Starting phenix.real_space_refine on Sun Mar 17 23:21:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/03_2024/6z9f_11122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/03_2024/6z9f_11122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/03_2024/6z9f_11122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/03_2024/6z9f_11122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/03_2024/6z9f_11122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/03_2024/6z9f_11122_updated.pdb" } resolution = 1.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.156 sd= 10.228 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 41020 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 23040 2.51 5 N 6528 2.21 5 O 11300 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41020 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "1" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "K" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "a" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "B" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "E" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "e" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "r" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "G" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "I" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "M" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "O" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "Q" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "S" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "U" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "W" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "Y" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "2" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "4" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "F" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "H" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "P" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "X" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 Chain: "6" Number of atoms: 1534 Number of conformers: 2 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: 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 bond proxies already assigned to first conformer: 1319 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: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "1" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "K" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "a" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "E" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "e" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "r" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "I" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "M" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "O" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "Q" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "S" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "U" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "W" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "Y" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "2" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "4" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "H" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "P" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "X" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 171 Classifications: {'water': 171} Link IDs: {None: 170} Chain: "6" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Residues with excluded nonbonded symmetry interactions: 312 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 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 residue: pdb=" N AGLU A 162 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 162 " occ=0.50 ... (remaining 300 not shown) Time building chain proxies: 26.20, per 1000 atoms: 0.64 Number of scatterers: 41020 At special positions: 0 Unit cell: (136.284, 136.284, 136.284, 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 11300 8.00 N 6528 7.00 C 23040 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: 15.20 Conformation dependent library (CDL) restraints added in 8.3 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 72.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 76 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 2736 hydrogen bonds defined for protein. 8448 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: 11.74 Time building geometry restraints manager: 16.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6750 1.31 - 1.44: 9924 1.44 - 1.57: 20910 1.57 - 1.70: 0 1.70 - 1.83: 216 Bond restraints: 37800 Sorted by residual: bond pdb=" CE1 HIS I 13 " pdb=" NE2 HIS I 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" CE1 HIS X 13 " pdb=" NE2 HIS X 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" CE1 HIS 1 13 " pdb=" NE2 HIS 1 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS P 13 " pdb=" NE2 HIS P 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS S 13 " pdb=" NE2 HIS S 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 ... (remaining 37795 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.88: 504 105.88 - 112.93: 18104 112.93 - 119.99: 17658 119.99 - 127.04: 14638 127.04 - 134.10: 360 Bond angle restraints: 51264 Sorted by residual: angle pdb=" CA LEU P 138 " pdb=" C LEU P 138 " pdb=" O LEU P 138 " ideal model delta sigma weight residual 120.82 115.30 5.52 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU e 138 " pdb=" C LEU e 138 " pdb=" O LEU e 138 " ideal model delta sigma weight residual 120.82 115.30 5.52 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU 1 138 " pdb=" C LEU 1 138 " pdb=" O LEU 1 138 " ideal model delta sigma weight residual 120.82 115.31 5.51 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU M 138 " pdb=" C LEU M 138 " pdb=" O LEU M 138 " ideal model delta sigma weight residual 120.82 115.32 5.50 1.05e+00 9.07e-01 2.74e+01 angle pdb=" CA LEU B 138 " pdb=" C LEU B 138 " pdb=" O LEU B 138 " ideal model delta sigma weight residual 120.82 115.32 5.50 1.05e+00 9.07e-01 2.74e+01 ... (remaining 51259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 21023 16.14 - 32.28: 1295 32.28 - 48.42: 490 48.42 - 64.55: 328 64.55 - 80.69: 72 Dihedral angle restraints: 23208 sinusoidal: 9672 harmonic: 13536 Sorted by residual: dihedral pdb=" C TYR H 39 " pdb=" N TYR H 39 " pdb=" CA TYR H 39 " pdb=" CB TYR H 39 " ideal model delta harmonic sigma weight residual -122.60 -132.85 10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C TYR A 39 " pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " ideal model delta harmonic sigma weight residual -122.60 -132.84 10.24 0 2.50e+00 1.60e-01 1.68e+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 -132.80 10.20 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 23205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3297 0.079 - 0.158: 1397 0.158 - 0.237: 467 0.237 - 0.316: 71 0.316 - 0.396: 48 Chirality restraints: 5280 Sorted by residual: chirality pdb=" CA ASN r 50 " pdb=" N ASN r 50 " pdb=" C ASN r 50 " pdb=" CB ASN r 50 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ASN H 50 " pdb=" N ASN H 50 " pdb=" C ASN H 50 " pdb=" CB ASN H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ASN 4 50 " pdb=" N ASN 4 50 " pdb=" C ASN 4 50 " pdb=" CB ASN 4 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 5277 not shown) Planarity restraints: 6936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.083 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR P 137 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 137 " -0.083 2.00e-02 2.50e+03 5.00e-02 4.99e+01 pdb=" CG TYR 2 137 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 137 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 137 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 137 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 137 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR 2 137 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR 2 137 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 137 " -0.082 2.00e-02 2.50e+03 5.00e-02 4.99e+01 pdb=" CG TYR H 137 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR H 137 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR H 137 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR H 137 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR H 137 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR H 137 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR H 137 " -0.066 2.00e-02 2.50e+03 ... (remaining 6933 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 319 2.41 - 3.03: 29082 3.03 - 3.65: 73806 3.65 - 4.28: 124655 4.28 - 4.90: 190002 Nonbonded interactions: 417864 Sorted by model distance: nonbonded pdb=" OE2 GLU K 101 " pdb=" NH2BARG K 156 " model vdw 1.782 2.520 nonbonded pdb=" OE2 GLU B 101 " pdb=" NH2BARG B 156 " model vdw 1.783 2.520 nonbonded pdb=" OE2 GLU a 101 " pdb=" NH2BARG a 156 " model vdw 1.783 2.520 nonbonded pdb=" OE2 GLU E 101 " pdb=" NH2BARG E 156 " model vdw 1.783 2.520 nonbonded pdb=" OE2 GLU G 101 " pdb=" NH2BARG G 156 " model vdw 1.783 2.520 ... (remaining 417859 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.360 Construct map_model_manager: 0.050 Extract box with map and model: 21.960 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 99.550 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.210 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 : 0.015 0.078 37800 Z= 0.996 Angle : 1.742 8.541 51264 Z= 1.258 Chirality : 0.098 0.396 5280 Planarity : 0.011 0.050 6936 Dihedral : 15.506 80.693 14616 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.66 % Allowed : 3.05 % Favored : 93.29 % Cbeta Deviations : 1.12 % 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: 2.70 (0.11), residues: 4920 helix: 2.12 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.36 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.019 TRP 4 93 HIS 0.019 0.008 HIS a 118 PHE 0.052 0.012 PHE W 41 TYR 0.083 