Starting phenix.real_space_refine on Thu Dec 14 07:52:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/12_2023/6z9f_11122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/12_2023/6z9f_11122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/12_2023/6z9f_11122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/12_2023/6z9f_11122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/12_2023/6z9f_11122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/12_2023/6z9f_11122_updated.pdb" } resolution = 1.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.156 sd= 10.228 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 41020 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 Na 32 4.78 5 C 23040 2.51 5 N 6528 2.21 5 O 11300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 9": "NH1" <-> "NH2" Residue "1 ASP 15": "OD1" <-> "OD2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "1 ASP 91": "OD1" <-> "OD2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "1 ASP 123": "OD1" <-> "OD2" Residue "1 ASP 131": "OD1" <-> "OD2" Residue "1 GLU 134": "OE1" <-> "OE2" Residue "1 GLU 140": "OE1" <-> "OE2" Residue "1 GLU 147": "OE1" <-> "OE2" Residue "1 ASP 150": "OD1" <-> "OD2" Residue "1 ARG 156": "NH1" <-> "NH2" Residue "1 ARG 156": "NH1" <-> "NH2" Residue "1 GLU 167": "OE1" <-> "OE2" Residue "1 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "K ASP 150": "OD1" <-> "OD2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ASP 15": "OD1" <-> "OD2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ASP 91": "OD1" <-> "OD2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "a ASP 123": "OD1" <-> "OD2" Residue "a ASP 131": "OD1" <-> "OD2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 140": "OE1" <-> "OE2" Residue "a GLU 147": "OE1" <-> "OE2" Residue "a ASP 150": "OD1" <-> "OD2" Residue "a ARG 156": "NH1" <-> "NH2" Residue "a ARG 156": "NH1" <-> "NH2" Residue "a GLU 167": "OE1" <-> "OE2" Residue "a TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E ASP 131": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 9": "NH1" <-> "NH2" Residue "e ASP 15": "OD1" <-> "OD2" Residue "e GLU 61": "OE1" <-> "OE2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "e ASP 131": "OD1" <-> "OD2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "e GLU 140": "OE1" <-> "OE2" Residue "e GLU 147": "OE1" <-> "OE2" Residue "e ASP 150": "OD1" <-> "OD2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e GLU 167": "OE1" <-> "OE2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ASP 15": "OD1" <-> "OD2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ASP 91": "OD1" <-> "OD2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Residue "r ASP 123": "OD1" <-> "OD2" Residue "r ASP 131": "OD1" <-> "OD2" Residue "r GLU 134": "OE1" <-> "OE2" Residue "r GLU 140": "OE1" <-> "OE2" Residue "r GLU 147": "OE1" <-> "OE2" Residue "r ASP 150": "OD1" <-> "OD2" Residue "r ARG 156": "NH1" <-> "NH2" Residue "r ARG 156": "NH1" <-> "NH2" Residue "r GLU 167": "OE1" <-> "OE2" Residue "r TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I ASP 123": "OD1" <-> "OD2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 150": "OD1" <-> "OD2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 9": "NH1" <-> "NH2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 123": "OD1" <-> "OD2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 150": "OD1" <-> "OD2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 9": "NH1" <-> "NH2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O ASP 123": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 147": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 9": "NH1" <-> "NH2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 147": "OE1" <-> "OE2" Residue "Q ASP 150": "OD1" <-> "OD2" Residue "Q ARG 156": "NH1" <-> "NH2" Residue "Q ARG 156": "NH1" <-> "NH2" Residue "Q GLU 167": "OE1" <-> "OE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 9": "NH1" <-> "NH2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "S GLU 134": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S ASP 150": "OD1" <-> "OD2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S GLU 167": "OE1" <-> "OE2" Residue "S TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 9": "NH1" <-> "NH2" Residue "U ASP 15": "OD1" <-> "OD2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "U ASP 123": "OD1" <-> "OD2" Residue "U ASP 131": "OD1" <-> "OD2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U GLU 147": "OE1" <-> "OE2" Residue "U ASP 150": "OD1" <-> "OD2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 9": "NH1" <-> "NH2" Residue "W ASP 15": "OD1" <-> "OD2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ASP 123": "OD1" <-> "OD2" Residue "W ASP 131": "OD1" <-> "OD2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W GLU 147": "OE1" <-> "OE2" Residue "W ASP 150": "OD1" <-> "OD2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "W TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Y GLU 61": "OE1" <-> "OE2" Residue "Y ARG 63": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y ASP 123": "OD1" <-> "OD2" Residue "Y ASP 131": "OD1" <-> "OD2" Residue "Y GLU 134": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "Y GLU 147": "OE1" <-> "OE2" Residue "Y ASP 150": "OD1" <-> "OD2" Residue "Y ARG 156": "NH1" <-> "NH2" Residue "Y ARG 156": "NH1" <-> "NH2" Residue "Y GLU 167": "OE1" <-> "OE2" Residue "Y TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 9": "NH1" <-> "NH2" Residue "2 ASP 15": "OD1" <-> "OD2" Residue "2 GLU 61": "OE1" <-> "OE2" Residue "2 ARG 63": "NH1" <-> "NH2" Residue "2 ASP 91": "OD1" <-> "OD2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "2 ASP 123": "OD1" <-> "OD2" Residue "2 ASP 131": "OD1" <-> "OD2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 GLU 140": "OE1" <-> "OE2" Residue "2 GLU 147": "OE1" <-> "OE2" Residue "2 ASP 150": "OD1" <-> "OD2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 GLU 167": "OE1" <-> "OE2" Residue "2 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 9": "NH1" <-> "NH2" Residue "4 ASP 15": "OD1" <-> "OD2" Residue "4 GLU 61": "OE1" <-> "OE2" Residue "4 ARG 63": "NH1" <-> "NH2" Residue "4 ASP 91": "OD1" <-> "OD2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 116": "OE1" <-> "OE2" Residue "4 ASP 123": "OD1" <-> "OD2" Residue "4 ASP 131": "OD1" <-> "OD2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 GLU 140": "OE1" <-> "OE2" Residue "4 GLU 147": "OE1" <-> "OE2" Residue "4 ASP 150": "OD1" <-> "OD2" Residue "4 ARG 156": "NH1" <-> "NH2" Residue "4 ARG 156": "NH1" <-> "NH2" Residue "4 GLU 167": "OE1" <-> "OE2" Residue "4 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H ASP 131": "OD1" <-> "OD2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 9": "NH1" <-> "NH2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P ASP 123": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 9": "NH1" <-> "NH2" Residue "X ASP 15": "OD1" <-> "OD2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X ARG 63": "NH1" <-> "NH2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X ASP 123": "OD1" <-> "OD2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 147": "OE1" <-> "OE2" Residue "X ASP 150": "OD1" <-> "OD2" Residue "X ARG 156": "NH1" <-> "NH2" Residue "X ARG 156": "NH1" <-> "NH2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 9": "NH1" <-> "NH2" Residue "6 ASP 15": "OD1" <-> "OD2" Residue "6 GLU 61": "OE1" <-> "OE2" Residue "6 ARG 63": "NH1" <-> "NH2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 ASP 123": "OD1" <-> "OD2" Residue "6 ASP 131": "OD1" <-> "OD2" Residue "6 GLU 134": "OE1" <-> "OE2" Residue "6 GLU 140": "OE1" <-> "OE2" Residue "6 GLU 147": "OE1" <-> "OE2" Residue "6 ASP 150": "OD1" <-> "OD2" Residue "6 ARG 156": "NH1" <-> "NH2" Residue "6 ARG 156": "NH1" <-> "NH2" Residue "6 GLU 167": "OE1" <-> "OE2" Residue "6 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 41020 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "1" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "K" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "a" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "B" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "E" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "e" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "r" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "G" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "I" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "M" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "O" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "Q" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "S" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "U" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "W" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "Y" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "2" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "4" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "F" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "H" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "P" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "X" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "6" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "1" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "K" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "a" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "E" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "e" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "r" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "I" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "M" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "O" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "Q" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "S" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "U" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "W" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "Y" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "2" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "4" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "H" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "P" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "X" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 171 Classifications: {'water': 171} Link IDs: {None: 170} Chain: "6" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Residues with excluded nonbonded symmetry interactions: 312 residue: pdb=" N ALYS A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 49 " occ=0.50 residue: pdb=" N ALYS A 53 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 53 " occ=0.50 residue: pdb=" N AGLU A 64 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.50 residue: pdb=" N ALYS A 68 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 68 " occ=0.50 residue: pdb=" N ALYS A 71 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 71 " occ=0.50 residue: pdb=" N ALEU A 72 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 72 " occ=0.50 residue: pdb=" N AGLN A 75 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 75 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N AASN A 109 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 109 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 residue: pdb=" N AARG A 156 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 156 " occ=0.50 residue: pdb=" N AGLU A 162 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 162 " occ=0.50 ... (remaining 300 not shown) Time building chain proxies: 27.16, per 1000 atoms: 0.66 Number of scatterers: 41020 At special positions: 0 Unit cell: (136.284, 136.284, 136.