Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 18:29:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/07_2023/7a6a_11668_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/07_2023/7a6a_11668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/07_2023/7a6a_11668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/07_2023/7a6a_11668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/07_2023/7a6a_11668_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/07_2023/7a6a_11668_updated.pdb" } resolution = 1.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 41613 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 Na 32 4.78 5 C 23112 2.51 5 N 6552 2.21 5 O 11797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 9": "NH1" <-> "NH2" Residue "1 ASP 15": "OD1" <-> "OD2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "1 ASP 91": "OD1" <-> "OD2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "1 ASP 123": "OD1" <-> "OD2" Residue "1 ASP 131": "OD1" <-> "OD2" Residue "1 GLU 134": "OE1" <-> "OE2" Residue "1 GLU 140": "OE1" <-> "OE2" Residue "1 GLU 147": "OE1" <-> "OE2" Residue "1 ASP 150": "OD1" <-> "OD2" Residue "1 ARG 156": "NH1" <-> "NH2" Residue "1 ARG 156": "NH1" <-> "NH2" Residue "1 GLU 167": "OE1" <-> "OE2" Residue "1 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "K ASP 150": "OD1" <-> "OD2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ASP 15": "OD1" <-> "OD2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ASP 91": "OD1" <-> "OD2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "a ASP 123": "OD1" <-> "OD2" Residue "a ASP 131": "OD1" <-> "OD2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 140": "OE1" <-> "OE2" Residue "a GLU 147": "OE1" <-> "OE2" Residue "a ASP 150": "OD1" <-> "OD2" Residue "a ARG 156": "NH1" <-> "NH2" Residue "a ARG 156": "NH1" <-> "NH2" Residue "a GLU 167": "OE1" <-> "OE2" Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E ASP 131": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 9": "NH1" <-> "NH2" Residue "e ASP 15": "OD1" <-> "OD2" Residue "e GLU 61": "OE1" <-> "OE2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 131": "OD1" <-> "OD2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "e GLU 140": "OE1" <-> "OE2" Residue "e GLU 147": "OE1" <-> "OE2" Residue "e ASP 150": "OD1" <-> "OD2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e GLU 167": "OE1" <-> "OE2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ASP 15": "OD1" <-> "OD2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ASP 91": "OD1" <-> "OD2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Residue "r ASP 123": "OD1" <-> "OD2" Residue "r ASP 131": "OD1" <-> "OD2" Residue "r GLU 134": "OE1" <-> "OE2" Residue "r GLU 140": "OE1" <-> "OE2" Residue "r GLU 147": "OE1" <-> "OE2" Residue "r ASP 150": "OD1" <-> "OD2" Residue "r ARG 156": "NH1" <-> "NH2" Residue "r ARG 156": "NH1" <-> "NH2" Residue "r GLU 167": "OE1" <-> "OE2" Residue "r TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I ASP 123": "OD1" <-> "OD2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 150": "OD1" <-> "OD2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 9": "NH1" <-> "NH2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 123": "OD1" <-> "OD2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 150": "OD1" <-> "OD2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O ASP 123": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "Q ASP 150": "OD1" <-> "OD2" Residue "Q ARG 156": "NH1" <-> "NH2" Residue "Q ARG 156": "NH1" <-> "NH2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 9": "NH1" <-> "NH2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "S GLU 134": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S ASP 150": "OD1" <-> "OD2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S GLU 167": "OE1" <-> "OE2" Residue "S TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 9": "NH1" <-> "NH2" Residue "U ASP 15": "OD1" <-> "OD2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "U ASP 123": "OD1" <-> "OD2" Residue "U ASP 131": "OD1" <-> "OD2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U GLU 147": "OE1" <-> "OE2" Residue "U ASP 150": "OD1" <-> "OD2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 9": "NH1" <-> "NH2" Residue "W ASP 15": "OD1" <-> "OD2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ASP 123": "OD1" <-> "OD2" Residue "W ASP 131": "OD1" <-> "OD2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ASP 150": "OD1" <-> "OD2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "W TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Y GLU 61": "OE1" <-> "OE2" Residue "Y ARG 63": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y ASP 123": "OD1" <-> "OD2" Residue "Y ASP 131": "OD1" <-> "OD2" Residue "Y GLU 134": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "Y GLU 147": "OE1" <-> "OE2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "Y ARG 156": "NH1" <-> "NH2" Residue "Y ARG 156": "NH1" <-> "NH2" Residue "Y GLU 167": "OE1" <-> "OE2" Residue "Y TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 9": "NH1" <-> "NH2" Residue "2 ASP 15": "OD1" <-> "OD2" Residue "2 GLU 61": "OE1" <-> "OE2" Residue "2 ARG 63": "NH1" <-> "NH2" Residue "2 ASP 91": "OD1" <-> "OD2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "2 ASP 123": "OD1" <-> "OD2" Residue "2 ASP 131": "OD1" <-> "OD2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 GLU 140": "OE1" <-> "OE2" Residue "2 GLU 147": "OE1" <-> "OE2" Residue "2 ASP 150": "OD1" <-> "OD2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 GLU 167": "OE1" <-> "OE2" Residue "2 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 9": "NH1" <-> "NH2" Residue "4 ASP 15": "OD1" <-> "OD2" Residue "4 GLU 61": "OE1" <-> "OE2" Residue "4 ARG 63": "NH1" <-> "NH2" Residue "4 ASP 91": "OD1" <-> "OD2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 116": "OE1" <-> "OE2" Residue "4 ASP 123": "OD1" <-> "OD2" Residue "4 ASP 131": "OD1" <-> "OD2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 GLU 140": "OE1" <-> "OE2" Residue "4 GLU 147": "OE1" <-> "OE2" Residue "4 ASP 150": "OD1" <-> "OD2" Residue "4 ARG 156": "NH1" <-> "NH2" Residue "4 ARG 156": "NH1" <-> "NH2" Residue "4 GLU 167": "OE1" <-> "OE2" Residue "4 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H ASP 131": "OD1" <-> "OD2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P ASP 123": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 9": "NH1" <-> "NH2" Residue "X ASP 15": "OD1" <-> "OD2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X ARG 63": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X ASP 123": "OD1" <-> "OD2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 147": "OE1" <-> "OE2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X ARG 156": "NH1" <-> "NH2" Residue "X ARG 156": "NH1" <-> "NH2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 9": "NH1" <-> "NH2" Residue "6 ASP 15": "OD1" <-> "OD2" Residue "6 GLU 61": "OE1" <-> "OE2" Residue "6 ARG 63": "NH1" <-> "NH2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 ASP 123": "OD1" <-> "OD2" Residue "6 ASP 131": "OD1" <-> "OD2" Residue "6 GLU 134": "OE1" <-> "OE2" Residue "6 GLU 140": "OE1" <-> "OE2" Residue "6 GLU 147": "OE1" <-> "OE2" Residue "6 ASP 150": "OD1" <-> "OD2" Residue "6 ARG 156": "NH1" <-> "NH2" Residue "6 ARG 156": "NH1" <-> "NH2" Residue "6 GLU 167": "OE1" <-> "OE2" Residue "6 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 41613 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "1" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "K" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "a" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "B" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "E" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "e" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "r" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "G" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "I" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "M" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "O" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "Q" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "S" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "U" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "W" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "Y" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "2" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "4" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "F" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "H" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "P" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "X" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "6" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "1" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "K" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "a" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "B" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "e" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "r" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "I" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "M" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "O" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "Q" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "S" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "U" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "W" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "Y" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "2" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "4" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "F" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "H" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "P" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "X" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "6" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Residues