0.020 TYR P 137 ARG 0.022 0.003 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 600 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6545 (mp10) REVERT: A 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6978 (mp0) REVERT: A 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6913 (mttm) REVERT: A 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: 1 86 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6499 (mp10) REVERT: 1 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6983 (mp0) REVERT: 1 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6915 (mttm) REVERT: 1 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6705 (mtmt) REVERT: K 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6460 (mp10) REVERT: K 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6966 (mp0) REVERT: K 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6910 (mttm) REVERT: K 157 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6710 (mtmt) REVERT: a 86 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6461 (mp10) REVERT: a 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6956 (mp0) REVERT: a 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6910 (mttm) REVERT: a 157 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6713 (mtmt) REVERT: B 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6496 (mp10) REVERT: B 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6972 (mp0) REVERT: B 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6913 (mttm) REVERT: B 157 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6718 (mtmt) REVERT: E 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6490 (mp10) REVERT: E 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6973 (mp0) REVERT: E 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6913 (mttm) REVERT: E 157 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6717 (mtmt) REVERT: e 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6490 (mp10) REVERT: e 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6979 (mp0) REVERT: e 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6908 (mttm) REVERT: e 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: r 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6495 (mp10) REVERT: r 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6961 (mp0) REVERT: r 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6912 (mttm) REVERT: r 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6708 (mtmt) REVERT: G 86 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6498 (mp10) REVERT: G 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6979 (mp0) REVERT: G 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6912 (mttm) REVERT: G 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6704 (mtmt) REVERT: I 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6489 (mp10) REVERT: I 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6976 (mp0) REVERT: I 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6911 (mttm) REVERT: I 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: M 86 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6458 (mp10) REVERT: M 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6975 (mp0) REVERT: M 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6911 (mttm) REVERT: M 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: O 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6495 (mp10) REVERT: O 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6971 (mp0) REVERT: O 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6909 (mttm) REVERT: O 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6716 (mtmt) REVERT: Q 86 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6460 (mp10) REVERT: Q 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6980 (mp0) REVERT: Q 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6913 (mttm) REVERT: Q 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: S 86 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6459 (mp10) REVERT: S 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6966 (mp0) REVERT: S 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6912 (mttm) REVERT: S 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: U 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6495 (mp10) REVERT: U 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6981 (mp0) REVERT: U 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6912 (mttm) REVERT: U 157 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: W 86 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6456 (mp10) REVERT: W 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6966 (mp0) REVERT: W 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6914 (mttm) REVERT: W 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6708 (mtmt) REVERT: Y 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6459 (mp10) REVERT: Y 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6971 (mp0) REVERT: Y 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6912 (mttm) REVERT: Y 157 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6717 (mtmt) REVERT: 2 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6457 (mp10) REVERT: 2 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6980 (mp0) REVERT: 2 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6911 (mttm) REVERT: 2 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6705 (mtmt) REVERT: 4 86 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6460 (mp10) REVERT: 4 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6975 (mp0) REVERT: 4 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6912 (mttm) REVERT: 4 157 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6710 (mtmt) REVERT: F 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6459 (mp10) REVERT: F 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6979 (mp0) REVERT: F 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6908 (mttm) REVERT: F 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6714 (mtmt) REVERT: H 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6545 (mp10) REVERT: H 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6971 (mp0) REVERT: H 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6913 (mttm) REVERT: H 157 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6718 (mtmt) REVERT: P 86 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6463 (mp10) REVERT: P 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6980 (mp0) REVERT: P 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6913 (mttm) REVERT: P 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (mtmt) REVERT: X 86 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6463 (mp10) REVERT: X 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6972 (mp0) REVERT: X 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6912 (mttm) REVERT: X 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6714 (mtmt) REVERT: 6 86 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6491 (mp10) REVERT: 6 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6969 (mp0) REVERT: 6 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6913 (mttm) REVERT: 6 157 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6708 (mtmt) outliers start: 48 outliers final: 24 residues processed: 624 average time/residue: 1.5241 time to fit residues: 1126.1030 Evaluate side-chains 496 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 448 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 157 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 157 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 157 LYS Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain r residue 157 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 157 LYS Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 157 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain W residue 157 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 157 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 157 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 157 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 157 LYS Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 157 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 75 GLN B A 83 GLN A 98 ASN A 112 GLN 1 14 GLN 1 60 HIS 1 75 GLN B 1 83 GLN 1 98 ASN K 14 GLN K 60 HIS K 75 GLN B K 83 GLN K 98 ASN K 105 HIS K 112 GLN a 14 GLN a 60 HIS a 75 GLN B a 83 GLN a 98 ASN a 112 GLN B 14 GLN B 60 HIS B 75 GLN B B 83 GLN B 98 ASN E 14 GLN E 60 HIS E 75 GLN B E 83 GLN E 98 ASN e 14 GLN e 60 HIS e 75 GLN B e 83 GLN e 98 ASN e 112 GLN r 14 GLN r 60 HIS r 75 GLN B r 83 GLN r 98 ASN G 14 GLN G 60 HIS G 75 GLN B G 83 GLN G 98 ASN G 112 GLN I 14 GLN I 60 HIS I 75 GLN B I 83 GLN I 98 ASN I 112 GLN M 14 GLN M 60 HIS M 75 GLN B M 83 GLN M 98 ASN M 112 GLN O 14 GLN O 60 HIS O 75 GLN B O 83 GLN O 98 ASN O 112 GLN Q 14 GLN Q 60 HIS Q 75 GLN B Q 83 GLN Q 98 ASN Q 112 GLN S 14 GLN S 60 HIS S 75 GLN B S 83 GLN S 98 ASN S 112 GLN U 14 GLN U 60 HIS U 75 GLN B U 83 GLN U 98 ASN U 112 GLN W 14 GLN W 60 HIS W 75 GLN B W 83 GLN W 98 ASN Y 14 GLN Y 60 HIS Y 75 GLN B Y 83 GLN Y 98 ASN 2 14 GLN 2 60 HIS 2 75 GLN B 2 83 GLN 2 98 ASN 2 112 GLN 4 14 GLN 4 60 HIS 4 75 GLN B 4 83 GLN 4 98 ASN 4 112 GLN F 14 GLN F 60 HIS F 75 GLN B F 83 GLN F 98 ASN F 112 GLN H 14 GLN H 60 HIS H 75 GLN B H 83 GLN H 98 ASN P 14 GLN P 60 HIS P 75 GLN B P 83 GLN P 98 ASN P 105 HIS P 112 GLN X 14 GLN X 60 HIS X 75 GLN B X 83 GLN X 98 ASN X 105 HIS 6 14 GLN 6 60 HIS 6 75 GLN B 6 83 GLN 6 98 ASN 6 105 HIS 6 112 GLN Total number of N/Q/H flips: 140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 37800 Z= 0.195 Angle : 0.655 5.743 51264 Z= 0.358 Chirality : 0.039 0.160 5280 Planarity : 0.004 0.036 6936 Dihedral : 7.158 47.194 5304 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.66 % Allowed : 3.66 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.11), residues: 4920 helix: 3.30 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.59 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP Q 93 HIS 0.009 0.001 HIS Y 60 PHE 0.027 0.003 PHE H 41 TYR 0.021 0.003 TYR P 39 ARG 0.007 0.001 ARG e 