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Na 32 11.00 O 11300 8.00 N 6528 7.00 C 23040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.80 Conformation dependent library (CDL) restraints added in 8.5 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 72.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 76 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 76 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 76 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 76 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 76 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 76 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 76 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 76 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 76 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 76 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 76 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 76 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 76 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 76 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 76 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 76 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 76 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 76 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 76 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 2736 hydrogen bonds defined for protein. 8448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.79 Time building geometry restraints manager: 16.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6750 1.31 - 1.44: 9924 1.44 - 1.57: 20910 1.57 - 1.70: 0 1.70 - 1.83: 216 Bond restraints: 37800 Sorted by residual: bond pdb=" CE1 HIS I 13 " pdb=" NE2 HIS I 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" CE1 HIS X 13 " pdb=" NE2 HIS X 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" CE1 HIS 1 13 " pdb=" NE2 HIS 1 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS P 13 " pdb=" NE2 HIS P 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS S 13 " pdb=" NE2 HIS S 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 ... (remaining 37795 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.88: 504 105.88 - 112.93: 18104 112.93 - 119.99: 17658 119.99 - 127.04: 14638 127.04 - 134.10: 360 Bond angle restraints: 51264 Sorted by residual: angle pdb=" CA LEU P 138 " pdb=" C LEU P 138 " pdb=" O LEU P 138 " ideal model delta sigma weight residual 120.82 115.30 5.52 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU e 138 " pdb=" C LEU e 138 " pdb=" O LEU e 138 " ideal model delta sigma weight residual 120.82 115.30 5.52 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU 1 138 " pdb=" C LEU 1 138 " pdb=" O LEU 1 138 " ideal model delta sigma weight residual 120.82 115.31 5.51 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU M 138 " pdb=" C LEU M 138 " pdb=" O LEU M 138 " ideal model delta sigma weight residual 120.82 115.32 5.50 1.05e+00 9.07e-01 2.74e+01 angle pdb=" CA LEU B 138 " pdb=" C LEU B 138 " pdb=" O LEU B 138 " ideal model delta sigma weight residual 120.82 115.32 5.50 1.05e+00 9.07e-01 2.74e+01 ... (remaining 51259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 21023 16.14 - 32.28: 1295 32.28 - 48.42: 490 48.42 - 64.55: 328 64.55 - 80.69: 72 Dihedral angle restraints: 23208 sinusoidal: 9672 harmonic: 13536 Sorted by residual: dihedral pdb=" C TYR H 39 " pdb=" N TYR H 39 " pdb=" CA TYR H 39 " pdb=" CB TYR H 39 " ideal model delta harmonic sigma weight residual -122.60 -132.85 10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C TYR A 39 " pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " ideal model delta harmonic sigma weight residual -122.60 -132.84 10.24 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C TYR G 39 " pdb=" N TYR G 39 " pdb=" CA TYR G 39 " pdb=" CB TYR G 39 " ideal model delta harmonic sigma weight residual -122.60 -132.80 10.20 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 23205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3297 0.079 - 0.158: 1397 0.158 - 0.237: 467 0.237 - 0.316: 71 0.316 - 0.396: 48 Chirality restraints: 5280 Sorted by residual: chirality pdb=" CA ASN r 50 " pdb=" N ASN r 50 " pdb=" C ASN r 50 " pdb=" CB ASN r 50 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ASN H 50 " pdb=" N ASN H 50 " pdb=" C ASN H 50 " pdb=" CB ASN H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ASN 4 50 " pdb=" N ASN 4 50 " pdb=" C ASN 4 50 " pdb=" CB ASN 4 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 5277 not shown) Planarity restraints: 6936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.083 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR P 137 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 137 " -0.083 2.00e-02 2.50e+03 5.00e-02 4.99e+01 pdb=" CG TYR 2 137 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 137 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 137 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 137 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 137 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR 2 137 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR 2 137 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 137 " -0.082 2.00e-02 2.50e+03 5.00e-02 4.99e+01 pdb=" CG TYR H 137 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR H 137 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR H 137 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR H 137 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR H 137 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR H 137 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR H 137 " -0.066 2.00e-02 2.50e+03 ... (remaining 6933 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 319 2.41 - 3.03: 29082 3.03 - 3.65: 73806 3.65 - 4.28: 124655 4.28 - 4.90: 190002 Nonbonded interactions: 