Starting phenix.real_space_refine on Sat Mar 23 18:10:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/03_2024/7k3v_22657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/03_2024/7k3v_22657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/03_2024/7k3v_22657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/03_2024/7k3v_22657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/03_2024/7k3v_22657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3v_22657/03_2024/7k3v_22657.pdb" } resolution = 1.34 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= 0.007 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 254 6.06 5 S 192 5.16 5 Na 80 4.78 5 C 22248 2.51 5 N 6096 2.21 5 O 9536 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D ASP 126": "OD1" <-> "OD2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "F PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "G PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 84": "OD1" <-> "OD2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ASP 126": "OD1" <-> "OD2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I ASP 126": "OD1" <-> "OD2" Residue "I PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "J PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 84": "OD1" <-> "OD2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J ASP 126": "OD1" <-> "OD2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 84": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K ASP 126": "OD1" <-> "OD2" Residue "K PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "M PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 126": "OD1" <-> "OD2" Residue "M PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "N PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N GLU 94": "OE1" <-> "OE2" Residue "N GLU 94": "OE1" <-> "OE2" Residue "N GLU 116": "OE1" <-> "OE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "O PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 84": "OD1" <-> "OD2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "P PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 84": "OD1" <-> "OD2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 84": "OD1" <-> "OD2" Residue "R GLU 94": "OE1" <-> "OE2" Residue "R GLU 94": "OE1" <-> "OE2" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R ASP 126": "OD1" <-> "OD2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "S PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S ASP 126": "OD1" <-> "OD2" Residue "S PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "T PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T GLU 116": "OE1" <-> "OE2" Residue "T ASP 126": "OD1" <-> "OD2" Residue "T PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "U PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 84": "OD1" <-> "OD2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "U ASP 126": "OD1" <-> "OD2" Residue "U PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 84": "OD1" <-> "OD2" Residue "V GLU 94": "OE1" <-> "OE2" Residue "V GLU 94": "OE1" <-> "OE2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "V ASP 126": "OD1" <-> "OD2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "W PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 84": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ASP 126": "OD1" <-> "OD2" Residue "W PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 134": "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 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 ASP 44": "OD1" <-> "OD2" 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 GLU 67": "OE1" <-> "OE2" Residue "X PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 84": "OD1" <-> "OD2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X ASP 126": "OD1" <-> "OD2" Residue "X PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 134": "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 ASP 171": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38406 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "B" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "C" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "D" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "E" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "F" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "G" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "H" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "I" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "J" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "K" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "L" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "M" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "N" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "O" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "P" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "Q" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "R" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "S" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "T" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "U" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "V" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "W" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "X" Number of atoms: 1475 Number of conformers: 3 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: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "G" 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: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "K" 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: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "M" 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: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "O" 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: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "Q" 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: "R" 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: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "T" 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: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "V" 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: "W" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} 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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} 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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "P" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} 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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 46.79, per 1000 atoms: 1.22 Number of scatterers: 38406 At special positions: 0 Unit cell: (137.2, 137.2, 137.2, 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 254 29.99 S 192 16.00 Na 80 11.00 O 9536 8.00 N 6096 7.00 C 22248 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: 16.40 Conformation dependent library (CDL) restraints added in 16.