PHE 0.018 0.003 PHE X 41 TYR 0.022 0.003 TYR A 39 ARG 0.002 0.001 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.631 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.6048 time to fit residues: 839.3274 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 30.0000 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 0.8980 chunk 194 optimal weight: 30.0000 chunk 353 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 36744 Z= 0.152 Angle : 0.581 6.588 49464 Z= 0.312 Chirality : 0.036 0.141 5304 Planarity : 0.004 0.029 6408 Dihedral : 4.467 18.611 4560 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.50 (0.13), residues: 4080 helix: 3.37 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.24 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 93 HIS 0.003 0.001 HIS A 128 PHE 0.015 0.003 PHE D 41 TYR 0.020 0.002 TYR W 39 ARG 0.001 0.000 ARG Q 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.410 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.5172 time to fit residues: 756.0806 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 336 optimal weight: 0.0970 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 36744 Z= 0.120 Angle : 0.507 6.047 49464 Z= 0.270 Chirality : 0.034 0.135 5304 Planarity : 0.003 0.026 6408 Dihedral : 4.314 19.173 4560 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.06 (0.13), residues: 4080 helix: 3.77 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.41 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 93 HIS 0.003 0.001 HIS M 128 PHE 0.011 0.002 PHE X 41 TYR 0.017 0.002 TYR E 39 ARG 0.001 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.770 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.5820 time to fit residues: 918.1372 Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.0440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 36744 Z= 0.219 Angle : 0.659 6.720 49464 Z= 0.361 Chirality : 0.040 0.139 5304 Planarity : 0.005 0.033 6408 Dihedral : 4.543 18.096 4560 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.13), residues: 4080 helix: 3.11 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.32 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 93 HIS 0.005 0.002 HIS P 57 PHE 0.021 0.003 PHE C 41 TYR 0.024 0.003 TYR C 39 ARG 0.003 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.659 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.6300 time to fit residues: 850.5986 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 393 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.0416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 36744 Z= 0.238 Angle : 0.685 6.851 49464 Z= 0.375 Chirality : 0.040 0.143 5304 Planarity : 0.005 0.035 6408 Dihedral : 4.574 17.877 4560 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.13), residues: 4080 helix: 2.90 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.26 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.006 0.002 HIS J 57 PHE 0.021 0.004 PHE U 41 TYR 0.024 0.003 TYR B 39 ARG 0.003 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.634 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.6119 time to fit residues: 842.3041 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 76 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.0496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 36744 Z= 0.176 Angle : 0.611 6.717 49464 Z= 0.332 Chirality : 0.038 0.140 5304 Planarity : 0.004 0.030 6408 Dihedral : 4.518 18.122 4560 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.13), residues: 4080 helix: 3.17 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.29 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 93 HIS 0.004 0.001 HIS C 57 PHE 0.017 0.003 PHE X 41 TYR 0.022 0.003 TYR V 39 ARG 0.002 0.001 ARG K 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.262 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.6130 time to fit residues: 840.5397 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 331 optimal weight: 10.0000 chunk 346 optimal weight: 30.0000 chunk 365 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.0432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 36744 Z= 0.258 Angle : 0.708 6.912 49464 Z= 0.388 Chirality : 0.041 0.143 5304 Planarity : 0.005 0.040 6408 Dihedral : 4.588 17.616 4560 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.13), residues: 4080 helix: 2.83 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.22 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 93 HIS 0.007 0.002 HIS H 57 PHE 0.023 0.004 PHE A 41 TYR 0.026 0.003 TYR I 39 ARG 0.003 0.001 ARG U 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.5955 time to fit residues: 832.2008 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 4.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS P 112 GLN Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 36744 Z= 0.148 Angle : 0.568 6.508 49464 Z= 0.307 Chirality : 0.036 0.140 5304 Planarity : 0.003 0.028 6408 Dihedral : 4.488 18.268 4560 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.13), residues: 4080 helix: 3.37 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.32 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 93 HIS 0.004 0.001 HIS E 57 PHE 0.015 0.002 PHE U 41 TYR 0.020 0.002 TYR U 39 ARG 0.001 0.000 ARG A 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.5871 time to fit residues: 827.5486 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 7.9990 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 332 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.213252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146216 restraints weight = 49203.334| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 0.67 r_work: 0.3595 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.3260 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 36744 Z= 0.225 Angle : 0.669 6.852 49464 Z= 0.366 Chirality : 0.040 0.144 5304 Planarity : 0.005 0.033 6408 Dihedral : 4.551 17.885 4560 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.13), residues: 4080 helix: 3.00 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.27 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 93 HIS 0.005 0.002 HIS U 57 PHE 0.020 0.003 PHE A 41 TYR 0.025 0.003 TYR U 39 ARG 0.003 0.001 ARG P 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20837.51 seconds wall clock time: 367 minutes 48.41 seconds (22068.41 seconds total)