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 495 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6389 (mp10) REVERT: A 140 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6936 (mp0) REVERT: A 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6956 (mttm) REVERT: A 157 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6771 (mtmt) REVERT: 1 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6391 (mp10) REVERT: 1 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6941 (mp0) REVERT: 1 143 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6963 (mttm) REVERT: 1 157 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6769 (mtmt) REVERT: K 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6371 (mp10) REVERT: K 140 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6926 (mp0) REVERT: K 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6957 (mttm) REVERT: K 157 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6771 (mtmt) REVERT: a 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6366 (mp10) REVERT: a 140 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6920 (mp0) REVERT: a 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6936 (mttm) REVERT: a 157 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6784 (mtmt) REVERT: B 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6391 (mp10) REVERT: B 140 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6933 (mp0) REVERT: B 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6959 (mttm) REVERT: B 157 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6788 (mtmt) REVERT: E 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6391 (mp10) REVERT: E 140 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6935 (mp0) REVERT: E 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6936 (mttm) REVERT: E 157 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6787 (mtmt) REVERT: e 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6389 (mp10) REVERT: e 140 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6937 (mp0) REVERT: e 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6966 (mttm) REVERT: e 157 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6772 (mtmt) REVERT: r 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6391 (mp10) REVERT: r 140 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6923 (mp0) REVERT: r 143 LYS cc_start: 0.7277 (mtmt) cc_final: 0.6960 (mttm) REVERT: r 157 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6784 (mtmt) REVERT: G 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6391 (mp10) REVERT: G 140 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6940 (mp0) REVERT: G 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6966 (mttm) REVERT: G 157 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6771 (mtmt) REVERT: I 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6390 (mp10) REVERT: I 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6943 (mp0) REVERT: I 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6958 (mttm) REVERT: I 157 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6782 (mtmt) REVERT: M 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6368 (mp10) REVERT: M 140 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6931 (mp0) REVERT: M 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6965 (mttm) REVERT: M 157 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: O 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6389 (mp10) REVERT: O 140 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6914 (mp0) REVERT: O 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6964 (mttm) REVERT: O 157 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6785 (mtmt) REVERT: Q 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6370 (mp10) REVERT: Q 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6940 (mp0) REVERT: Q 143 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6970 (mttm) REVERT: Q 157 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6771 (mtmt) REVERT: S 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6370 (mp10) REVERT: S 140 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6930 (mp0) REVERT: S 143 LYS cc_start: 0.7278 (mtmt) cc_final: 0.6962 (mttm) REVERT: S 157 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6782 (mtmt) REVERT: U 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6390 (mp10) REVERT: U 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6939 (mp0) REVERT: U 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6962 (mttm) REVERT: U 157 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6769 (mtmt) REVERT: W 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6368 (mp10) REVERT: W 140 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6932 (mp0) REVERT: W 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6959 (mttm) REVERT: W 157 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6771 (mtmt) REVERT: Y 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6369 (mp10) REVERT: Y 140 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6927 (mp0) REVERT: Y 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6963 (mttm) REVERT: Y 157 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6772 (mtmt) REVERT: 2 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6369 (mp10) REVERT: 2 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6943 (mp0) REVERT: 2 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6958 (mttm) REVERT: 2 157 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6789 (mtmt) REVERT: 4 86 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6370 (mp10) REVERT: 4 140 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6939 (mp0) REVERT: 4 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6960 (mttm) REVERT: 4 157 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: F 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6366 (mp10) REVERT: F 140 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6939 (mp0) REVERT: F 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6964 (mttm) REVERT: F 157 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6784 (mtmt) REVERT: H 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6389 (mp10) REVERT: H 140 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6932 (mp0) REVERT: H 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6960 (mttm) REVERT: H 157 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6772 (mtmt) REVERT: P 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6369 (mp10) REVERT: P 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6942 (mp0) REVERT: P 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6957 (mttm) REVERT: P 157 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: X 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6369 (mp10) REVERT: X 140 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6937 (mp0) REVERT: X 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6958 (mttm) REVERT: X 157 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6769 (mtmt) REVERT: 6 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6393 (mp10) REVERT: 6 140 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6926 (mp0) REVERT: 6 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6961 (mttm) REVERT: 6 157 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6774 (mtmt) outliers start: 48 outliers final: 24 residues processed: 519 average time/residue: 1.3677 time to fit residues: 856.0905 Evaluate side-chains 507 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 459 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 157 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 157 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 157 LYS Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain r residue 157 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 157 LYS Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 157 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain W residue 157 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 157 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 157 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 157 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 157 LYS Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 157 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 139 ASN 1 14 GLN 1 139 ASN K 14 GLN K 139 ASN a 14 GLN a 139 ASN B 14 GLN B 139 ASN E 14 GLN E 139 ASN e 14 GLN e 139 ASN r 14 GLN r 139 ASN G 14 GLN G 139 ASN I 14 GLN I 139 ASN M 14 GLN M 139 ASN O 14 GLN O 139 ASN Q 14 GLN Q 139 ASN S 14 GLN S 139 ASN U 14 GLN U 139 ASN W 14 GLN W 139 ASN Y 14 GLN 2 14 GLN 2 139 ASN 4 14 GLN 4 139 ASN F 14 GLN H 14 GLN H 139 ASN P 14 GLN P 139 ASN X 14 GLN X 139 ASN 6 14 GLN 6 139 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 37800 Z= 0.324 Angle : 0.813 6.384 51264 Z= 0.442 Chirality : 0.043 0.161 5280 Planarity : 0.005 0.037 6936 Dihedral : 7.160 59.975 5304 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 3.81 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.11), residues: 4920 helix: 3.02 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.52 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.005 TRP r 93 HIS 0.005 0.002 HIS e 136 PHE 0.032 0.005 PHE r 41 TYR 0.024 0.004 TYR F 39 ARG 0.010 0.002 ARG W 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 477 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6412 (mp10) REVERT: A 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6927 (mp0) REVERT: A 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6978 (mttm) REVERT: 1 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6417 (mp10) REVERT: 1 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6928 (mp0) REVERT: 1 143 LYS cc_start: 0.7308 (mtmt) cc_final: 0.6990 (mttm) REVERT: K 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6399 (mp10) REVERT: K 140 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6910 (mp0) REVERT: K 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6971 (mttm) REVERT: a 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6396 (mp10) REVERT: a 