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - 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 203 " pdb="ZN ZN G 203 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 208 " pdb="ZN ZN J 208 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 204 " pdb="ZN ZN M 204 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 208 " pdb="ZN ZN N 208 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 204 " pdb="ZN ZN O 204 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 208 " pdb="ZN ZN P 208 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 209 " pdb="ZN ZN Q 209 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 209 " pdb="ZN ZN R 209 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 208 " pdb="ZN ZN S 208 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 209 " pdb="ZN ZN T 209 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 208 " pdb="ZN ZN U 208 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 209 " pdb="ZN ZN V 209 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 208 " pdb="ZN ZN W 208 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 208 " pdb="ZN ZN X 208 " - 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: 8496 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: 2.81 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: 12.87 Time building geometry restraints manager: 17.45 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: 11952 1.34 - 1.46: 6288 1.46 - 1.58: 17592 1.58 - 1.70: 0 1.70 - 1.81: 288 Bond restraints: 36120 Sorted by residual: bond pdb=" CB ARG N 79 " pdb=" CG ARG N 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG Q 79 " pdb=" CG ARG Q 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG P 79 " pdb=" CG ARG P 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG S 79 " pdb=" CG ARG S 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CB ARG O 79 " pdb=" CG ARG O 79 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 ... (remaining 36115 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.73: 384 105.73 - 112.77: 19272 112.77 - 119.81: 12816 119.81 - 126.85: 15792 126.85 - 133.89: 408 Bond angle restraints: 48672 Sorted by residual: angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP X 93 " pdb=" N GLU X 94 " pdb=" CA GLU X 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 ... (remaining 48667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 21816 35.98 - 71.96: 456 71.96 - 107.94: 24 107.94 - 143.92: 24 143.92 - 179.90: 96 Dihedral angle restraints: 22416 sinusoidal: 9576 harmonic: 12840 Sorted by residual: dihedral pdb=" CB CGLU C 162 " pdb=" CG CGLU C 162 " pdb=" CD CGLU C 162 " pdb=" OE1CGLU C 162 " ideal model delta sinusoidal sigma weight residual 0.00 179.90 -179.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CGLU H 162 " pdb=" CG CGLU H 162 " pdb=" CD CGLU H 162 " pdb=" OE1CGLU H 162 " ideal model delta sinusoidal sigma weight residual 0.00 179.90 -179.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CGLU I 162 " pdb=" CG CGLU I 162 " pdb=" CD CGLU I 162 " pdb=" OE1CGLU I 162 " ideal model delta sinusoidal sigma weight residual 0.00 179.90 -179.90 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 22413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3240 0.033 - 0.065: 1296 0.065 - 0.098: 480 0.098 - 0.131: 120 0.131 - 0.164: 48 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CG LEU K 72 " pdb=" CB LEU K 72 " pdb=" CD1 LEU K 72 " pdb=" CD2 LEU K 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CG LEU J 72 " pdb=" CB LEU J 72 " pdb=" CD1 LEU J 72 " pdb=" CD2 LEU J 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CG LEU W 72 " pdb=" CB LEU W 72 " pdb=" CD1 LEU W 72 " pdb=" CD2 LEU W 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 5181 not shown) Planarity restraints: 6360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU S 94 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU S 94 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU S 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER S 95 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 94 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU N 94 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU N 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER N 95 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 94 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLU K 94 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU K 94 " 0.012 2.00e-02 2.50e+03 pdb=" N SER K 95 " 0.012 2.00e-02 2.50e+03 ... (remaining 6357 not shown) Histogram of nonbonded interaction distances: 0.21 - 1.15: 84 1.15 - 2.09: 140 2.09 - 3.02: 26276 3.02 - 3.96: 124464 3.96 - 4.90: 223228 Warning: very small nonbonded interaction distances. Nonbonded interactions: 374192 Sorted by model distance: nonbonded pdb=" O HOH O 318 " pdb=" O HOH O 338 " model vdw 0.211 2.440 nonbonded pdb=" O HOH X 318 " pdb=" O HOH X 338 " model vdw 0.211 2.440 nonbonded pdb=" O HOH E 318 " pdb=" O HOH E 338 " model vdw 0.211 2.440 nonbonded pdb=" O HOH G 318 " pdb=" O HOH G 339 " model vdw 0.211 2.440 nonbonded pdb=" O HOH C 318 " pdb=" O HOH C 339 " model vdw 0.211 2.440 ... (remaining 374187 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) 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 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 204 or resid 211 through 212)) } 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=0.33 max=1.00 mean=0.96 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: 6.270 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: 19.290 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 143.650 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 0.030 36120 Z= 0.315 Angle : 0.786 7.609 48672 Z= 0.442 Chirality : 0.044 0.164 5184 Planarity : 0.004 0.020 6360 Dihedral : 21.253 179.899 13920 Min Nonbonded Distance : 0.211 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 3.60 (0.13), residues: 4080 helix: 2.75 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.89 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP R 93 HIS 0.005 0.002 HIS G 118 PHE 0.027 0.004 PHE V 41 TYR 0.028 0.004 TYR B 39 ARG 0.002 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 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.8191 time to fit residues: 1127.3872 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.830 ------------------------------------------------------------------------------- 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: 0.