with excluded nonbonded symmetry interactions: 336 residue: pdb=" N ALYS A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 49 " occ=0.50 residue: pdb=" N ALYS A 53 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 53 " occ=0.50 residue: pdb=" N AGLU A 64 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.50 residue: pdb=" N ALYS A 68 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 68 " occ=0.50 residue: pdb=" N ALYS A 71 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 71 " occ=0.50 residue: pdb=" N ALEU A 72 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 72 " occ=0.50 residue: pdb=" N AGLN A 75 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 75 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N AASN A 109 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 109 " occ=0.50 residue: pdb=" N ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG CSER A 113 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 residue: pdb=" N AARG A 156 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 156 " occ=0.50 ... (remaining 324 not shown) Time building chain proxies: 35.12, per 1000 atoms: 0.84 Number of scatterers: 41613 At special positions: 0 Unit cell: (135.3, 135.3, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Na 32 11.00 O 11797 8.00 N 6552 7.00 C 23112 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: 15.56 Conformation dependent library (CDL) restraints added in 9.1 seconds 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 75 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 75 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 75 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 75 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 75 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 75 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 75 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 75 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 75 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 75 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 75 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 75 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 75 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 75 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 75 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 75 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 75 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 75 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 75 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 75 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 75 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 75 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 2712 hydrogen bonds defined for protein. 8352 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: 12.54 Time building geometry restraints manager: 16.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 6102 1.26 - 1.40: 10242 1.40 - 1.54: 21197 1.54 - 1.69: 211 1.69 - 1.83: 216 Bond restraints: 37968 Sorted by residual: bond pdb=" C CSER 6 113 " pdb=" O CSER 6 113 " ideal model delta sigma weight residual 1.237 1.117 0.120 1.17e-02 7.31e+03 1.05e+02 bond pdb=" C CSER P 113 " pdb=" O CSER P 113 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.15e-02 7.56e+03 1.98e+01 bond pdb=" C CSER 2 113 " pdb=" N LEU 2 114 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.31e-02 5.83e+03 1.89e+01 bond pdb=" C ARG M 43 " pdb=" O ARG M 43 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.24e-02 6.50e+03 1.88e+01 bond pdb=" C ARG X 43 " pdb=" O ARG X 43 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.24e-02 6.50e+03 1.88e+01 ... (remaining 37963 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.27: 593 106.27 - 113.17: 17629 113.17 - 120.08: 17023 120.08 - 126.98: 15856 126.98 - 133.88: 427 Bond angle restraints: 51528 Sorted by residual: angle pdb=" CA ASP G 150 " pdb=" CB ASP G 150 " pdb=" CG ASP G 150 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASP 4 150 " pdb=" CB ASP 4 150 " pdb=" CG ASP 4 150 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASP P 150 " pdb=" CB ASP P 150 " pdb=" CG ASP P 150 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" CA ASP M 150 " pdb=" CB ASP M 150 " pdb=" CG ASP M 150 