Starting phenix.real_space_refine on Mon Mar 18 02:18:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/03_2024/7a6a_11668_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/03_2024/7a6a_11668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/03_2024/7a6a_11668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/03_2024/7a6a_11668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/03_2024/7a6a_11668_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6a_11668/03_2024/7a6a_11668_updated.pdb" } resolution = 1.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 41613 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 Na 32 4.78 5 C 23112 2.51 5 N 6552 2.21 5 O 11797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 9": "NH1" <-> "NH2" Residue "1 ASP 15": "OD1" <-> "OD2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "1 ASP 91": "OD1" <-> "OD2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "1 ASP 123": "OD1" <-> "OD2" Residue "1 ASP 131": "OD1" <-> "OD2" Residue "1 GLU 134": "OE1" <-> "OE2" Residue "1 GLU 140": "OE1" <-> "OE2" Residue "1 GLU 147": "OE1" <-> "OE2" Residue "1 ASP 150": "OD1" <-> "OD2" Residue "1 ARG 156": "NH1" <-> "NH2" Residue "1 ARG 156": "NH1" <-> "NH2" Residue "1 GLU 167": "OE1" <-> "OE2" Residue "1 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "K ASP 150": "OD1" <-> "OD2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ASP 15": "OD1" <-> "OD2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ASP 91": "OD1" <-> "OD2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "a ASP 123": "OD1" <-> "OD2" Residue "a ASP 131": "OD1" <-> "OD2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 140": "OE1" <-> "OE2" Residue "a GLU 147": "OE1" <-> "OE2" Residue "a ASP 150": "OD1" <-> "OD2" Residue "a ARG 156": "NH1" <-> "NH2" Residue "a ARG 156": "NH1" <-> "NH2" Residue "a GLU 167": "OE1" <-> "OE2" Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E ASP 131": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 9": "NH1" <-> "NH2" Residue "e ASP 15": "OD1" <-> "OD2" Residue "e GLU 61": "OE1" <-> "OE2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 131": "OD1" <-> "OD2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "e GLU 140": "OE1" <-> "OE2" Residue "e GLU 147": "OE1" <-> "OE2" Residue "e ASP 150": "OD1" <-> "OD2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e GLU 167": "OE1" <-> "OE2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ASP 15": "OD1" <-> "OD2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ASP 91": "OD1" <-> "OD2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Residue "r ASP 123": "OD1" <-> "OD2" Residue "r ASP 131": "OD1" <-> "OD2" Residue "r GLU 134": "OE1" <-> "OE2" Residue "r GLU 140": "OE1" <-> "OE2" Residue "r GLU 147": "OE1" <-> "OE2" Residue "r ASP 150": "OD1" <-> "OD2" Residue "r ARG 156": "NH1" <-> "NH2" Residue "r ARG 156": "NH1" <-> "NH2" Residue "r GLU 167": "OE1" <-> "OE2" Residue "r TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I ASP 123": "OD1" <-> "OD2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 150": "OD1" <-> "OD2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 9": "NH1" <-> "NH2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 123": "OD1" <-> "OD2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 150": "OD1" <-> "OD2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O ASP 123": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "Q ASP 150": "OD1" <-> "OD2" Residue "Q ARG 156": "NH1" <-> "NH2" Residue "Q ARG 156": "NH1" <-> "NH2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 9": "NH1" <-> "NH2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "S GLU 134": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S ASP 150": "OD1" <-> "OD2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S GLU 167": "OE1" <-> "OE2" Residue "S TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 9": "NH1" <-> "NH2" Residue "U ASP 15": "OD1" <-> "OD2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "U ASP 123": "OD1" <-> "OD2" Residue "U ASP 131": "OD1" <-> "OD2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U GLU 147": "OE1" <-> "OE2" Residue "U ASP 150": "OD1" <-> "OD2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 9": "NH1" <-> "NH2" Residue "W ASP 15": "OD1" <-> "OD2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ASP 123": "OD1" <-> "OD2" Residue "W ASP 131": "OD1" <-> "OD2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ASP 150": "OD1" <-> "OD2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "W TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Y GLU 61": "OE1" <-> "OE2" Residue "Y ARG 63": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y ASP 123": "OD1" <-> "OD2" Residue "Y ASP 131": "OD1" <-> "OD2" Residue "Y GLU 134": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "Y GLU 147": "OE1" <-> "OE2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "Y ARG 156": "NH1" <-> "NH2" Residue "Y ARG 156": "NH1" <-> "NH2" Residue "Y GLU 167": "OE1" <-> "OE2" Residue "Y TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 9": "NH1" <-> "NH2" Residue "2 ASP 15": "OD1" <-> "OD2" Residue "2 GLU 61": "OE1" <-> "OE2" Residue "2 ARG 63": "NH1" <-> "NH2" Residue "2 ASP 91": "OD1" <-> "OD2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "2 ASP 123": "OD1" <-> "OD2" Residue "2 ASP 131": "OD1" <-> "OD2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 GLU 140": "OE1" <-> "OE2" Residue "2 GLU 147": "OE1" <-> "OE2" Residue "2 ASP 150": "OD1" <-> "OD2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 GLU 167": "OE1" <-> "OE2" Residue "2 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 9": "NH1" <-> "NH2" Residue "4 ASP 15": "OD1" <-> "OD2" Residue "4 GLU 61": "OE1" <-> "OE2" Residue "4 ARG 63": "NH1" <-> "NH2" Residue "4 ASP 91": "OD1" <-> "OD2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 116": "OE1" <-> "OE2" Residue "4 ASP 123": "OD1" <-> "OD2" Residue "4 ASP 131": "OD1" <-> "OD2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 GLU 140": "OE1" <-> "OE2" Residue "4 GLU 147": "OE1" <-> "OE2" Residue "4 ASP 150": "OD1" <-> "OD2" Residue "4 ARG 156": "NH1" <-> "NH2" Residue "4 ARG 156": "NH1" <-> "NH2" Residue "4 GLU 167": "OE1" <-> "OE2" Residue "4 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H ASP 131": "OD1" <-> "OD2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P ASP 123": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 9": "NH1" <-> "NH2" Residue "X ASP 15": "OD1" <-> "OD2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X ARG 63": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X ASP 123": "OD1" <-> "OD2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 147": "OE1" <-> "OE2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X ARG 156": "NH1" <-> "NH2" Residue "X ARG 156": "NH1" <-> "NH2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 9": "NH1" <-> "NH2" Residue "6 ASP 15": "OD1" <-> "OD2" Residue "6 GLU 61": "OE1" <-> "OE2" Residue "6 ARG 63": "NH1" <-> "NH2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 ASP 123": "OD1" <-> "OD2" Residue "6 ASP 131": "OD1" <-> "OD2" Residue "6 GLU 134": "OE1" <-> "OE2" Residue "6 GLU 140": "OE1" <-> "OE2" Residue "6 GLU 147": "OE1" <-> "OE2" Residue "6 ASP 150": "OD1" <-> "OD2" Residue "6 ARG 156": "NH1" <-> "NH2" Residue "6 ARG 156": "NH1" <-> "NH2" Residue "6 GLU 167": "OE1" <-> "OE2" Residue "6 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41613 