417864 Sorted by model distance: nonbonded pdb=" OE2 GLU K 101 " pdb=" NH2BARG K 156 " model vdw 1.782 2.520 nonbonded pdb=" OE2 GLU B 101 " pdb=" NH2BARG B 156 " model vdw 1.783 2.520 nonbonded pdb=" OE2 GLU a 101 " pdb=" NH2BARG a 156 " model vdw 1.783 2.520 nonbonded pdb=" OE2 GLU E 101 " pdb=" NH2BARG E 156 " model vdw 1.783 2.520 nonbonded pdb=" OE2 GLU G 101 " pdb=" NH2BARG G 156 " model vdw 1.783 2.520 ... (remaining 417859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '1' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain '2' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain '4' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain '6' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'Y' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'a' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'e' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'r' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.400 Construct map_model_manager: 0.040 Extract box with map and model: 22.470 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 102.240 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.078 37800 Z= 0.996 Angle : 1.742 8.541 51264 Z= 1.258 Chirality : 0.098 0.396 5280 Planarity : 0.011 0.050 6936 Dihedral : 15.506 80.693 14616 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.66 % Allowed : 3.05 % Favored : 93.29 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.11), residues: 4920 helix: 2.12 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.36 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.019 TRP 4 93 HIS 0.019 0.008 HIS a 118 PHE 0.052 0.012 PHE W 41 TYR 0.083 0.020 TYR P 137 ARG 0.022 0.003 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 600 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 624 average time/residue: 1.5757 time to fit residues: 1164.8774 Evaluate side-chains 456 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 432 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.1903 ------------------------------------------------------------------------------- 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: 10.0000 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS ** A 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 98 ASN A 105 HIS A 112 GLN 1 14 GLN 1 60 HIS ** 1 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 GLN ** 1 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 98 ASN 1 105 HIS K 14 GLN K 60 HIS ** K 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** K 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN K 105 HIS K 112 GLN a 14 GLN a 60 HIS ** a 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 GLN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN a 105 HIS a 112 GLN B 14 GLN B 60 HIS ** B 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN B 105 HIS E 14 GLN E 60 HIS ** E 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 105 HIS e 14 GLN e 60 HIS ** e 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 GLN e 98 ASN e 105 HIS e 112 GLN r 14 GLN r 60 HIS ** r 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 GLN ** r 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 98 ASN r 105 HIS G 14 GLN G 60 HIS ** G 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN G 105 HIS G 112 GLN I 14 GLN I 60 HIS ** I 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN I 105 HIS I 112 GLN M 14 GLN M 60 HIS ** M 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN M 98 ASN M 105 HIS M 112 GLN O 14 GLN O 60 HIS ** O 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 ASN O 105 HIS O 112 GLN Q 14 GLN Q 60 HIS ** Q 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN Q 105 HIS Q 112 GLN S 14 GLN S 60 HIS ** S 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN S 105 HIS S 112 GLN U 14 GLN U 60 HIS ** U 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN U 105 HIS U 112 GLN W 14 GLN W 60 HIS ** W 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 GLN ** W 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 ASN W 105 HIS Y 14 GLN Y 60 HIS ** Y 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN Y 105 HIS 2 14 GLN 2 60 HIS ** 2 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** 2 83 GLN ** 2 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 98 ASN 2 105 HIS 2 112 GLN 4 14 GLN 4 60 HIS ** 4 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** 4 83 GLN ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 ASN 4 105 HIS 4 112 GLN F 14 GLN F 60 HIS ** F 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 105 HIS F 112 GLN H 14 GLN H 60 HIS ** H 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN H 98 ASN H 105 HIS P 14 GLN P 60 HIS ** P 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN P 105 HIS P 112 GLN X 14 GLN X 60 HIS ** X 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** X 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN X 105 HIS 6 14 GLN 6 60 HIS ** 6 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** 6 83 GLN 6 98 ASN 6 105 HIS 6 112 GLN Total number of N/Q/H flips: 136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 37800 Z= 0.172 Angle : 0.611 5.461 51264 Z= 0.333 Chirality : 0.037 0.159 5280 Planarity : 0.004 0.030 6936 Dihedral : 4.552 19.153 5160 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 3.71 % Favored : 93.24 % 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: 4.49 (0.11), residues: 4920 helix: 3.42 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.59 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP Q 93 HIS 0.008 0.001 HIS F 60 PHE 0.023 0.003 PHE W 41 TYR 0.019 0.002 TYR S 39 ARG 0.006 0.001 ARG P 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 472 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 496 average time/residue: 1.4144 time to fit residues: 848.0130 Evaluate side-chains 420 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 396 time to evaluate : 3.340 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.2197 ------------------------------------------------------------------------------- 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: 1.