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" CA ASP 1 150 " pdb=" CB ASP 1 150 " pdb=" CG ASP 1 150 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 ... (remaining 51523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 20808 15.77 - 31.54: 1708 31.54 - 47.30: 500 47.30 - 63.07: 240 63.07 - 78.84: 72 Dihedral angle restraints: 23328 sinusoidal: 9696 harmonic: 13632 Sorted by residual: dihedral pdb=" C TYR 1 39 " pdb=" N TYR 1 39 " pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" C TYR G 39 " pdb=" N TYR G 39 " pdb=" CA TYR G 39 " pdb=" CB TYR G 39 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" C TYR 2 39 " pdb=" N TYR 2 39 " pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " ideal model delta harmonic sigma weight residual -122.60 -134.43 11.83 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 23325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2426 0.110 - 0.219: 2012 0.219 - 0.329: 722 0.329 - 0.438: 72 0.438 - 0.548: 72 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CG LEU 6 117 " pdb=" CB LEU 6 117 " pdb=" CD1 LEU 6 117 " pdb=" CD2 LEU 6 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" CG LEU X 117 " pdb=" CB LEU X 117 " pdb=" CD1 LEU X 117 " pdb=" CD2 LEU X 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CG LEU P 117 " pdb=" CB LEU P 117 " pdb=" CD1 LEU P 117 " pdb=" CD2 LEU P 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.12e+00 ... (remaining 5301 not shown) Planarity restraints: 6984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 137 " -0.139 2.00e-02 2.50e+03 7.67e-02 1.18e+02 pdb=" CG TYR 6 137 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 137 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 137 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 137 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 137 " 0.061 2.00e-02 2.50e+03 pdb=" CZ TYR 6 137 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR 6 137 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.139 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR P 137 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " -0.060 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.139 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR a 137 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.106 2.00e-02 2.50e+03 ... (remaining 6981 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 260 2.47 - 3.07: 35098 3.07 - 3.68: 76655 3.68 - 4.29: 127541 4.29 - 4.90: 190295 Nonbonded interactions: 429849 Sorted by model distance: nonbonded pdb=" OE2 GLU X 101 " pdb=" NH2BARG X 156 " model vdw 1.857 2.520 nonbonded pdb=" OE2 GLU P 101 " pdb=" NH2BARG P 156 " model vdw 1.859 2.520 nonbonded pdb=" OE2 GLU H 101 " pdb=" NH2BARG H 156 " model vdw 1.860 2.520 nonbonded pdb=" OE2 GLU F 101 " pdb=" NH2BARG F 156 " model vdw 1.862 2.520 nonbonded pdb=" OE2 GLU 4 101 " pdb=" NH2BARG 4 156 " model vdw 1.863 2.520 ... (remaining 429844 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 '1' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'Y' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'a' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'e' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'r' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) } 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=0.50 max=1.00 mean=0.93 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.030 Extract box with map and model: 25.300 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 112.540 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.260 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 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 : 0.018 0.120 37968 Z= 1.200 Angle : 1.695 11.100 51528 Z= 1.150 Chirality : 0.160 0.548 5304 Planarity : 0.013 0.077 6984 Dihedral : 14.684 78.837 14688 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.56 % 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: 2.45 (0.11), residues: 4992 helix: 1.92 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.41 (0.23), residues: 888 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 936 time to evaluate : 3.279 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: 48 outliers final: 0 residues processed: 960 average time/residue: 1.5949 time to fit residues: 1811.8027 Evaluate side-chains 696 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1781 ------------------------------------------------------------------------------- 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: 0.6980 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 105 HIS A 112 GLN A 136 HIS 1 98 ASN 1 105 HIS 1 136 HIS K 98 ASN K 105 HIS K 136 HIS a 98 ASN a 105 HIS a 136 HIS B 98 ASN B 105 HIS B 112 GLN B 136 HIS E 98 ASN E 105 HIS E 112 GLN E 136 HIS e 98 ASN e 105 HIS