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "1" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "K" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "a" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "B" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "E" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "e" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "r" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "G" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "I" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "M" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "O" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "Q" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "S" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "U" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "W" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "Y" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "2" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "4" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "F" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "H" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "P" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "X" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "6" Number of atoms: 1540 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 1412 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Conformer: "C" Number of residues, atoms: 160, 1302 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 156} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1312 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "1" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "K" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "a" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "B" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "e" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "r" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "I" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "M" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "O" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "Q" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "S" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "U" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "W" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "Y" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "2" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "4" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "F" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 191 Classifications: {'water': 191} Link IDs: {None: 190} Chain: "H" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "P" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "X" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "6" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Residues with excluded nonbonded symmetry interactions: 336 residue: pdb=" N ALYS A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 49 " occ=0.50 residue: pdb=" N ALYS A 53 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 53 " occ=0.50 residue: pdb=" N AGLU A 64 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.50 residue: pdb=" N ALYS A 68 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 68 " occ=0.50 residue: pdb=" N ALYS A 71 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 71 " occ=0.50 residue: pdb=" N ALEU A 72 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 72 " occ=0.50 residue: pdb=" N AGLN A 75 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 75 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N AASN A 109 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 109 " occ=0.50 residue: pdb=" N ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG CSER A 113 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 residue: pdb=" N AARG A 156 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 156 " occ=0.50 ... (remaining 324 not shown) Time building chain proxies: 38.05, per 1000 atoms: 0.91 Number of scatterers: 41613 At special positions: 0 Unit cell: (135.3, 135.3, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Na 32 11.00 O 11797 8.00 N 6552 7.00 C 23112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.03 Conformation dependent library (CDL) restraints added in 13.0 seconds 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 75 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 75 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 75 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 75 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 75 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 75 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 75 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 75 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 75 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 75 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 75 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 75 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 75 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 75 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 75 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 75 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 75 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 75 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 75 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 75 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 75 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 75 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 2712 hydrogen bonds defined for protein. 8352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.43 Time building geometry restraints manager: 19.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 6102 1.26 - 1.40: 10242 1.40 - 1.54: 21197 1.54 - 1.69: 211 1.69 - 1.83: 216 Bond restraints: 37968 Sorted by residual: bond pdb=" C CSER 6 113 " pdb=" O CSER 6 113 " ideal model delta sigma weight residual 1.237 1.117 0.120 1.17e-02 7.31e+03 1.05e+02 bond pdb=" C CSER P 113 " pdb=" O CSER P 113 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.15e-02 7.56e+03 1.98e+01 bond pdb=" C CSER 2 113 " pdb=" N LEU 2 114 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.31e-02 5.83e+03 1.89e+01 bond pdb=" C ARG M 43 " pdb=" O ARG M 43 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.24e-02 6.50e+03 1.88e+01 bond pdb=" C ARG X 43 " pdb=" O ARG X 43 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.24e-02 6.50e+03 1.88e+01 ... (remaining 37963 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.27: 593 106.27 - 113.17: 17629 113.17 - 120.08: 17023 120.08 - 126.98: 15856 126.98 - 133.88: 427 Bond angle restraints: 51528 Sorted by residual: angle pdb=" CA ASP G 150 " pdb=" CB ASP G 150 " pdb=" CG ASP G 150 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASP 4 150 " pdb=" CB ASP 4 150 " pdb=" CG ASP 4 150 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASP P 150 " pdb=" CB ASP P 150 " pdb=" CG ASP P 150 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" CA ASP M 150 " pdb=" CB ASP M 150 " pdb=" CG ASP M 150 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" CA ASP 1 150 " pdb=" CB ASP 1 150 " pdb=" CG ASP 1 150 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 ... (remaining 51523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 20808 15.77 - 31.54: 1708 31.54 - 47.30: 500 47.30 - 63.07: 240 63.07 - 78.84: 72 Dihedral angle restraints: 23328 sinusoidal: 9696 harmonic: 13632 Sorted by residual: dihedral pdb=" C TYR 1 39 " pdb=" N TYR 1 39 " pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" C TYR G 39 " pdb=" N TYR G 39 " pdb=" CA TYR G 39 " pdb=" CB TYR G 39 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" C TYR 2 39 " pdb=" N TYR 2 39 " pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " ideal model delta harmonic sigma weight residual -122.60 -134.43 11.83 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 23325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2426 0.110 - 0.219: 2012 0.219 - 