140 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6913 (mp0) REVERT: a 143 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6985 (mttm) REVERT: B 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6417 (mp10) REVERT: B 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6914 (mp0) REVERT: B 143 LYS cc_start: 0.7306 (mtmt) cc_final: 0.6990 (mttm) REVERT: E 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6418 (mp10) REVERT: E 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6922 (mp0) REVERT: E 143 LYS cc_start: 0.7304 (mtmt) cc_final: 0.6988 (mttm) REVERT: e 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6411 (mp10) REVERT: e 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6928 (mp0) REVERT: e 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6981 (mttm) REVERT: r 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6418 (mp10) REVERT: r 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6909 (mp0) REVERT: r 143 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6984 (mttm) REVERT: G 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6417 (mp10) REVERT: G 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6926 (mp0) REVERT: G 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6978 (mttm) REVERT: I 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6415 (mp10) REVERT: I 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6929 (mp0) REVERT: I 143 LYS cc_start: 0.7308 (mtmt) cc_final: 0.6991 (mttm) REVERT: M 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6396 (mp10) REVERT: M 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6922 (mp0) REVERT: M 143 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6986 (mttm) REVERT: O 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6420 (mp10) REVERT: O 140 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6908 (mp0) REVERT: O 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6981 (mttm) REVERT: Q 86 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6402 (mp10) REVERT: Q 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6924 (mp0) REVERT: Q 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6978 (mttm) REVERT: S 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6407 (mp10) REVERT: S 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6923 (mp0) REVERT: S 143 LYS cc_start: 0.7307 (mtmt) cc_final: 0.6991 (mttm) REVERT: U 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6414 (mp10) REVERT: U 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6923 (mp0) REVERT: U 143 LYS cc_start: 0.7304 (mtmt) cc_final: 0.6986 (mttm) REVERT: W 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6396 (mp10) REVERT: W 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6923 (mp0) REVERT: W 143 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6986 (mttm) REVERT: Y 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6396 (mp10) REVERT: Y 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6910 (mp0) REVERT: Y 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6972 (mttm) REVERT: 2 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6395 (mp10) REVERT: 2 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6930 (mp0) REVERT: 2 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6977 (mttm) REVERT: 4 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6399 (mp10) REVERT: 4 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6930 (mp0) REVERT: 4 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6985 (mttm) REVERT: F 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6397 (mp10) REVERT: F 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6924 (mp0) REVERT: F 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6973 (mttm) REVERT: H 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6416 (mp10) REVERT: H 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6922 (mp0) REVERT: H 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6971 (mttm) REVERT: P 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6398 (mp10) REVERT: P 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6928 (mp0) REVERT: P 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6981 (mttm) REVERT: X 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6400 (mp10) REVERT: X 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6928 (mp0) REVERT: X 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6980 (mttm) REVERT: 6 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6418 (mp10) REVERT: 6 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6915 (mp0) REVERT: 6 143 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6984 (mttm) outliers start: 24 outliers final: 24 residues processed: 501 average time/residue: 1.3601 time to fit residues: 824.9154 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 447 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 0.0770 chunk 177 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN a 14 GLN B 14 GLN e 14 GLN r 14 GLN G 14 GLN I 14 GLN O 14 GLN U 14 GLN Y 14 GLN 4 14 GLN F 14 GLN H 14 GLN 6 14 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 37800 Z= 0.150 Angle : 0.573 5.376 51264 Z= 0.311 Chirality : 0.036 0.149 5280 Planarity : 0.004 0.047 6936 Dihedral : 5.380 44.602 5208 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 3.68 % Favored : 93.27 % 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: 4.75 (0.12), residues: 4920 helix: 3.60 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP 2 93 HIS 0.004 0.001 HIS M 60 PHE 0.019 0.002 PHE 6 41 TYR 0.017 0.002 TYR B 39 ARG 0.007 0.001 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 443 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6433 (mp10) REVERT: A 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6930 (mp0) REVERT: A 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6982 (mttm) REVERT: 1 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6431 (mp10) REVERT: 1 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6776 (mp0) REVERT: 1 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6886 (mttm) REVERT: K 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6416 (mp10) REVERT: K 140 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6919 (mp0) REVERT: K 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6980 (mttm) REVERT: a 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6420 (mp10) REVERT: a 140 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6915 (mp0) REVERT: a 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6980 (mttm) REVERT: B 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6431 (mp10) REVERT: B 140 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6770 (mp0) REVERT: B 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6885 (mttm) REVERT: E 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6429 (mp10) REVERT: E 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6928 (mp0) REVERT: E 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6980 (mttm) REVERT: e 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6434 (mp10) REVERT: e 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6930 (mp0) REVERT: e 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6977 (mttm) REVERT: r 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6431 (mp10) REVERT: r 140 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6916 (mp0) REVERT: r 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6980 (mttm) REVERT: G 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6434 (mp10) REVERT: G 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6933 (mp0) REVERT: G 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6986 (mttm) REVERT: I 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6430 (mp10) REVERT: I 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6775 (mp0) REVERT: I 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6880 (mttm) REVERT: M 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6418 (mp10) REVERT: M 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6926 (mp0) REVERT: M 143 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6973 (mttm) REVERT: O 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6438 (mp10) REVERT: O 140 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6762 (mp0) REVERT: O 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6894 (mttm) REVERT: Q 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6416 (mp10) REVERT: Q 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6932 (mp0) REVERT: Q 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6984 (mttm) REVERT: S 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6416 (mp10) REVERT: S 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6925 (mp0) REVERT: S 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6975 (mttm) REVERT: U 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6434 (mp10) REVERT: U 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6775 (mp0) REVERT: U 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6883 (mttm) REVERT: W 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6410 (mp10) REVERT: W 140 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6926 (mp0) REVERT: W 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6982 (mttm) REVERT: Y 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6413 (mp10) REVERT: Y 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6929 (mp0) REVERT: Y 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6980 (mttm) REVERT: 2 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6415 (mp10) REVERT: 2 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6933 (mp0) REVERT: 2 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6975 (mttm) REVERT: 4 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6412 (mp10) REVERT: 4 140 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6933 (mp0) REVERT: 4 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6973 (mttm) REVERT: F 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6410 (mp10) REVERT: F 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6942 (mp0) REVERT: F 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6979 (mttm) REVERT: H 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6427 (mp10) REVERT: H 140 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6925 (mp0) REVERT: H 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6985 (mttm) REVERT: P 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6414 (mp10) REVERT: P 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6932 (mp0) REVERT: P 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6971 (mttm) REVERT: X 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6412 (mp10) REVERT: X 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6933 (mp0) REVERT: X 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6981 (mttm) REVERT: 6 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6434 (mp10) REVERT: 6 140 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6920 (mp0) REVERT: 6 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6974 (mttm) outliers start: 24 outliers final: 24 residues processed: 467 average time/residue: 1.3290 time to fit residues: 754.7344 Evaluate side-chains 465 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 441 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 139 ASN F 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 37800 Z= 0.216 Angle : 0.672 6.064 51264 Z= 0.364 Chirality : 0.039 0.150 5280 Planarity : 0.004 0.033 6936 Dihedral : 5.478 45.414 5208 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 4.55 % Favored : 92.40 % 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 (0.11), residues: 4920 helix: 3.37 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.68 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Q 93 HIS 0.004 0.001 HIS M 60 PHE 0.024 0.004 PHE W 41 TYR 0.021 0.003 TYR F 39 ARG 0.003 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6430 (mp10) REVERT: A 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6971 (mttm) REVERT: 1 86 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6432 (mp10) REVERT: 1 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6952 (mp0) REVERT: 1 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6981 (mttm) REVERT: K 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6416 (mp10) REVERT: K 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6937 (mp0) REVERT: K 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6972 (mttm) REVERT: a 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6417 (mp10) REVERT: a 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6936 (mp0) REVERT: a 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6983 (mttm) REVERT: B 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6433 (mp10) REVERT: B 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6945 (mp0) REVERT: B 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6980 (mttm) REVERT: E 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6432 (mp10) REVERT: E 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6942 (mp0) REVERT: E 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6981 (mttm) REVERT: e 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6431 (mp10) REVERT: e 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6948 (mp0) REVERT: e 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6974 (mttm) REVERT: r 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6434 (mp10) REVERT: r 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6934 (mp0) REVERT: r 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6983 (mttm) REVERT: G 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6434 (mp10) REVERT: G 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6951 (mp0) REVERT: G 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6982 (mttm) REVERT: I 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6432 (mp10) REVERT: I 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6953 (mp0) REVERT: I 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6978 (mttm) REVERT: M 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6418 (mp10) REVERT: M 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6944 (mp0) REVERT: M 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6980 (mttm) REVERT: O 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6434 (mp10) REVERT: O 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6938 (mp0) REVERT: O 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6979 (mttm) REVERT: Q 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6417 (mp10) REVERT: Q 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6945 (mp0) REVERT: Q 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6979 (mttm) REVERT: S 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6415 (mp10) REVERT: S 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6941 (mp0) REVERT: S 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6980 (mttm) REVERT: U 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6432 (mp10) REVERT: U 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6952 (mp0) REVERT: U 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6976 (mttm) REVERT: W 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6415 (mp10) REVERT: W 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6945 (mp0) REVERT: W 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6982 (mttm) REVERT: Y 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6415 (mp10) REVERT: Y 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6936 (mp0) REVERT: Y 143 LYS cc_start: 0.7307 (mtmt) cc_final: 0.6991 (mttm) REVERT: 2 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6416 (mp10) REVERT: 2 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6952 (mp0) REVERT: 2 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6978 (mttm) REVERT: 4 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6417 (mp10) REVERT: 4 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6950 (mp0) REVERT: 4 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6978 (mttm) REVERT: F 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6413 (mp10) REVERT: F 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6945 (mp0) REVERT: F 143 LYS cc_start: 0.7305 (mtmt) cc_final: 0.6990 (mttm) REVERT: H 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6425 (mp10) REVERT: H 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6944 (mp0) REVERT: H 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6977 (mttm) REVERT: P 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6416 (mp10) REVERT: P 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6951 (mp0) REVERT: P 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6975 (mttm) REVERT: X 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6416 (mp10) REVERT: X 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6951 (mp0) REVERT: X 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6979 (mttm) REVERT: 6 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6434 (mp10) REVERT: 6 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6939 (mp0) REVERT: 6 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6978 (mttm) outliers start: 24 outliers final: 24 residues processed: 478 average time/residue: 1.3049 time to fit residues: 759.0500 Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 0.0010 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 37800 Z= 0.227 Angle : 0.686 6.132 51264 Z= 0.372 Chirality : 0.039 0.152 5280 Planarity : 0.004 0.030 6936 Dihedral : 5.477 45.395 5208 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.05 % Allowed : 4.57 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.11), residues: 4920 helix: 3.29 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.67 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP Q 93 HIS 0.004 0.001 HIS E 128 PHE 0.025 0.004 PHE E 41 TYR 0.023 0.003 TYR H 39 ARG 0.003 0.001 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6436 (mp10) REVERT: A 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6939 (mp0) REVERT: A 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6992 (mttm) REVERT: 1 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6439 (mp10) REVERT: 1 140 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6947 (mp0) REVERT: 1 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6994 (mttm) REVERT: K 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6419 (mp10) REVERT: K 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6926 (mp0) REVERT: K 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6993 (mttm) REVERT: a 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6423 (mp10) REVERT: a 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6925 (mp0) REVERT: a 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6994 (mttm) REVERT: B 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6436 (mp10) REVERT: B 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6938 (mp0) REVERT: B 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6995 (mttm) REVERT: E 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6439 (mp10) REVERT: E 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6942 (mp0) REVERT: E 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6993 (mttm) REVERT: e 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6433 (mp10) REVERT: e 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6945 (mp0) REVERT: e 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6993 (mttm) REVERT: r 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6438 (mp10) REVERT: r 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6928 (mp0) REVERT: r 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6995 (mttm) REVERT: G 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6439 (mp10) REVERT: G 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6937 (mp0) REVERT: G 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6996 (mttm) REVERT: I 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6438 (mp10) REVERT: I 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6943 (mp0) REVERT: I 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6993 (mttm) REVERT: M 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6424 (mp10) REVERT: M 