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 0.9980 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 0.0870 chunk 297 optimal weight: 3.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** 1 14 GLN ** 1 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN ** K 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 GLN ** a 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 14 GLN ** e 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 14 GLN ** r 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 GLN ** G 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 GLN ** I 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 GLN ** M 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 GLN ** O 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 GLN ** Q 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 GLN ** S 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 14 GLN ** U 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 14 GLN ** W 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 GLN ** Y 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 14 GLN ** 2 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** 4 14 GLN ** 4 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN ** F 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN ** H 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 GLN ** P 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 GLN ** X 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 14 GLN ** 6 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 37800 Z= 0.202 Angle : 0.658 5.804 51264 Z= 0.358 Chirality : 0.039 0.153 5280 Planarity : 0.004 0.027 6936 Dihedral : 4.553 19.226 5160 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 3.71 % Favored : 93.24 % 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: 4.46 (0.11), residues: 4920 helix: 3.41 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.55 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP 1 93 HIS 0.004 0.001 HIS H 128 PHE 0.024 0.003 PHE E 41 TYR 0.022 0.003 TYR e 39 ARG 0.007 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 425 average time/residue: 1.2484 time to fit residues: 658.2651 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.286 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.1715 ------------------------------------------------------------------------------- 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: 8.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 177 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 0.9980 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 0.5980 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 105 HIS 1 105 HIS K 14 GLN ** K 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS a 105 HIS B 105 HIS E 105 HIS e 105 HIS r 14 GLN r 105 HIS G 105 HIS I 105 HIS M 105 HIS ** O 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 HIS Q 105 HIS S 105 HIS U 105 HIS W 105 HIS ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 HIS ** 2 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 105 HIS 4 14 GLN 4 105 HIS F 105 HIS H 105 HIS ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 HIS X 105 HIS ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 105 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 37800 Z= 0.125 Angle : 0.511 4.985 51264 Z= 0.278 Chirality : 0.035 0.140 5280 Planarity : 0.003 0.042 6936 Dihedral : 4.323 19.273 5160 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 3.40 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.14 (0.12), residues: 4920 helix: 3.89 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.73 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 93 HIS 0.004 0.001 HIS G 60 PHE 0.015 0.002 PHE r 41 TYR 0.017 0.002 TYR Q 39 ARG 0.003 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 413 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 437 average time/residue: 1.2266 time to fit residues: 666.7294 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.321 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.1817 ------------------------------------------------------------------------------- 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: 0.7980 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 37800 Z= 0.157 Angle : 0.576 5.436 51264 Z= 0.314 Chirality : 0.037 0.144 5280 Planarity : 0.004 0.047 6936 Dihedral : 4.403 19.352 5160 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 3.40 % Favored : 93.55 % 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: 4.89 (0.12), residues: 4920 helix: 3.71 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP a 93 HIS 0.005 0.001 HIS K 60 PHE 0.019 0.003 PHE F 41 TYR 0.017 0.002 TYR H 39 ARG 0.007 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 425 average time/residue: 1.2965 time to fit residues: 684.8602 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.382 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.8387 ------------------------------------------------------------------------------- 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: 4.9990 chunk 355 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 37800 Z= 0.143 Angle : 0.553 5.266 51264 Z= 0.301 Chirality : 0.036 0.141 5280 Planarity : 0.003 0.038 6936 Dihedral : 4.361 19.355 5160 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 3.96 % Favored : 92.99 % 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: 4.97 (0.12), residues: 4920 helix: 3.77 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.67 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 1 93 HIS 