0.329: 722 0.329 - 0.438: 72 0.438 - 0.548: 72 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CG LEU 6 117 " pdb=" CB LEU 6 117 " pdb=" CD1 LEU 6 117 " pdb=" CD2 LEU 6 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" CG LEU X 117 " pdb=" CB LEU X 117 " pdb=" CD1 LEU X 117 " pdb=" CD2 LEU X 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" CG LEU P 117 " pdb=" CB LEU P 117 " pdb=" CD1 LEU P 117 " pdb=" CD2 LEU P 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.12e+00 ... (remaining 5301 not shown) Planarity restraints: 6984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 137 " -0.139 2.00e-02 2.50e+03 7.67e-02 1.18e+02 pdb=" CG TYR 6 137 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 137 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 137 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 137 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 137 " 0.061 2.00e-02 2.50e+03 pdb=" CZ TYR 6 137 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR 6 137 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.139 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR P 137 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " -0.060 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.139 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR a 137 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.106 2.00e-02 2.50e+03 ... (remaining 6981 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 260 2.47 - 3.07: 35098 3.07 - 3.68: 76655 3.68 - 4.29: 127541 4.29 - 4.90: 190295 Nonbonded interactions: 429849 Sorted by model distance: nonbonded pdb=" OE2 GLU X 101 " pdb=" NH2BARG X 156 " model vdw 1.857 2.520 nonbonded pdb=" OE2 GLU P 101 " pdb=" NH2BARG P 156 " model vdw 1.859 2.520 nonbonded pdb=" OE2 GLU H 101 " pdb=" NH2BARG H 156 " model vdw 1.860 2.520 nonbonded pdb=" OE2 GLU F 101 " pdb=" NH2BARG F 156 " model vdw 1.862 2.520 nonbonded pdb=" OE2 GLU 4 101 " pdb=" NH2BARG 4 156 " model vdw 1.863 2.520 ... (remaining 429844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'Y' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'a' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'e' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) selection = (chain 'r' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 112 or resid 114 throu \ gh 132 or resid 134 through 155 or resid 157 through 161 or resid 163 through 17 \ 1 or resid 173 through 176 or resid 300)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.040 Extract box with map and model: 23.960 Check model and map are aligned: 0.470 Set scattering table: 0.310 Process input model: 123.880 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.120 37968 Z= 1.200 Angle : 1.695 11.100 51528 Z= 1.150 Chirality : 0.160 0.548 5304 Planarity : 0.013 0.077 6984 Dihedral : 14.684 78.837 14688 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.03 % Allowed : 3.03 % Favored : 93.94 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.11), residues: 4992 helix: 1.92 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.41 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.010 TRP Q 93 HIS 0.035 0.010 HIS 6 65 PHE 0.057 0.016 PHE U 81 TYR 0.139 0.030 TYR H 137 ARG 0.030 0.004 ARG 1 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 936 time to evaluate : 3.338 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 14 GLN cc_start: 0.5865 (mm110) cc_final: 0.5432 (pm20) REVERT: A 61 GLU cc_start: 0.6207 (mm-30) cc_final: 0.6007 (mm-30) REVERT: A 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6045 (tttp) REVERT: 1 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5431 (pm20) REVERT: 1 61 GLU cc_start: 0.6207 (mm-30) cc_final: 0.6006 (mm-30) REVERT: 1 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: K 14 GLN cc_start: 0.5865 (mm110) cc_final: 0.5433 (pm20) REVERT: K 61 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6004 (mm-30) REVERT: K 119 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6047 (tttp) REVERT: a 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5430 (pm20) REVERT: a 61 GLU cc_start: 0.6208 (mm-30) cc_final: 0.6007 (mm-30) REVERT: a 119 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6046 (tttp) REVERT: B 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5429 (pm20) REVERT: B 61 GLU cc_start: 0.6203 (mm-30) cc_final: 0.6003 (mm-30) REVERT: B 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6045 (tttp) REVERT: E 14 GLN cc_start: 0.5865 (mm110) cc_final: 0.5430 (pm20) REVERT: E 61 GLU cc_start: 0.6204 (mm-30) cc_final: 0.6003 (mm-30) REVERT: E 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6045 (tttp) REVERT: e 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5431 (pm20) REVERT: e 61 GLU cc_start: 0.6208 (mm-30) cc_final: 0.6007 (mm-30) REVERT: e 119 LYS cc_start: 0.6341 (ttmm) cc_final: 0.6044 (tttp) REVERT: r 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5430 (pm20) REVERT: r 61 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6005 (mm-30) REVERT: r 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: G 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5430 (pm20) REVERT: G 61 GLU cc_start: 0.6205 (mm-30) cc_final: 0.6005 (mm-30) REVERT: G 119 LYS cc_start: 0.6341 (ttmm) cc_final: 0.6045 (tttp) REVERT: I 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5428 (pm20) REVERT: I 61 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6006 (mm-30) REVERT: I 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: M 14 GLN cc_start: 0.5865 (mm110) cc_final: 0.5431 (pm20) REVERT: M 61 GLU cc_start: 0.6202 (mm-30) cc_final: 0.6002 (mm-30) REVERT: M 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: O 14 GLN cc_start: 0.5865 (mm110) cc_final: 0.5432 (pm20) REVERT: O 61 GLU cc_start: 0.6205 (mm-30) cc_final: 0.6003 (mm-30) REVERT: O 119 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6047 (tttp) REVERT: Q 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5430 (pm20) REVERT: Q 61 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6005 (mm-30) REVERT: Q 119 LYS cc_start: 0.6341 (ttmm) cc_final: 0.6045 (tttp) REVERT: S 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5430 (pm20) REVERT: S 61 GLU cc_start: 0.6203 (mm-30) cc_final: 0.6002 (mm-30) REVERT: S 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: U 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5429 (pm20) REVERT: U 61 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6006 (mm-30) REVERT: U 119 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6046 (tttp) REVERT: W 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5431 (pm20) REVERT: W 61 GLU cc_start: 0.6202 (mm-30) cc_final: 0.6002 (mm-30) REVERT: W 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: Y 14 GLN cc_start: 0.5865 (mm110) cc_final: 0.5432 (pm20) REVERT: Y 61 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6004 (mm-30) REVERT: Y 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: 2 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5429 (pm20) REVERT: 2 61 GLU cc_start: 0.6207 (mm-30) cc_final: 0.6006 (mm-30) REVERT: 2 119 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6047 (tttp) REVERT: 4 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5430 (pm20) REVERT: 4 61 GLU cc_start: 0.6205 (mm-30) cc_final: 0.6005 (mm-30) REVERT: 4 119 LYS cc_start: 0.6341 (ttmm) cc_final: 0.6045 (tttp) REVERT: F 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5431 (pm20) REVERT: F 61 GLU cc_start: 0.6208 (mm-30) cc_final: 0.6007 (mm-30) REVERT: F 119 LYS cc_start: 0.6341 (ttmm) cc_final: 0.6044 (tttp) REVERT: H 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5430 (pm20) REVERT: H 61 GLU cc_start: 0.6205 (mm-30) cc_final: 0.6004 (mm-30) REVERT: H 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6045 (tttp) REVERT: P 14 GLN cc_start: 0.5864 (mm110) cc_final: 0.5431 (pm20) REVERT: P 61 GLU cc_start: 0.6207 (mm-30) cc_final: 0.6005 (mm-30) REVERT: P 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6045 (tttp) REVERT: X 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5431 (pm20) REVERT: X 61 GLU cc_start: 0.6207 (mm-30) cc_final: 0.6005 (mm-30) REVERT: X 119 LYS cc_start: 0.6342 (ttmm) cc_final: 0.6046 (tttp) REVERT: 6 14 GLN cc_start: 0.5863 (mm110) cc_final: 0.5430 (pm20) REVERT: 6 119 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6046 (tttp) outliers start: 48 outliers final: 0 residues processed: 960 average time/residue: 1.5806 time to fit residues: 1794.3306 Evaluate side-chains 909 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 909 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.7980 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 98 ASN A 105 HIS A 136 HIS 1 14 GLN 1 98 ASN 1 105 HIS 1 136 HIS K 14 GLN K 98 ASN K 105 HIS K 136 HIS a 14 GLN a 98 ASN a 105 HIS a 136 HIS B 14 GLN B 98 ASN B 105 HIS B 112 GLN B 136 HIS E 14 GLN E 98 ASN E 105 HIS E 112 GLN E 136 HIS e 14 GLN e 98 ASN e 105 HIS e 136 HIS r 14 GLN r 98 ASN r 105 HIS r 136 HIS G 14 GLN G 98 ASN G 105 HIS G 136 HIS I 14 GLN I 98 ASN I 105 HIS I 112 GLN I 136 HIS M 14 GLN M 98 ASN M 105 HIS M 112 GLN M 136 HIS O 14 GLN O 98 ASN O 105 HIS O 136 HIS Q 14 GLN Q 98 ASN Q 105 HIS Q 136 HIS S 14 GLN S 98 ASN S 105 HIS S 112 GLN S 136 HIS U 14 GLN U 98 ASN U 105 HIS U 136 HIS W 14 GLN W 98 ASN W 105 HIS W 136 HIS Y 14 GLN Y 98 ASN Y 105 HIS Y 136 HIS 2 14 GLN 2 98 ASN 2 105 HIS 2 136 HIS 4 14 GLN 4 98 ASN 4 105 HIS 4 136 HIS F 14 GLN F 98 ASN F 105 HIS F 136 HIS H 14 GLN H 98 ASN H 105 HIS H 136 HIS P 14 GLN P 98 ASN P 105 HIS P 136 HIS X 14 GLN X 98 ASN X 105 HIS X 136 HIS 6 14 GLN 6 98 ASN 6 105 HIS 6 136 HIS Total number of N/Q/H flips: 101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 37968 Z= 0.165 Angle : 0.585 5.669 51528 Z= 0.326 Chirality : 0.039 0.160 5304 Planarity : 0.004 0.026 6984 Dihedral : 4.466 18.857 5208 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.42 % Allowed : 3.06 % Favored : 94.52 % 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: 4.29 (0.11), residues: 4992 helix: 3.19 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP P 93 HIS 0.004 0.001 HIS B 60 PHE 0.022 0.003 PHE 1 41 TYR 0.021 0.003 TYR 1 39 ARG 0.006 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 906 time to evaluate : 3.357 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 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5345 (pm20) REVERT: A 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6106 (tttp) REVERT: 1 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5346 (pm20) REVERT: 1 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: K 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5345 (pm20) REVERT: K 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6104 (tttp) REVERT: a 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5346 (pm20) REVERT: a 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: B 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5345 (pm20) REVERT: B 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: E 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5345 (pm20) REVERT: E 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: e 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5345 (pm20) REVERT: e 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6105 (tttp) REVERT: r 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5347 (pm20) REVERT: r 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6105 (tttp) REVERT: G 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5344 (pm20) REVERT: G 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: I 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5345 (pm20) REVERT: I 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: M 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5346 (pm20) REVERT: M 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: O 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5345 (pm20) REVERT: O 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6105 (tttp) REVERT: Q 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5344 (pm20) REVERT: Q 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6107 (tttp) REVERT: S 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5345 (pm20) REVERT: S 119 LYS cc_start: 0.6400 (ttmm) cc_final: 0.6106 (tttp) REVERT: U 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5346 (pm20) REVERT: U 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6105 (tttp) REVERT: W 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5345 (pm20) REVERT: W 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: Y 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5345 (pm20) REVERT: Y 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6105 (tttp) REVERT: 2 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5345 (pm20) REVERT: 2 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6105 (tttp) REVERT: 4 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5344 (pm20) REVERT: 4 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6107 (tttp) REVERT: F 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5345 (pm20) REVERT: F 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6105 (tttp) REVERT: H 14 GLN cc_start: 0.5789 (mm-40) cc_final: 0.5346 (pm20) REVERT: H 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6106 (tttp) REVERT: P 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5346 (pm20) REVERT: P 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: X 14 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5345 (pm20) REVERT: X 119 LYS cc_start: 0.6399 (ttmm) cc_final: 0.6106 (tttp) REVERT: 6 14 GLN cc_start: 0.5787 (mm-40) cc_final: 0.5346 (pm20) REVERT: 6 119 LYS cc_start: 0.6398 (ttmm) cc_final: 0.6107 (tttp) outliers start: 24 outliers final: 0 residues processed: 906 average time/residue: 1.2988 time to fit residues: 1436.7377 Evaluate side-chains 779 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 779 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 400 optimal weight: 0.9980 chunk 330 optimal weight: 0.9980 chunk 368 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B A 105 HIS A 109 ASN A A 112 GLN A 139 ASN 1 75 GLN B 1 105 HIS 1 109 ASN A 1 112 GLN 1 139 ASN K 75 GLN B K 105 HIS K 109 ASN A K 112 GLN K 139 ASN a 75 GLN B a 105 HIS a 112 GLN a 139 ASN B 75 GLN B B 105 HIS B 109 ASN A B 112 GLN B 139 ASN E 75 GLN B E 105 HIS E 109 ASN A E 112 GLN E 139 ASN e 75 GLN B e 105 HIS e 112 GLN e 139 ASN r 75 GLN B r 105 HIS r 109 ASN A r 112 GLN r 139 ASN G 75 GLN B G 105 HIS G 109 ASN A G 112 GLN G 139 ASN I 75 GLN B I 105 HIS I 109 ASN A I 112 GLN I 139 ASN M 75 GLN B M 105 HIS M 109 ASN A M 112 GLN M 139 ASN ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN B O 105 HIS O 109 ASN A O 112 GLN O 139 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN B Q 105 HIS Q 109 ASN A Q 112 GLN Q 139 ASN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 GLN B S 105 HIS S 109 ASN A S 112 GLN S 139 ASN U 75 GLN B U 105 HIS U 109 ASN A U 139 ASN ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN B W 105 HIS W 109 ASN A W 112 GLN W 139 ASN ** Y 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 75 GLN B Y 105 HIS Y 109 ASN A Y 112 GLN Y 139 ASN ** 2 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN B 2 105 HIS 2 109 ASN A 2 112 GLN 2 139 ASN ** 4 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 75 GLN B 4 105 HIS 4 109 ASN A 4 112 GLN 4 139 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN B F 105 HIS F 109 ASN A F 112 GLN F 139 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN B H 105 HIS H 109 ASN A H 112 GLN H 139 ASN ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN B P 105 HIS P 109 ASN A P 112 GLN P 139 ASN ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 75 GLN B X 105 HIS X 109 ASN A X 139 ASN ** 6 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 75 GLN B 6 105 HIS 6 109 ASN A 6 139 ASN Total number of N/Q/H flips: 115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 37968 Z= 0.252 Angle : 0.717 6.414 51528 Z= 0.397 Chirality : 0.042 0.153 5304 Planarity : 0.005 0.026 6984 Dihedral : 4.725 18.121 5208 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.82 % Allowed : 3.54 % Favored : 94.65 % 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: 3.87 (0.11), residues: 4992 helix: 2.90 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP 4 93 HIS 0.007 0.002 HIS 6 60 PHE 0.025 0.004 PHE 6 41 TYR 0.021 0.004 TYR O 39 ARG 0.008 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 755 time to evaluate : 3.285 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 14 GLN cc_start: 0.5849 (mm-40) cc_final: 0.5417 (pm20) REVERT: A 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6146 (tttp) REVERT: 1 14 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5417 (pm20) REVERT: 1 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6147 (tttp) REVERT: K 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5418 (pm20) REVERT: K 119 LYS cc_start: 0.6402 (ttmm) cc_final: 0.6143 (tttp) REVERT: a 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5418 (pm20) REVERT: a 119 LYS cc_start: 0.6400 (ttmm) cc_final: 0.6142 (tttp) REVERT: B 14 GLN cc_start: 0.5849 (mm-40) cc_final: 0.5418 (pm20) REVERT: B 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6147 (tttp) REVERT: E 14 GLN cc_start: 0.5849 (mm-40) cc_final: 0.5418 (pm20) REVERT: E 119 LYS cc_start: 0.6405 (ttmm) cc_final: 0.6146 (tttp) REVERT: e 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5417 (pm20) REVERT: e 119 LYS cc_start: 0.6405 (ttmm) cc_final: 0.6145 (tttp) REVERT: r 14 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5418 (pm20) REVERT: r 119 LYS cc_start: 0.6400 (ttmm) cc_final: 0.6142 (tttp) REVERT: G 14 GLN cc_start: 0.5849 (mm-40) cc_final: 0.5417 (pm20) REVERT: G 119 LYS cc_start: 0.6402 (ttmm) cc_final: 0.6143 (tttp) REVERT: I 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5416 (pm20) REVERT: I 119 LYS cc_start: 0.6407 (ttmm) cc_final: 0.6148 (tttp) REVERT: M 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5417 (pm20) REVERT: M 119 LYS cc_start: 0.6407 (ttmm) cc_final: 0.6148 (tttp) REVERT: O 14 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5418 (pm20) REVERT: O 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6147 (tttp) REVERT: Q 14 GLN cc_start: 0.5849 (mm-40) cc_final: 0.5417 (pm20) REVERT: Q 119 LYS cc_start: 0.6402 (ttmm) cc_final: 0.6143 (tttp) REVERT: S 14 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5416 (pm20) REVERT: S 119 LYS cc_start: 0.6407 (ttmm) cc_final: 0.6148 (tttp) REVERT: U 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5416 (pm20) REVERT: U 119 LYS cc_start: 0.6402 (ttmm) cc_final: 0.6143 (tttp) REVERT: W 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5417 (pm20) REVERT: W 119 LYS cc_start: 0.6407 (ttmm) cc_final: 0.6148 (tttp) REVERT: Y 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5418 (pm20) REVERT: Y 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6147 (tttp) REVERT: 2 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5416 (pm20) REVERT: 2 119 LYS cc_start: 0.6401 (ttmm) cc_final: 0.6143 (tttp) REVERT: 4 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5417 (pm20) REVERT: 4 119 LYS cc_start: 0.6403 (ttmm) cc_final: 0.6143 (tttp) REVERT: F 14 GLN cc_start: 0.5849 (mm-40) cc_final: 0.5417 (pm20) REVERT: F 119 LYS cc_start: 0.6408 (ttmm) cc_final: 0.6148 (tttp) REVERT: H 14 GLN cc_start: 0.5850 (mm-40) cc_final: 0.5418 (pm20) REVERT: H 119 LYS cc_start: 0.6401 (ttmm) cc_final: 0.6142 (tttp) REVERT: P 14 GLN cc_start: 0.5848 (mm-40) cc_final: 0.5417 (pm20) REVERT: P 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6147 (tttp) REVERT: X 14 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5417 (pm20) REVERT: X 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6147 (tttp) REVERT: 6 14 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5418 (pm20) REVERT: 6 119 LYS cc_start: 0.6406 (ttmm) cc_final: 0.6146 (tttp) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 1.4505 time to fit residues: 1312.6295 Evaluate side-chains 745 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 745 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 112 GLN A 139 ASN 1 105 HIS 1 112 GLN 1 139 ASN K 105 HIS K 112 GLN K 139 ASN a 105 HIS a 109 ASN A a 112 GLN a 139 ASN B 105 HIS B 112 GLN B 139 ASN E 105 HIS E 112 GLN E 139 ASN e 105 HIS e 109 ASN A e 112 GLN e 139 ASN r 105 HIS r 112 GLN r 139 ASN G 105 HIS G 112 GLN G 139 ASN I 105 HIS I 112 GLN I 139 ASN M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 112 GLN O 139 ASN Q 60 HIS Q 105 HIS Q 112 GLN Q 139 ASN S 60 HIS S 105 HIS S 112 GLN S 139 ASN U 105 HIS U 112 GLN U 139 ASN W 60 HIS W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 60 HIS 4 105 HIS 4 112 GLN 4 139 ASN F 60 HIS F 105 HIS F 112 GLN F 139 ASN H 60 HIS H 105 HIS H 112 GLN H 139 ASN P 60 HIS P 105 HIS P 112 GLN P 139 ASN X 60 HIS X 105 HIS X 112 GLN X 139 ASN 6 60 HIS 6 105 HIS 6 112 GLN 6 139 ASN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37968 Z= 0.204 Angle : 0.646 6.977 51528 Z= 0.358 Chirality : 0.039 0.144 5304 Planarity : 0.004 0.046 6984 Dihedral : 4.583 18.224 5208 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 3.11 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.11), residues: 4992 helix: 3.08 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 4 93 HIS 0.004 0.001 HIS M 128 PHE 0.021 0.003 PHE W 41 TYR 0.019 0.003 TYR U 39 ARG 0.007 0.001 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 816 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5391 (pm20) REVERT: A 119 LYS cc_start: 0.6418 (ttmm) cc_final: 0.6158 (tttp) REVERT: 1 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5392 (pm20) REVERT: 1 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6157 (tttp) REVERT: K 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5391 (pm20) REVERT: K 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6157 (tttp) REVERT: a 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5392 (pm20) REVERT: a 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6158 (tttp) REVERT: B 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5388 (pm20) REVERT: B 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6155 (tttp) REVERT: E 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5389 (pm20) REVERT: E 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6158 (tttp) REVERT: e 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5391 (pm20) REVERT: e 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6158 (tttp) REVERT: r 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5393 (pm20) REVERT: r 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6157 (tttp) REVERT: G 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5390 (pm20) REVERT: G 119 LYS cc_start: 0.6418 (ttmm) cc_final: 0.6159 (tttp) REVERT: I 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5391 (pm20) REVERT: I 119 LYS cc_start: 0.6419 (ttmm) cc_final: 0.6161 (tttp) REVERT: M 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5391 (pm20) REVERT: M 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6159 (tttp) REVERT: O 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5392 (pm20) REVERT: O 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6158 (tttp) REVERT: Q 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5388 (pm20) REVERT: Q 119 LYS cc_start: 