e 136 HIS r 98 ASN r 105 HIS r 136 HIS G 98 ASN G 105 HIS G 136 HIS I 98 ASN I 105 HIS I 112 GLN I 136 HIS M 98 ASN M 105 HIS M 112 GLN M 136 HIS O 98 ASN O 105 HIS O 136 HIS Q 98 ASN Q 105 HIS Q 136 HIS S 98 ASN S 105 HIS S 112 GLN S 136 HIS U 98 ASN U 105 HIS U 136 HIS W 98 ASN W 105 HIS W 112 GLN W 136 HIS Y 98 ASN Y 105 HIS Y 136 HIS 2 98 ASN 2 105 HIS 2 136 HIS 4 98 ASN 4 105 HIS 4 136 HIS F 98 ASN F 105 HIS F 136 HIS H 98 ASN H 105 HIS H 136 HIS P 98 ASN P 105 HIS P 136 HIS X 98 ASN X 105 HIS X 136 HIS 6 98 ASN 6 105 HIS 6 136 HIS Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 37968 Z= 0.167 Angle : 0.588 5.691 51528 Z= 0.328 Chirality : 0.039 0.160 5304 Planarity : 0.004 0.026 6984 Dihedral : 4.471 18.787 5208 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 2.42 % 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: 4.27 (0.11), residues: 4992 helix: 3.17 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.91 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1049 time to evaluate : 3.354 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: 24 outliers final: 0 residues processed: 1049 average time/residue: 1.4213 time to fit residues: 1798.3860 Evaluate side-chains 788 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 788 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1202 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 0.8980 chunk 308 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 2.9990 chunk 400 optimal weight: 0.9980 chunk 330 optimal weight: 0.5980 chunk 368 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 chunk 297 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 139 ASN 1 105 HIS 1 139 ASN K 75 GLN B K 105 HIS K 139 ASN a 105 HIS a 139 ASN B 75 GLN B B 105 HIS B 139 ASN E 75 GLN B E 105 HIS E 139 ASN e 105 HIS e 139 ASN r 105 HIS r 139 ASN G 105 HIS G 139 ASN I 105 HIS I 139 ASN M 105 HIS M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 75 GLN B S 105 HIS S 139 ASN U 105 HIS U 139 ASN W 60 HIS W 75 GLN B W 105 HIS W 139 ASN Y 60 HIS Y 75 GLN B Y 105 HIS Y 139 ASN 2 60 HIS 2 75 GLN B 2 105 HIS 2 139 ASN 4 60 HIS 4 75 GLN B 4 105 HIS 4 139 ASN F 105 HIS F 139 ASN H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 60 HIS X 75 GLN B X 105 HIS X 139 ASN 6 75 GLN B 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 37968 Z= 0.151 Angle : 0.563 5.509 51528 Z= 0.311 Chirality : 0.037 0.146 5304 Planarity : 0.003 0.021 6984 Dihedral : 4.409 18.858 5208 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 1.82 % 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: 4.65 (0.12), residues: 4992 helix: 3.45 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.94 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 782 time to evaluate : 3.245 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: 782 average time/residue: 1.4701 time to fit residues: 1379.4688 Evaluate side-chains 768 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 768 time to evaluate : 3.244 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 0.5980 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B A 105 HIS A 109 ASN A A 139 ASN 1 75 GLN B 1 105 HIS 1 139 ASN K 105 HIS K 139 ASN a 75 GLN B a 105 HIS a 139 ASN B 105 HIS B 139 ASN E 105 HIS E 109 ASN A E 139 ASN e 75 GLN B e 105 HIS e 139 ASN r 75 GLN B r 105 HIS r 109 ASN A r 139 ASN G 75 GLN B G 105 HIS G 139 ASN I 75 GLN B I 105 HIS I 109 ASN A I 139 ASN M 75 GLN B M 105 HIS M 109 ASN A M 139 ASN O 75 GLN B O 105 HIS O 139 ASN Q 75 GLN B Q 105 HIS Q 112 GLN Q 139 ASN S 105 HIS S 109 ASN A S 139 ASN U 75 GLN B U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 105 HIS Y 109 ASN A Y 112 GLN Y 139 ASN 2 105 HIS 2 109 ASN A 2 112 GLN 2 139 ASN 4 105 HIS 4 112 GLN 4 139 ASN F 75 GLN B F 105 HIS F 112 GLN F 139 ASN H 75 GLN B H 105 HIS H 112 GLN H 139 ASN P 75 GLN B P 105 HIS P 112 GLN P 139 ASN X 105 HIS X 139 ASN 6 105 HIS 6 109 ASN A 6 112 GLN 6 139 ASN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 37968 Z= 0.150 Angle : 0.556 6.217 51528 Z= 0.308 Chirality : 0.037 0.138 5304 Planarity : 0.003 0.022 6984 Dihedral : 4.387 19.014 5208 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.70 (0.12), residues: 4992 helix: 3.48 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.99 (0.25), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 792 time to evaluate : 3.177 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: 792 average time/residue: 1.4081 time to fit residues: 1348.0643 Evaluate side-chains 853 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 853 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1658 ------------------------------------------------------------------------------- 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: 7.9990 chunk 