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6946 (mp0) REVERT: M 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6992 (mttm) REVERT: O 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6440 (mp10) REVERT: O 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6937 (mp0) REVERT: O 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6993 (mttm) REVERT: Q 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6421 (mp10) REVERT: Q 140 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6947 (mp0) REVERT: Q 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6997 (mttm) REVERT: S 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6419 (mp10) REVERT: S 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6938 (mp0) REVERT: S 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6995 (mttm) REVERT: U 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6436 (mp10) REVERT: U 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6951 (mp0) REVERT: U 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6993 (mttm) REVERT: W 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6418 (mp10) REVERT: W 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6939 (mp0) REVERT: W 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6998 (mttm) REVERT: Y 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6419 (mp10) REVERT: Y 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6930 (mp0) REVERT: Y 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6986 (mttm) REVERT: 2 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6423 (mp10) REVERT: 2 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6944 (mp0) REVERT: 2 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6994 (mttm) REVERT: 4 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6421 (mp10) REVERT: 4 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6943 (mp0) REVERT: 4 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6987 (mttm) REVERT: F 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6418 (mp10) REVERT: F 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6942 (mp0) REVERT: F 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6991 (mttm) REVERT: H 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6435 (mp10) REVERT: H 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6930 (mp0) REVERT: H 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6997 (mttm) REVERT: P 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6420 (mp10) REVERT: P 140 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6952 (mp0) REVERT: P 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6992 (mttm) REVERT: X 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6420 (mp10) REVERT: X 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6946 (mp0) REVERT: X 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6988 (mttm) REVERT: 6 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6438 (mp10) REVERT: 6 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6932 (mp0) REVERT: 6 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6993 (mttm) outliers start: 24 outliers final: 24 residues processed: 478 average time/residue: 1.3348 time to fit residues: 776.1853 Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 0.0980 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN a 14 GLN B 14 GLN e 14 GLN G 14 GLN I 14 GLN O 14 GLN U 14 GLN 4 14 GLN F 14 GLN H 14 GLN 6 14 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 37800 Z= 0.188 Angle : 0.631 5.762 51264 Z= 0.343 Chirality : 0.038 0.149 5280 Planarity : 0.004 0.027 6936 Dihedral : 5.423 45.025 5208 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.92 % Allowed : 4.70 % Favored : 92.38 % 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: 4.54 (0.12), residues: 4920 helix: 3.44 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.71 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP e 93 HIS 0.003 0.001 HIS E 128 PHE 0.022 0.003 PHE E 41 TYR 0.020 0.002 TYR P 39 ARG 0.003 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6427 (mp10) REVERT: A 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6945 (mp0) REVERT: A 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6985 (mttm) REVERT: 1 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6429 (mp10) REVERT: 1 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6943 (mp0) REVERT: 1 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6990 (mttm) REVERT: K 86 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6410 (mp10) REVERT: K 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6932 (mp0) REVERT: K 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6986 (mttm) REVERT: a 86 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6411 (mp10) REVERT: a 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6933 (mp0) REVERT: a 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6991 (mttm) REVERT: B 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6429 (mp10) REVERT: B 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6943 (mp0) REVERT: B 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6995 (mttm) REVERT: E 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6431 (mp10) REVERT: E 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6939 (mp0) REVERT: E 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6990 (mttm) REVERT: e 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6430 (mp10) REVERT: e 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6947 (mp0) REVERT: e 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6985 (mttm) REVERT: r 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6426 (mp10) REVERT: r 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6933 (mp0) REVERT: r 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6987 (mttm) REVERT: G 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6429 (mp10) REVERT: G 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6944 (mp0) REVERT: G 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6986 (mttm) REVERT: I 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6427 (mp10) REVERT: I 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6951 (mp0) REVERT: I 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6985 (mttm) REVERT: M 86 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6412 (mp10) REVERT: M 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6943 (mp0) REVERT: M 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6988 (mttm) REVERT: O 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6430 (mp10) REVERT: O 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6933 (mp0) REVERT: O 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6993 (mttm) REVERT: Q 86 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6410 (mp10) REVERT: Q 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6943 (mp0) REVERT: Q 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6988 (mttm) REVERT: S 86 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6409 (mp10) REVERT: S 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6948 (mp0) REVERT: S 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6985 (mttm) REVERT: U 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6430 (mp10) REVERT: U 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6948 (mp0) REVERT: U 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6983 (mttm) REVERT: W 86 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6411 (mp10) REVERT: W 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6941 (mp0) REVERT: W 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6989 (mttm) REVERT: Y 86 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6410 (mp10) REVERT: Y 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6931 (mp0) REVERT: Y 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6975 (mttm) REVERT: 2 86 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6410 (mp10) REVERT: 2 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6945 (mp0) REVERT: 2 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6985 (mttm) REVERT: 4 86 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6412 (mp10) REVERT: 4 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6945 (mp0) REVERT: 4 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6987 (mttm) REVERT: F 86 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6406 (mp10) REVERT: F 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6944 (mp0) REVERT: F 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6982 (mttm) REVERT: H 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6431 (mp10) REVERT: H 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6934 (mp0) REVERT: H 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6988 (mttm) REVERT: P 86 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6406 (mp10) REVERT: P 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6944 (mp0) REVERT: P 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6987 (mttm) REVERT: X 86 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6412 (mp10) REVERT: X 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6949 (mp0) REVERT: X 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6996 (mttm) REVERT: 6 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6433 (mp10) REVERT: 6 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6931 (mp0) REVERT: 6 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6988 (mttm) outliers start: 24 outliers final: 24 residues processed: 478 average time/residue: 1.3288 time to fit residues: 771.9917 Evaluate side-chains 475 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 451 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN a 14 GLN B 14 GLN e 14 GLN G 14 GLN I 14 GLN O 14 GLN U 14 GLN 4 14 GLN F 14 GLN H 14 GLN 6 14 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 37800 Z= 0.190 Angle : 0.638 5.833 51264 Z= 0.346 Chirality : 0.038 0.149 5280 Planarity : 0.004 0.026 6936 Dihedral : 5.430 45.239 5208 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.52 % Allowed : 5.11 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.12), residues: 4920 helix: 3.43 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 