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 0.0670 chunk 370 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 105 HIS O 105 HIS P 105 HIS Q 105 HIS R 105 HIS S 105 HIS T 105 HIS U 105 HIS V 105 HIS W 105 HIS X 105 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 36120 Z= 0.169 Angle : 0.606 6.605 48672 Z= 0.334 Chirality : 0.037 0.148 5184 Planarity : 0.004 0.022 6360 Dihedral : 4.519 20.231 4536 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 4.39 (0.13), residues: 4080 helix: 3.33 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.02 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 93 HIS 0.003 0.001 HIS O 128 PHE 0.019 0.003 PHE B 41 TYR 0.021 0.003 TYR V 39 ARG 0.005 0.001 ARG M 63 *********************** 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 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 1.8272 time to fit residues: 1082.0028 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.959 ------------------------------------------------------------------------------- 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: 9.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 0.0060 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 36120 Z= 0.165 Angle : 0.603 6.493 48672 Z= 0.332 Chirality : 0.037 0.146 5184 Planarity : 0.003 0.022 6360 Dihedral : 4.496 20.241 4536 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 4.47 (0.13), residues: 4080 helix: 3.40 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.00 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 93 HIS 0.003 0.001 HIS R 128 PHE 0.020 0.003 PHE R 41 TYR 0.022 0.003 TYR S 39 ARG 0.002 0.001 ARG D 63 *********************** 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 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 1.8179 time to fit residues: 1028.9882 Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.294 ------------------------------------------------------------------------------- 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: 9.9990 chunk 279 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 394 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 60 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 60 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 36120 Z= 0.188 Angle : 0.638 6.707 48672 Z= 0.352 Chirality : 0.039 0.148 5184 Planarity : 0.004 0.025 6360 Dihedral : 4.523 20.086 4536 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 4.33 (0.13), residues: 4080 helix: 3.29 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.99 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP J 93 HIS 0.003 0.001 HIS B 128 PHE 0.022 0.003 PHE D 41 TYR 0.024 0.003 TYR V 39 ARG 0.002 0.000 ARG I 79 *********************** 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 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.9245 time to fit residues: 1193.8578 Evaluate side-chains 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.074 ------------------------------------------------------------------------------- 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: 10.0000 chunk 223 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 105 HIS B 57 HIS B 105 HIS C 57 HIS C 105 HIS D 57 HIS D 105 HIS E 57 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 105 HIS H 57 HIS H 105 HIS I 57 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 105 HIS L 57 HIS L 105 HIS M 57 HIS M 105 HIS N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 57 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 57 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36120 Z= 0.239 Angle : 0.703 7.177 48672 Z= 0.387 Chirality : 0.041 0.156 5184 Planarity : 0.004 0.029 6360 Dihedral : 4.568 19.619 4536 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 4.11 (0.13), residues: 4080 helix: 3.12 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.01 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 93 HIS 0.004 0.001 HIS L 118 PHE 0.024 0.004 PHE L 41 TYR 0.026 0.004 TYR J 39 ARG 0.004 0.001 ARG L 63 *********************** 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 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.8497 time to fit residues: 1145.9264 Evaluate side-chains 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.724 ------------------------------------------------------------------------------- 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: 1.9990 chunk 355 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 0.6980 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 141 GLN B 105 HIS C 105 HIS D 105 HIS E 105 HIS F 105 HIS G 105 HIS H 105 HIS I 105 HIS I 141 GLN J 60 HIS J 105 HIS K 105 HIS L 105 HIS M 105 HIS N 105 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 105 HIS S 60 HIS S 105 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 36120 Z= 0.133 Angle : 0.547 7.436 48672 Z= 0.300 Chirality : 0.035 0.142 5184 Planarity : 0.003 0.021 6360 Dihedral : 4.405 20.203 4536 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 4.87 (0.13), residues: 4080 helix: 3.68 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.10 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 93 HIS 0.003 0.001 HIS O 128 PHE 0.015 0.002 PHE O 41 TYR 0.018 0.002 TYR Q 39 ARG 0.003 0.000 ARG C 63 *********************** 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 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.844 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 2.0165 time to fit residues: 1232.6833 Evaluate side-chains 528 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.423 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 20.0000 chunk 246 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 60 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 57 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 57 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 36120 Z= 0.313 Angle : 0.777 7.438 48672 Z= 0.430 Chirality : 0.045 0.175 5184 Planarity : 0.005 0.038 6360 Dihedral : 4.593 19.007 4536 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.61 % Allowed : 3.03 % Favored : 96.36 % 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: 2.94 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.00 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP L 93 HIS 0.007 0.002 HIS S 60 PHE 0.026 0.005 PHE E 41 TYR 0.028 0.004 TYR Q 39 ARG 0.003 0.001 ARG F 76 *********************** 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 570 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 546 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: B 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: C 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: D 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: E 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: F 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: G 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: H 119 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7948 (tttm) REVERT: I 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: J 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: K 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: L 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: M 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: N 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: O 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: P 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: Q 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: R 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: S 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: T 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: U 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: V 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: W 119 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: X 119 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (tttm) outliers start: 24 outliers final: 0 residues processed: 546 average time/residue: 1.7916 time to fit residues: 1151.4152 Evaluate side-chains 546 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 522 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS B 60 HIS B 105 HIS C 60 HIS C 105 HIS D 60 HIS D 105 HIS E 60 HIS E 105 HIS F 60 HIS F 105 HIS G 60 HIS G 105 HIS H 60 HIS H 105 HIS I 60 HIS I 105 HIS J 60 HIS J 105 HIS K 60 HIS K 105 HIS L 60 HIS L 105 HIS M 60 HIS M 105 HIS N 60 HIS N 105 HIS O 60 HIS O 105 HIS P 60 HIS P 105 HIS Q 60 HIS Q 105 HIS R 60 HIS R 105 HIS S 60 HIS S 105 HIS T 60 HIS T 105 HIS U 60 HIS U 105 HIS V 60 HIS V 105 HIS W 60 HIS W 105 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 36120 Z= 0.174 Angle : 0.606 6.712 48672 Z= 0.335 Chirality : 0.038 0.146 5184 Planarity : 0.004 0.024 6360 Dihedral : 4.530 19.864 4536 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 4.33 (0.13), residues: 4080 helix: 3.27 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.09 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 93 HIS 0.003 0.001 HIS S 128 PHE 0.021 0.003 PHE B 41 TYR 0.023 0.003 TYR P 39 ARG 0.002 0.000 ARG U 63 *********************** 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 511 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 1.8304 time to fit residues: 1099.9326 Evaluate side-chains 511 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 4.044 ------------------------------------------------------------------------------- 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: 20.0000 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 60 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 57 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 57 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 36120 Z= 0.271 Angle : 0.728 7.344 48672 Z= 0.403 Chirality : 0.042 0.160 5184 Planarity : 0.005 0.032 6360 Dihedral : 4.606 19.433 4536 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 3.93 (0.13), residues: 4080 helix: 2.97 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.05 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 93 HIS 0.004 0.002 HIS W 118 PHE 0.027 0.004 PHE W 41 TYR 0.027 0.004 TYR E 39 ARG 0.003 0.001 ARG U 76 *********************** 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 522 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 1.9564 time to fit residues: 1204.4671 Evaluate side-chains 522 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.336 ------------------------------------------------------------------------------- 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: 0.8980 chunk 387 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 chunk 323 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 60 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 57 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 57 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 36120 Z= 0.246 Angle : 0.701 7.233 48672 Z= 0.388 Chirality : 0.041 0.156 5184 Planarity : 0.004 0.031 6360 Dihedral : 4.609 19.355 4536 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 3.96 (0.13), residues: 4080 helix: 2.99 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.04 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 93 HIS 0.004 0.001 HIS M 57 PHE 0.025 0.004 PHE J 41 TYR 0.026 0.004 TYR K 39 ARG 0.002 0.001 ARG N 76 ********************** 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 522 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 1.8731 time to fit residues: 1145.8142 Evaluate side-chains 522 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.087 ------------------------------------------------------------------------------- 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: 9.9990 chunk 344 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 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 57 HIS A 60 HIS A 105 HIS B 57 HIS B 60 HIS B 105 HIS C 57 HIS C 60 HIS C 105 HIS D 57 HIS D 60 HIS D 105 HIS E 57 HIS E 60 HIS E 105 HIS F 57 HIS F 60 HIS F 105 HIS G 57 HIS G 60 HIS G 105 HIS H 57 HIS H 60 HIS H 105 HIS I 57 HIS I 60 HIS I 105 HIS J 57 HIS J 60 HIS J 105 HIS K 57 HIS K 60 HIS K 105 HIS L 57 HIS L 60 HIS L 105 HIS M 57 HIS M 60 HIS M 105 HIS N 57 HIS N 60 HIS N 105 HIS O 57 HIS O 60 HIS O 105 HIS P 57 HIS P 60 HIS P 105 HIS Q 57 HIS Q 60 HIS Q 105 HIS R 57 HIS R 60 HIS R 105 HIS S 57 HIS S 60 HIS S 105 HIS T 57 HIS T 60 HIS T 105 HIS U 57 HIS U 60 HIS U 105 HIS V 57 HIS V 60 HIS V 105 HIS W 57 HIS W 60 HIS W 105 HIS X 57 HIS X 60 HIS X 105 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.221682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157855 restraints weight = 33601.266| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 0.52 r_work: 0.3621 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work: 0.3245 rms_B_bonded: 3.15 restraints_weight: 0.1250 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 36120 Z= 0.230 Angle : 0.683 7.156 48672 Z= 0.379 Chirality : 0.041 0.155 5184 Planarity : 0.004 0.030 6360 Dihedral : 4.603 19.448 4536 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 4.01 (0.13), residues: 4080 helix: 3.04 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.04 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 93 HIS 0.003 0.001 HIS M 118 PHE 0.025 0.004 PHE X 41 TYR 0.026 0.003 TYR K 39 ARG 0.002 0.001 ARG N 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20702.38 seconds wall clock time: 365 minutes 40.08 seconds (21940.08 seconds total)