0.6418 (ttmm) cc_final: 0.6159 (tttp) REVERT: S 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5388 (pm20) REVERT: S 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6159 (tttp) REVERT: U 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5389 (pm20) REVERT: U 119 LYS cc_start: 0.6419 (ttmm) cc_final: 0.6161 (tttp) REVERT: W 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5391 (pm20) REVERT: W 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6159 (tttp) REVERT: Y 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5391 (pm20) REVERT: Y 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6157 (tttp) REVERT: 2 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5391 (pm20) REVERT: 2 119 LYS cc_start: 0.6420 (ttmm) cc_final: 0.6160 (tttp) REVERT: 4 14 GLN cc_start: 0.5816 (mm-40) cc_final: 0.5390 (pm20) REVERT: 4 119 LYS cc_start: 0.6418 (ttmm) cc_final: 0.6160 (tttp) REVERT: F 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5389 (pm20) REVERT: F 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6157 (tttp) REVERT: H 14 GLN cc_start: 0.5819 (mm-40) cc_final: 0.5392 (pm20) REVERT: H 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6157 (tttp) REVERT: P 14 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5389 (pm20) REVERT: P 119 LYS cc_start: 0.6418 (ttmm) cc_final: 0.6159 (tttp) REVERT: X 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5391 (pm20) REVERT: X 119 LYS cc_start: 0.6417 (ttmm) cc_final: 0.6158 (tttp) REVERT: 6 14 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5392 (pm20) REVERT: 6 119 LYS cc_start: 0.6416 (ttmm) cc_final: 0.6159 (tttp) outliers start: 0 outliers final: 0 residues processed: 816 average time/residue: 1.3924 time to fit residues: 1369.2533 Evaluate side-chains 797 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 797 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 162 optimal weight: 0.4980 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 112 GLN A 139 ASN 1 105 HIS 1 139 ASN K 105 HIS K 139 ASN a 105 HIS a 139 ASN B 105 HIS B 112 GLN B 139 ASN E 105 HIS E 112 GLN E 139 ASN e 105 HIS e 139 ASN r 105 HIS r 139 ASN G 105 HIS G 139 ASN I 105 HIS I 112 GLN I 139 ASN M 105 HIS M 112 GLN M 139 ASN O 57 HIS O 60 HIS O 105 HIS O 139 ASN Q 57 HIS Q 60 HIS Q 105 HIS Q 139 ASN S 57 HIS S 60 HIS S 105 HIS S 112 GLN S 139 ASN U 105 HIS U 139 ASN W 57 HIS W 60 HIS W 105 HIS W 112 GLN W 139 ASN Y 57 HIS Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 57 HIS 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 57 HIS 4 60 HIS 4 105 HIS 4 139 ASN F 57 HIS F 60 HIS F 105 HIS F 139 ASN H 60 HIS H 105 HIS H 112 GLN H 139 ASN P 57 HIS P 60 HIS P 105 HIS P 112 GLN P 139 ASN X 57 HIS X 60 HIS X 105 HIS X 139 ASN 6 57 HIS 6 60 HIS 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 37968 Z= 0.143 Angle : 0.555 7.826 51528 Z= 0.306 Chirality : 0.036 0.141 5304 Planarity : 0.003 0.022 6984 Dihedral : 4.364 18.488 5208 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 3.23 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.12), residues: 4992 helix: 3.48 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.94 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 93 HIS 0.005 0.001 HIS a 60 PHE 0.017 0.002 PHE B 41 TYR 0.017 0.002 TYR I 39 ARG 0.008 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 3.323 Fit side-chains REVERT: A 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5272 (mp-120) REVERT: 1 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5296 (pm20) REVERT: K 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5294 (pm20) REVERT: a 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5295 (pm20) REVERT: B 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5294 (pm20) REVERT: E 14 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5294 (pm20) REVERT: e 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5294 (pm20) REVERT: r 14 GLN cc_start: 0.5723 (mm-40) cc_final: 0.5294 (pm20) REVERT: G 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5293 (pm20) REVERT: I 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5271 (mp-120) REVERT: M 14 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5295 (pm20) REVERT: O 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5294 (pm20) REVERT: Q 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5293 (pm20) REVERT: S 14 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5295 (pm20) REVERT: U 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5294 (pm20) REVERT: W 14 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5296 (pm20) REVERT: Y 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5294 (pm20) REVERT: 2 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5294 (pm20) REVERT: 4 14 GLN cc_start: 0.5723 (mm-40) cc_final: 0.5293 (pm20) REVERT: F 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5272 (mp-120) REVERT: H 14 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5295 (pm20) REVERT: P 14 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5296 (pm20) REVERT: X 14 GLN cc_start: 0.5725 (mm-40) cc_final: 0.5296 (pm20) REVERT: 6 14 GLN cc_start: 0.5724 (mm-40) cc_final: 0.5295 (pm20) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 1.3391 time to fit residues: 1264.6049 Evaluate side-chains 828 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 828 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9990 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 394 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS A 112 GLN A 139 ASN 1 60 HIS 1 105 HIS 1 112 GLN 1 139 ASN K 60 HIS K 105 HIS K 112 GLN K 139 ASN a 60 HIS a 105 HIS a 112 GLN a 139 ASN B 60 HIS B 105 HIS B 112 GLN B 139 ASN E 60 HIS E 105 HIS E 112 GLN E 139 ASN e 60 HIS e 105 HIS e 112 GLN e 139 ASN r 60 HIS r 105 HIS r 112 GLN r 139 ASN G 60 HIS G 105 HIS G 112 GLN G 139 ASN I 60 HIS I 105 HIS I 112 GLN I 139 ASN M 60 HIS M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 112 GLN S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 60 HIS 4 105 HIS 4 112 GLN 4 139 ASN F 60 HIS F 105 HIS F 139 ASN H 60 HIS H 105 HIS H 112 GLN H 139 ASN P 105 HIS P 112 GLN P 139 ASN X 60 HIS X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 37968 Z= 0.305 Angle : 0.758 6.697 51528 Z= 0.422 Chirality : 0.043 0.152 5304 Planarity : 0.005 0.040 6984 Dihedral : 4.776 19.514 5208 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 2.93 % Favored : 95.25 % 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: 3.73 (0.11), residues: 4992 helix: 2.80 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP U 93 HIS 0.007 0.002 HIS H 60 PHE 0.024 0.004 PHE r 41 TYR 0.025 0.004 TYR I 39 ARG 0.005 0.001 ARG Q 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 753 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5866 (mm-40) cc_final: 0.5434 (pm20) REVERT: 1 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5439 (pm20) REVERT: K 14 GLN cc_start: 0.5868 (mm-40) cc_final: 0.5437 (pm20) REVERT: a 14 GLN cc_start: 0.5867 (mm-40) cc_final: 0.5436 (pm20) REVERT: B 14 GLN cc_start: 0.5866 (mm-40) cc_final: 0.5433 (pm20) REVERT: E 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5437 (pm20) REVERT: e 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5437 (pm20) REVERT: r 14 GLN cc_start: 0.5868 (mm-40) cc_final: 0.5436 (pm20) REVERT: G 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5438 (pm20) REVERT: I 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5436 (pm20) REVERT: M 14 GLN cc_start: 0.5870 (mm-40) cc_final: 0.5438 (pm20) REVERT: O 14 GLN cc_start: 0.5868 (mm-40) cc_final: 0.5437 (pm20) REVERT: Q 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5438 (pm20) REVERT: S 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5438 (pm20) REVERT: U 14 GLN cc_start: 0.5870 (mm-40) cc_final: 0.5437 (pm20) REVERT: W 14 GLN cc_start: 0.5866 (mm-40) cc_final: 0.5434 (pm20) REVERT: Y 14 GLN cc_start: 0.5868 (mm-40) cc_final: 0.5438 (pm20) REVERT: 2 14 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5436 (pm20) REVERT: 4 14 GLN cc_start: 0.5865 (mm-40) cc_final: 0.5434 (pm20) REVERT: F 14 GLN cc_start: 0.5870 (mm-40) cc_final: 0.5438 (pm20) REVERT: H 14 GLN cc_start: 0.5866 (mm-40) cc_final: 0.5434 (pm20) REVERT: P 14 GLN cc_start: 0.5870 (mm-40) cc_final: 0.5439 (pm20) REVERT: X 14 GLN cc_start: 0.5865 (mm-40) cc_final: 0.5434 (pm20) REVERT: 6 14 GLN cc_start: 0.5864 (mm-40) cc_final: 0.5432 (pm20) outliers start: 0 outliers final: 0 residues processed: 753 average time/residue: 1.4735 time to fit residues: 1345.8560 Evaluate side-chains 752 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 752 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 0.3980 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS A 112 GLN A 139 ASN 1 60 HIS 1 105 HIS 1 112 GLN 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 112 GLN B 139 ASN E 60 HIS E 105 HIS E 112 GLN E 139 ASN e 60 HIS e 105 HIS e 112 GLN e 139 ASN r 60 HIS r 105 HIS r 112 GLN r 139 ASN G 60 HIS G 105 HIS G 112 GLN G 139 ASN I 60 HIS I 105 HIS I 112 GLN I 139 ASN M 60 HIS M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 112 GLN O 139 ASN Q 105 HIS Q 112 GLN Q 139 ASN S 105 HIS S 112 GLN S 139 ASN U 60 HIS U 105 HIS U 112 GLN U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 60 HIS 4 105 HIS 4 112 GLN 4 139 ASN F 60 HIS F 105 HIS F 112 GLN F 139 ASN H 60 HIS H 105 HIS H 112 GLN H 139 ASN P 105 HIS P 112 GLN P 139 ASN X 60 HIS X 105 HIS X 112 GLN X 139 ASN 6 105 HIS 6 112 GLN 6 139 ASN Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 37968 Z= 0.186 Angle : 0.609 5.921 51528 Z= 0.339 Chirality : 0.038 0.142 5304 Planarity : 0.004 0.022 6984 Dihedral : 4.557 17.903 5208 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 2.93 % Favored : 95.25 % 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: 4.22 (0.11), residues: 4992 helix: 3.13 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 93 HIS 0.004 0.001 HIS S 128 PHE 0.019 0.003 PHE W 41 TYR 0.020 0.003 TYR 4 39 ARG 0.003 0.001 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 766 time to evaluate : 3.342 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 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5381 (pm20) REVERT: 1 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5382 (pm20) REVERT: K 14 GLN cc_start: 0.5807 (mm-40) cc_final: 0.5382 (pm20) REVERT: a 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5382 (pm20) REVERT: B 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5382 (pm20) REVERT: E 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5382 (pm20) REVERT: e 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5381 (pm20) REVERT: r 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5382 (pm20) REVERT: G 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5381 (pm20) REVERT: I 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5382 (pm20) REVERT: M 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5382 (pm20) REVERT: O 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5381 (pm20) REVERT: Q 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5381 (pm20) REVERT: S 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5382 (pm20) REVERT: U 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5382 (pm20) REVERT: W 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5382 (pm20) REVERT: Y 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5379 (pm20) REVERT: 2 14 GLN cc_start: 0.5810 (mm-40) cc_final: 0.5379 (pm20) REVERT: 4 14 GLN cc_start: 0.5807 (mm-40) cc_final: 0.5380 (pm20) REVERT: F 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5381 (pm20) REVERT: H 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5383 (pm20) REVERT: P 14 GLN cc_start: 0.5809 (mm-40) cc_final: 0.5380 (pm20) REVERT: X 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5382 (pm20) REVERT: 6 14 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5382 (pm20) outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 1.3556 time to fit residues: 1257.6622 Evaluate side-chains 758 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 758 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 250 optimal weight: 20.0000 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS A 112 GLN A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 112 GLN B 139 ASN E 60 HIS E 105 HIS E 112 GLN E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 112 GLN I 139 ASN M 60 HIS M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 112 GLN S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 60 HIS 4 105 HIS 4 139 ASN F 60 HIS F 105 HIS F 139 ASN H 60 HIS H 105 HIS H 139 ASN P 105 HIS P 112 GLN P 139 ASN X 60 HIS X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 37968 Z= 0.168 Angle : 0.585 5.721 51528 Z= 0.325 Chirality : 0.037 0.139 5304 Planarity : 0.003 0.023 6984 Dihedral : 4.497 18.040 5208 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 2.93 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.12), residues: 4992 helix: 3.26 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.93 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 93 HIS 0.003 0.001 HIS W 128 PHE 0.018 0.003 PHE W 41 TYR 0.018 0.002 TYR W 39 ARG 0.002 0.000 ARG S 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5369 (pm20) REVERT: 1 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5369 (pm20) REVERT: K 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5368 (pm20) REVERT: a 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5369 (pm20) REVERT: B 14 GLN cc_start: 0.5799 (mm-40) cc_final: 0.5369 (pm20) REVERT: E 14 GLN cc_start: 0.5799 (mm-40) cc_final: 0.5370 (pm20) REVERT: e 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5369 (pm20) REVERT: r 14 GLN cc_start: 0.5801 (mm-40) cc_final: 0.5373 (pm20) REVERT: G 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5368 (pm20) REVERT: I 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5368 (pm20) REVERT: M 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5369 (pm20) REVERT: O 14 GLN cc_start: 0.5801 (mm-40) cc_final: 0.5372 (pm20) REVERT: Q 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5368 (pm20) REVERT: S 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5369 (pm20) REVERT: U 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5369 (pm20) REVERT: W 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5369 (pm20) REVERT: Y 14 GLN cc_start: 0.5801 (mm-40) cc_final: 0.5372 (pm20) REVERT: 2 14 GLN cc_start: 0.5803 (mm-40) cc_final: 0.5372 (pm20) REVERT: 4 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5368 (pm20) REVERT: F 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5369 (pm20) REVERT: H 14 GLN cc_start: 0.5804 (mm-40) cc_final: 0.5374 (pm20) REVERT: P 14 GLN cc_start: 0.5798 (mm-40) cc_final: 0.5369 (pm20) REVERT: X 14 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5368 (pm20) REVERT: 6 14 GLN cc_start: 0.5801 (mm-40) cc_final: 0.5372 (pm20) outliers start: 0 outliers final: 0 residues processed: 754 average time/residue: 1.3900 time to fit residues: 1266.5582 Evaluate side-chains 754 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.9990 chunk 376 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 331 optimal weight: 0.8980 chunk 346 optimal weight: 0.8980 chunk 365 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS A 112 GLN A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 112 GLN K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 112 GLN B 139 ASN E 60 HIS E 105 HIS E 112 GLN E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 112 GLN G 139 ASN I 60 HIS I 105 HIS I 112 GLN I 139 ASN M 60 