0.004 0.001 HIS K 60 PHE 0.018 0.003 PHE W 41 TYR 0.017 0.002 TYR F 39 ARG 0.004 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 413 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 437 average time/residue: 1.2338 time to fit residues: 669.4144 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.1181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 37800 Z= 0.237 Angle : 0.697 6.193 51264 Z= 0.378 Chirality : 0.040 0.144 5280 Planarity : 0.004 0.028 6936 Dihedral : 4.500 19.097 5160 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 3.66 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.11), residues: 4920 helix: 3.35 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP H 93 HIS 0.006 0.001 HIS r 60 PHE 0.026 0.004 PHE r 41 TYR 0.024 0.003 TYR F 39 ARG 0.005 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 425 average time/residue: 1.2728 time to fit residues: 670.0146 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.1845 ------------------------------------------------------------------------------- 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: 2.9990 chunk 157 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 37800 Z= 0.149 Angle : 0.571 5.861 51264 Z= 0.311 Chirality : 0.036 0.144 5280 Planarity : 0.003 0.026 6936 Dihedral : 4.409 19.304 5160 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.05 % Allowed : 3.66 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.12), residues: 4920 helix: 3.65 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.68 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 6 93 HIS 0.003 0.001 HIS e 60 PHE 0.018 0.003 PHE W 41 TYR 0.018 0.002 TYR F 39 ARG 0.005 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 425 average time/residue: 1.2944 time to fit residues: 681.7065 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.321 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.2045 ------------------------------------------------------------------------------- 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: 3.9990 chunk 376 optimal weight: 0.7980 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 346 optimal weight: 5.9990 chunk 365 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 37800 Z= 0.156 Angle : 0.590 7.606 51264 Z= 0.320 Chirality : 0.036 0.145 5280 Planarity : 0.003 0.067 6936 Dihedral : 4.398 19.383 5160 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 3.66 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.12), residues: 4920 helix: 3.63 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.69 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP O 93 HIS 0.005 0.001 HIS M 60 PHE 0.019 0.003 PHE r 41 TYR 0.019 0.002 TYR F 39 ARG 0.009 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.629 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 425 average time/residue: 1.3178 time to fit residues: 697.2561 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.2776 ------------------------------------------------------------------------------- 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: 8.9990 chunk 387 optimal weight: 0.9990 chunk 236 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 0.9980 chunk 374 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** a 60 HIS ** a 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 HIS ** e 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** r 60 HIS ** r 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 HIS ** G 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS ** O 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 HIS ** Q 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** S 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** F 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** X 60 HIS ** X 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** 6 60 HIS ** 6 75 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 37800 Z= 0.144 Angle : 0.548 7.001 51264 Z= 0.299 Chirality : 0.036 0.145 5280 Planarity : 0.003 0.078 6936 Dihedral : 4.368 19.277 5160 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 3.68 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.12), residues: 4920 helix: 3.70 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.68 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP O 93 HIS 0.005 0.001 HIS M 60 PHE 0.018 0.003 PHE r 41 TYR 0.017 0.002 TYR E 39 ARG 0.006 0.000 ARG M 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 402 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 426 average time/residue: 1.2689 time to fit residues: 668.7686 Evaluate side-chains 425 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 401 time to evaluate : 3.385 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.1663 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 60 HIS Y 60 HIS 2 60 HIS 4 60 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149665 restraints weight = 254152.841| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.20 r_work: 0.3376 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.3186 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work: 0.3131 rms_B_bonded: 4.63 restraints_weight: 0.0625 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37800 Z= 0.187 Angle : 0.620 7.450 51264 Z= 0.337 Chirality : 0.038 0.146 5280 Planarity : 0.004 0.089 6936 Dihedral : 4.441 19.450 5160 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 3.68 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.61 (0.12), residues: 4920 helix: 3.50 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.69 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP a 93 HIS 0.008 0.001 HIS M 60 PHE 0.022 0.003 PHE F 41 TYR 0.022 0.002 TYR I 39 ARG 0.010 0.001 ARG M 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16166.26 seconds wall clock time: 282 minutes 54.68 seconds (16974.68 seconds total)