223 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 0.4980 chunk 162 optimal weight: 0.1980 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 139 ASN 1 105 HIS 1 109 ASN A 1 139 ASN K 105 HIS K 109 ASN A K 139 ASN a 105 HIS a 109 ASN A a 139 ASN B 105 HIS B 109 ASN A B 139 ASN E 105 HIS E 139 ASN e 105 HIS e 109 ASN A e 139 ASN r 105 HIS r 139 ASN G 105 HIS G 109 ASN A G 139 ASN I 105 HIS I 139 ASN M 105 HIS M 139 ASN O 105 HIS O 109 ASN A O 139 ASN Q 105 HIS Q 109 ASN A Q 139 ASN S 105 HIS S 139 ASN U 105 HIS U 109 ASN A U 139 ASN W 105 HIS W 109 ASN A W 139 ASN Y 105 HIS Y 139 ASN 2 105 HIS 2 139 ASN 4 105 HIS 4 109 ASN A 4 139 ASN F 105 HIS F 109 ASN A F 139 ASN H 105 HIS H 109 ASN A H 139 ASN P 105 HIS P 109 ASN A P 139 ASN X 105 HIS X 109 ASN A X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 37968 Z= 0.134 Angle : 0.525 7.569 51528 Z= 0.291 Chirality : 0.036 0.133 5304 Planarity : 0.004 0.053 6984 Dihedral : 4.311 19.188 5208 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.92 (0.12), residues: 4992 helix: 3.63 (0.08), residues: 4152 sheet: None (None), residues: 0 loop : 1.02 (0.25), residues: 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 783 time to evaluate : 4.327 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: 783 average time/residue: 1.4345 time to fit residues: 1361.6382 Evaluate side-chains 796 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 796 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1059 ------------------------------------------------------------------------------- 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: 7.9990 chunk 355 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 231 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 0.3980 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 112 GLN 1 105 HIS 1 112 GLN K 105 HIS K 112 GLN a 105 HIS a 112 GLN B 105 HIS B 112 GLN E 105 HIS E 112 GLN e 105 HIS e 112 GLN r 105 HIS r 112 GLN G 105 HIS G 112 GLN I 105 HIS I 112 GLN M 105 HIS M 112 GLN O 60 HIS O 105 HIS O 112 GLN Q 60 HIS Q 105 HIS S 60 HIS S 105 HIS S 112 GLN U 105 HIS U 112 GLN W 60 HIS W 105 HIS Y 60 HIS Y 105 HIS Y 112 GLN 2 60 HIS 2 105 HIS 2 112 GLN 4 60 HIS 4 105 HIS F 60 HIS F 105 HIS H 60 HIS H 105 HIS P 60 HIS P 105 HIS P 112 GLN X 60 HIS X 105 HIS X 112 GLN 6 60 HIS 6 105 HIS 6 112 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 37968 Z= 0.157 Angle : 0.568 7.820 51528 Z= 0.315 Chirality : 0.037 0.134 5304 Planarity : 0.003 0.022 6984 Dihedral : 4.415 19.771 5208 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.73 (0.12), residues: 4992 helix: 3.50 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.97 (0.25), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 816 time to evaluate : 3.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 816 average time/residue: 1.3027 time to fit residues: 1308.9681 Evaluate side-chains 814 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 814 time to evaluate : 3.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2320 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 223 optimal weight: 0.5980 chunk 332 optimal weight: 0.0170 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 139 ASN E 60 HIS E 105 HIS E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 139 ASN M 60 HIS M 105 HIS M 139 ASN O 105 HIS O 139 ASN Q 105 HIS Q 112 GLN Q 139 ASN S 105 HIS S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 105 HIS Y 139 ASN 2 105 HIS 2 139 ASN 4 105 HIS 4 112 GLN 4 139 ASN F 105 HIS F 112 GLN F 139 ASN H 105 HIS H 112 GLN H 139 ASN P 105 HIS P 139 ASN X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 37968 Z= 0.161 Angle : 0.559 5.457 51528 Z= 0.312 Chirality : 0.037 0.135 5304 Planarity : 0.003 0.022 6984 Dihedral : 4.468 19.771 5208 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.62 (0.12), residues: 4992 helix: 3.42 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 826 time to evaluate : 3.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 826 average time/residue: 1.3375 time to fit residues: 1353.9708 Evaluate side-chains 817 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 817 time to evaluate : 3.