2 93 HIS 0.003 0.001 HIS E 128 PHE 0.022 0.003 PHE E 41 TYR 0.021 0.002 TYR W 39 ARG 0.005 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 466 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6425 (mp10) REVERT: A 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6941 (mp0) REVERT: A 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6992 (mttm) REVERT: 1 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6428 (mp10) REVERT: 1 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6946 (mp0) REVERT: 1 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6997 (mttm) REVERT: K 86 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6411 (mp10) REVERT: K 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6931 (mp0) REVERT: K 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6992 (mttm) REVERT: a 86 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6409 (mp10) REVERT: a 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6932 (mp0) REVERT: a 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.7001 (mttm) REVERT: B 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6427 (mp10) REVERT: B 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6942 (mp0) REVERT: B 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6996 (mttm) REVERT: E 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6429 (mp10) REVERT: E 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6941 (mp0) REVERT: E 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6989 (mttm) REVERT: e 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6430 (mp10) REVERT: e 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6947 (mp0) REVERT: e 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6993 (mttm) REVERT: r 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6428 (mp10) REVERT: r 140 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6927 (mp0) REVERT: r 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6994 (mttm) REVERT: G 86 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6427 (mp10) REVERT: G 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6946 (mp0) REVERT: G 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6995 (mttm) REVERT: I 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6425 (mp10) REVERT: I 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6941 (mp0) REVERT: I 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6994 (mttm) REVERT: M 86 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6411 (mp10) REVERT: M 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6943 (mp0) REVERT: M 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6994 (mttm) REVERT: O 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6433 (mp10) REVERT: O 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6935 (mp0) REVERT: O 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6993 (mttm) REVERT: Q 86 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6409 (mp10) REVERT: Q 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6949 (mp0) REVERT: Q 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6991 (mttm) REVERT: S 86 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6410 (mp10) REVERT: S 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6948 (mp0) REVERT: S 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6996 (mttm) REVERT: U 86 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6427 (mp10) REVERT: U 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6949 (mp0) REVERT: U 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6986 (mttm) REVERT: W 86 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6409 (mp10) REVERT: W 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6942 (mp0) REVERT: W 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6998 (mttm) REVERT: Y 86 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6411 (mp10) REVERT: Y 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6930 (mp0) REVERT: Y 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6988 (mttm) REVERT: 2 86 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6410 (mp10) REVERT: 2 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6943 (mp0) REVERT: 2 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6993 (mttm) REVERT: 4 86 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6407 (mp10) REVERT: 4 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6947 (mp0) REVERT: 4 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6992 (mttm) REVERT: F 86 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6408 (mp10) REVERT: F 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6940 (mp0) REVERT: F 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6988 (mttm) REVERT: H 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6433 (mp10) REVERT: H 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6939 (mp0) REVERT: H 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6997 (mttm) REVERT: P 86 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6407 (mp10) REVERT: P 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6944 (mp0) REVERT: P 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6986 (mttm) REVERT: X 86 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6412 (mp10) REVERT: X 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6946 (mp0) REVERT: X 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6994 (mttm) REVERT: 6 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6432 (mp10) REVERT: 6 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6933 (mp0) REVERT: 6 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6987 (mttm) outliers start: 24 outliers final: 24 residues processed: 490 average time/residue: 1.3086 time to fit residues: 781.3202 Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 287 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 0.0370 chunk 346 optimal weight: 10.0000 chunk 365 optimal weight: 0.5980 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN a 14 GLN B 14 GLN e 14 GLN G 14 GLN I 14 GLN O 14 GLN U 14 GLN 4 14 GLN F 14 GLN H 14 GLN 6 14 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 37800 Z= 0.150 Angle : 0.574 6.354 51264 Z= 0.312 Chirality : 0.036 0.146 5280 Planarity : 0.004 0.071 6936 Dihedral : 5.352 44.835 5208 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.46 % Allowed : 4.85 % Favored : 92.68 % 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: 4.82 (0.12), residues: 4920 helix: 3.65 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP W 93 HIS 0.005 0.001 HIS M 60 PHE 0.018 0.003 PHE I 41 TYR 0.017 0.002 TYR H 39 ARG 0.007 0.001 ARG S 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.250 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: A 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6425 (mp10) REVERT: A 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6941 (mp0) REVERT: A 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6991 (mttm) REVERT: 1 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6427 (mp10) REVERT: 1 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6946 (mp0) REVERT: 1 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6997 (mttm) REVERT: K 86 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6418 (mp10) REVERT: K 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6936 (mp0) REVERT: K 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6990 (mttm) REVERT: a 86 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6413 (mp10) REVERT: a 140 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6918 (mp0) REVERT: a 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6994 (mttm) REVERT: B 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6427 (mp10) REVERT: B 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6935 (mp0) REVERT: B 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6992 (mttm) REVERT: E 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6429 (mp10) REVERT: E 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6946 (mp0) REVERT: E 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6997 (mttm) REVERT: e 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6424 (mp10) REVERT: e 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6942 (mp0) REVERT: e 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6993 (mttm) REVERT: r 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6426 (mp10) REVERT: r 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6930 (mp0) REVERT: r 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6994 (mttm) REVERT: G 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6425 (mp10) REVERT: G 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6949 (mp0) REVERT: G 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6994 (mttm) REVERT: I 86 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6426 (mp10) REVERT: I 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6951 (mp0) REVERT: I 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6995 (mttm) REVERT: M 63 ARG cc_start: 0.7057 (ttp-170) cc_final: 0.6812 (tpt-90) REVERT: M 86 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6415 (mp10) REVERT: M 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6940 (mp0) REVERT: M 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6995 (mttm) REVERT: O 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6428 (mp10) REVERT: O 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6929 (mp0) REVERT: O 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6992 (mttm) REVERT: Q 86 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6409 (mp10) REVERT: Q 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6950 (mp0) REVERT: Q 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6997 (mttm) REVERT: S 86 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6418 (mp10) REVERT: S 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6938 (mp0) REVERT: S 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6996 (mttm) REVERT: U 86 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6425 (mp10) REVERT: U 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6944 (mp0) REVERT: U 