HIS M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 105 HIS Q 112 GLN Q 139 ASN S 105 HIS S 112 GLN S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 60 HIS 4 105 HIS 4 139 ASN F 60 HIS F 105 HIS F 112 GLN F 139 ASN H 60 HIS H 105 HIS H 112 GLN H 139 ASN P 105 HIS P 139 ASN X 60 HIS X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 37968 Z= 0.151 Angle : 0.553 5.520 51528 Z= 0.307 Chirality : 0.036 0.137 5304 Planarity : 0.003 0.023 6984 Dihedral : 4.424 18.194 5208 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 2.93 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.12), residues: 4992 helix: 3.38 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.92 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 93 HIS 0.003 0.001 HIS W 128 PHE 0.016 0.002 PHE B 41 TYR 0.016 0.002 TYR Y 39 ARG 0.002 0.000 ARG P 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: 1 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5326 (pm20) REVERT: K 14 GLN cc_start: 0.5750 (mm-40) cc_final: 0.5324 (pm20) REVERT: a 14 GLN cc_start: 0.5750 (mm-40) cc_final: 0.5324 (pm20) REVERT: B 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: E 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: e 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: r 14 GLN cc_start: 0.5749 (mm-40) cc_final: 0.5324 (pm20) REVERT: G 14 GLN cc_start: 0.5750 (mm-40) cc_final: 0.5323 (pm20) REVERT: I 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: M 14 GLN cc_start: 0.5752 (mm-40) cc_final: 0.5325 (pm20) REVERT: O 14 GLN cc_start: 0.5749 (mm-40) cc_final: 0.5324 (pm20) REVERT: Q 14 GLN cc_start: 0.5750 (mm-40) cc_final: 0.5323 (pm20) REVERT: S 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5325 (pm20) REVERT: U 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: W 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5325 (pm20) REVERT: Y 14 GLN cc_start: 0.5750 (mm-40) cc_final: 0.5324 (pm20) REVERT: 2 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: 4 14 GLN cc_start: 0.5749 (mm-40) cc_final: 0.5322 (pm20) REVERT: F 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: H 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5324 (pm20) REVERT: P 14 GLN cc_start: 0.5752 (mm-40) cc_final: 0.5326 (pm20) REVERT: X 14 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5326 (pm20) REVERT: 6 14 GLN cc_start: 0.5749 (mm-40) cc_final: 0.5324 (pm20) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 1.3532 time to fit residues: 1277.9399 Evaluate side-chains 764 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 764 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 4.9990 chunk 387 optimal weight: 0.9990 chunk 236 optimal weight: 0.0370 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.5980 chunk 374 optimal weight: 0.7980 chunk 323 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS A 112 GLN A 139 ASN 1 60 HIS 1 105 HIS 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 112 GLN B 139 ASN E 60 HIS E 105 HIS E 112 GLN E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 112 GLN I 139 ASN M 60 HIS M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 112 GLN S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 139 ASN 2 60 HIS 2 105 HIS 2 112 GLN 2 139 ASN 4 60 HIS 4 105 HIS 4 139 ASN F 60 HIS F 105 HIS F 139 ASN H 60 HIS H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 60 HIS X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 37968 Z= 0.132 Angle : 0.512 5.211 51528 Z= 0.284 Chirality : 0.036 0.136 5304 Planarity : 0.003 0.023 6984 Dihedral : 4.321 18.255 5208 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 2.93 % Favored : 95.25 % 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: 4.83 (0.12), residues: 4992 helix: 3.58 (0.08), residues: 4152 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP e 93 HIS 0.003 0.001 HIS S 128 PHE 0.015 0.002 PHE Q 41 TYR 0.016 0.002 TYR H 39 ARG 0.001 0.000 ARG 6 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 768 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5262 (pm20) REVERT: 1 14 GLN cc_start: 0.5679 (mm-40) cc_final: 0.5260 (pm20) REVERT: K 14 GLN cc_start: 0.5681 (mm-40) cc_final: 0.5260 (pm20) REVERT: a 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5263 (pm20) REVERT: B 14 GLN cc_start: 0.5679 (mm-40) cc_final: 0.5259 (pm20) REVERT: E 14 GLN cc_start: 0.5679 (mm-40) cc_final: 0.5259 (pm20) REVERT: e 14 GLN cc_start: 0.5682 (mm-40) cc_final: 0.5261 (pm20) REVERT: r 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5263 (pm20) REVERT: G 14 GLN cc_start: 0.5678 (mm-40) cc_final: 0.5257 (pm20) REVERT: I 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5261 (pm20) REVERT: M 14 GLN cc_start: 0.5679 (mm-40) cc_final: 0.5259 (pm20) REVERT: O 14 GLN cc_start: 0.5681 (mm-40) cc_final: 0.5260 (pm20) REVERT: Q 14 GLN cc_start: 0.5682 (mm-40) cc_final: 0.5261 (pm20) REVERT: S 14 GLN cc_start: 0.5678 (mm-40) cc_final: 0.5258 (pm20) REVERT: U 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5261 (pm20) REVERT: W 14 GLN cc_start: 0.5678 (mm-40) cc_final: 0.5258 (pm20) REVERT: Y 14 GLN cc_start: 0.5681 (mm-40) cc_final: 0.5260 (pm20) REVERT: 2 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5261 (pm20) REVERT: 4 14 GLN cc_start: 0.5677 (mm-40) cc_final: 0.5257 (pm20) REVERT: F 14 GLN cc_start: 0.5682 (mm-40) cc_final: 0.5261 (pm20) REVERT: H 14 GLN cc_start: 0.5684 (mm-40) cc_final: 0.5262 (pm20) REVERT: P 14 GLN cc_start: 0.5684 (mm-40) cc_final: 0.5264 (pm20) REVERT: X 14 GLN cc_start: 0.5679 (mm-40) cc_final: 0.5260 (pm20) REVERT: 6 14 GLN cc_start: 0.5683 (mm-40) cc_final: 0.5263 (pm20) outliers start: 0 outliers final: 0 residues processed: 768 average time/residue: 1.3886 time to fit residues: 1289.4868 Evaluate side-chains 816 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 816 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 332 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 105 HIS A 112 GLN A 139 ASN 1 60 HIS 1 105 HIS 1 112 GLN 1 139 ASN K 60 HIS K 105 HIS K 139 ASN a 60 HIS a 105 HIS a 139 ASN B 60 HIS B 105 HIS B 112 GLN B 139 ASN E 60 HIS E 105 HIS E 112 GLN E 139 ASN e 60 HIS e 105 HIS e 139 ASN r 60 HIS r 105 HIS r 112 GLN r 139 ASN G 60 HIS G 105 HIS G 139 ASN I 60 HIS I 105 HIS I 112 GLN I 139 ASN M 60 HIS M 105 HIS M 112 GLN M 139 ASN O 60 HIS O 105 HIS O 139 ASN Q 105 HIS Q 139 ASN S 105 HIS S 112 GLN S 139 ASN U 60 HIS U 105 HIS U 139 ASN W 105 HIS W 112 GLN W 139 ASN Y 60 HIS Y 105 HIS Y 112 GLN Y 139 ASN 2 60 HIS 2 105 HIS 2 139 ASN 4 60 HIS 4 105 HIS 4 112 GLN 4 139 ASN F 60 HIS F 105 HIS F 139 ASN H 60 HIS H 105 HIS H 139 ASN P 105 HIS P 139 ASN X 60 HIS X 105 HIS X 139 ASN 6 105 HIS 6 139 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.184320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.154164 restraints weight = 134996.141| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.46 r_work: 0.3239 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.3015 rms_B_bonded: 2.79 restraints_weight: 0.1250 r_work: 0.2974 rms_B_bonded: 4.34 restraints_weight: 0.0625 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 37968 Z= 0.161 Angle : 0.562 5.641 51528 Z= 0.312 Chirality : 0.037 0.134 5304 Planarity : 0.003 0.023 6984 Dihedral : 4.423 18.564 5208 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.82 % Allowed : 3.06 % Favored : 95.13 % 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: 4.63 (0.12), residues: 4992 helix: 3.43 (0.07), residues: 4152 sheet: None (None), residues: 0 loop : 0.94 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 93 HIS 0.003 0.001 HIS X 128 PHE 0.018 0.003 PHE B 41 TYR 0.016 0.002 TYR 2 39 ARG 0.002 0.000 ARG 4 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25949.25 seconds wall clock time: 447 minutes 49.20 seconds (26869.20 seconds total)