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 139 ASN E 60 HIS E 105 HIS E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 139 ASN M 60 HIS M 105 HIS M 139 ASN O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 139 ASN Y 105 HIS Y 139 ASN 2 105 HIS 2 139 ASN 4 105 HIS 4 139 ASN F 105 HIS F 139 ASN H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 37968 Z= 0.190 Angle : 0.605 5.851 51528 Z= 0.338 Chirality : 0.039 0.136 5304 Planarity : 0.004 0.023 6984 Dihedral : 4.554 19.689 5208 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.44 (0.12), residues: 4992 helix: 3.30 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.91 (0.24), residues: 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 828 time to evaluate : 3.282 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 outliers start: 0 outliers final: 0 residues processed: 828 average time/residue: 1.3324 time to fit residues: 1355.1325 Evaluate side-chains 756 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2642 ------------------------------------------------------------------------------- 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: 0.9990 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 0.1980 chunk 220 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 287 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 0.7980 chunk 365 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 139 ASN E 60 HIS E 105 HIS E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 139 ASN M 60 HIS M 105 HIS M 139 ASN O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 139 ASN Y 105 HIS Y 139 ASN 2 105 HIS 2 139 ASN 4 105 HIS 4 139 ASN F 105 HIS F 139 ASN H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 37968 Z= 0.137 Angle : 0.515 5.166 51528 Z= 0.287 Chirality : 0.036 0.138 5304 Planarity : 0.003 0.023 6984 Dihedral : 4.362 19.434 5208 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.80 (0.12), residues: 4992 helix: 3.55 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.94 (0.25), residues: 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 817 time to evaluate : 3.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 817 average time/residue: 1.2837 time to fit residues: 1290.8090 Evaluate side-chains 817 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 817 time to evaluate : 3.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1819 ------------------------------------------------------------------------------- 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: 3.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 9.9990 chunk 374 optimal weight: 0.3980 chunk 323 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 139 ASN E 60 HIS E 105 HIS E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 139 ASN M 60 HIS M 105 HIS M 139 ASN O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 139 ASN Y 105 HIS Y 139 ASN 2 105 HIS 2 139 ASN 4 105 HIS 4 139 ASN F 105 HIS F 139 ASN H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 105 HIS X 139 ASN 6 105 HIS 6 112 GLN 6 139 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 37968 Z= 0.153 Angle : 0.550 5.428 51528 Z= 0.306 Chirality : 0.037 0.136 5304 Planarity : 0.003 0.023 6984 Dihedral : 4.441 19.877 5208 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.70 (0.12), residues: 4992 helix: 3.48 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.99 (0.25), residues: 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 824 average time/residue: 1.3188 time to fit residues: 1331.8260 Evaluate side-chains 817 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 817 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1186 ------------------------------------------------------------------------------- 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: 0.8980 chunk 344 optimal weight: 0.1980 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 0.2980 chunk 332 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 139 ASN E 60 HIS E 105 HIS E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 139 ASN M 60 HIS M 105 HIS M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 60 HIS Q 105 HIS Q 139 ASN S 105 HIS S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 139 ASN Y 105 HIS Y 139 ASN 2 105 HIS 2 139 ASN 4 60 HIS 4 105 HIS 4 139 ASN F 60 HIS F 105 HIS F 139 ASN H 60 HIS H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 60 HIS X 105 HIS X 139 ASN 6 60 HIS 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.184031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.153288 restraints weight = 133686.462| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.49 r_work: 0.3232 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2989 rms_B_bonded: 3.05 restraints_weight: 0.1250 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 37968 Z= 0.174 Angle : 0.579 5.629 51528 Z= 0.324 Chirality : 0.038 0.135 5304 Planarity : 0.004 0.038 6984 Dihedral : 4.505 19.623 5208 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.82 % 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: 4.55 (0.12), residues: 4992 helix: 3.37 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.93 (0.24), residues: 840 =============================================================================== Job complete usr+sys time: 25026.48 seconds wall clock time: 431 minutes 55.27 seconds (25915.27 seconds total)