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6994 (mttm) REVERT: W 86 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6412 (mp10) REVERT: W 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6936 (mp0) REVERT: W 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6997 (mttm) REVERT: Y 86 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6414 (mp10) REVERT: Y 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6931 (mp0) REVERT: Y 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6988 (mttm) REVERT: 2 86 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6415 (mp10) REVERT: 2 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6947 (mp0) REVERT: 2 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6994 (mttm) REVERT: 4 86 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6412 (mp10) REVERT: 4 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6950 (mp0) REVERT: 4 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6991 (mttm) REVERT: F 86 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6409 (mp10) REVERT: F 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6944 (mp0) REVERT: F 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6987 (mttm) REVERT: H 86 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6424 (mp10) REVERT: H 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6941 (mp0) REVERT: H 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6994 (mttm) REVERT: P 86 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6408 (mp10) REVERT: P 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6948 (mp0) REVERT: P 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6992 (mttm) REVERT: X 86 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6409 (mp10) REVERT: X 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6946 (mp0) REVERT: X 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6994 (mttm) REVERT: 6 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6427 (mp10) REVERT: 6 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6938 (mp0) REVERT: 6 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6994 (mttm) outliers start: 24 outliers final: 24 residues processed: 478 average time/residue: 1.3068 time to fit residues: 760.2438 Evaluate side-chains 478 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 0.0060 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 0.6980 chunk 323 optimal weight: 0.0070 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 overall best weight: 0.9216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN a 14 GLN B 14 GLN e 14 GLN G 14 GLN I 14 GLN O 14 GLN U 14 GLN 4 14 GLN F 14 GLN H 14 GLN 6 14 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 37800 Z= 0.134 Angle : 0.547 7.909 51264 Z= 0.297 Chirality : 0.035 0.142 5280 Planarity : 0.004 0.125 6936 Dihedral : 5.271 44.617 5208 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.46 % Allowed : 4.85 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.00 (0.12), residues: 4920 helix: 3.79 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP S 93 HIS 0.005 0.001 HIS K 60 PHE 0.016 0.002 PHE r 41 TYR 0.015 0.002 TYR H 39 ARG 0.010 0.001 ARG H 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 448 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6413 (mp10) REVERT: A 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6943 (mp0) REVERT: A 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6990 (mttm) REVERT: 1 86 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6414 (mp10) REVERT: 1 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6942 (mp0) REVERT: 1 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6997 (mttm) REVERT: K 86 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6406 (mp10) REVERT: K 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6932 (mp0) REVERT: K 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6991 (mttm) REVERT: a 86 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6404 (mp10) REVERT: a 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6926 (mp0) REVERT: a 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6992 (mttm) REVERT: B 86 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6414 (mp10) REVERT: B 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6936 (mp0) REVERT: B 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6994 (mttm) REVERT: E 86 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6413 (mp10) REVERT: E 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6938 (mp0) REVERT: E 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6993 (mttm) REVERT: e 86 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6414 (mp10) REVERT: e 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6945 (mp0) REVERT: e 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6989 (mttm) REVERT: r 86 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6413 (mp10) REVERT: r 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6930 (mp0) REVERT: r 143 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6989 (mttm) REVERT: G 86 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6414 (mp10) REVERT: G 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6945 (mp0) REVERT: G 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6993 (mttm) REVERT: I 86 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6412 (mp10) REVERT: I 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6944 (mp0) REVERT: I 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6992 (mttm) REVERT: M 63 ARG cc_start: 0.6995 (ttp-170) cc_final: 0.6776 (tpt-90) REVERT: M 86 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6404 (mp10) REVERT: M 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6940 (mp0) REVERT: M 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6991 (mttm) REVERT: O 86 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6417 (mp10) REVERT: O 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6930 (mp0) REVERT: O 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6991 (mttm) REVERT: Q 86 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6403 (mp10) REVERT: Q 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6947 (mp0) REVERT: Q 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6994 (mttm) REVERT: S 86 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6404 (mp10) REVERT: S 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6941 (mp0) REVERT: S 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6993 (mttm) REVERT: U 86 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6412 (mp10) REVERT: U 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6944 (mp0) REVERT: U 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6991 (mttm) REVERT: W 86 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6401 (mp10) REVERT: W 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6937 (mp0) REVERT: W 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6995 (mttm) REVERT: Y 86 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6403 (mp10) REVERT: Y 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6927 (mp0) REVERT: Y 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6994 (mttm) REVERT: 2 86 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6402 (mp10) REVERT: 2 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6945 (mp0) REVERT: 2 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6991 (mttm) REVERT: 4 86 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6404 (mp10) REVERT: 4 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6945 (mp0) REVERT: 4 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6994 (mttm) REVERT: F 86 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6396 (mp10) REVERT: F 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6941 (mp0) REVERT: F 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6995 (mttm) REVERT: H 86 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6412 (mp10) REVERT: H 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6934 (mp0) REVERT: H 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6995 (mttm) REVERT: P 86 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6399 (mp10) REVERT: P 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6945 (mp0) REVERT: P 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6993 (mttm) REVERT: X 86 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6400 (mp10) REVERT: X 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6946 (mp0) REVERT: X 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6995 (mttm) REVERT: 6 86 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6415 (mp10) REVERT: 6 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6933 (mp0) REVERT: 6 143 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6994 (mttm) outliers start: 24 outliers final: 24 residues processed: 472 average time/residue: 1.3289 time to fit residues: 761.4592 Evaluate side-chains 472 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 448 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS K 60 HIS B 60 HIS e 14 GLN e 60 HIS S 60 HIS 4 14 GLN 4 60 HIS F 60 HIS X 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149820 restraints weight = 251459.980| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.37 r_work: 0.3410 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3247 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work: 0.3189 rms_B_bonded: 4.62 restraints_weight: 0.0625 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37800 Z= 0.164 Angle : 0.596 7.082 51264 Z= 0.324 Chirality : 0.037 0.145 5280 Planarity : 0.004 0.131 6936 Dihedral : 5.360 45.153 5208 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.46 % Allowed : 4.85 % Favored : 92.68 % 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: 4.81 (0.12), residues: 4920 helix: 3.64 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.71 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 93 HIS 0.006 0.001 HIS G 60 PHE 0.019 0.003 PHE r 41 TYR 0.018 0.002 TYR K 39 ARG 0.006 0.001 ARG 2 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17653.65 seconds wall clock time: 307 minutes 38.30 seconds (18458.30 seconds total)