Starting phenix.real_space_refine (version: dev) on Fri Dec 16 00:36:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/12_2022/7a6b_11669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/12_2022/7a6b_11669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/12_2022/7a6b_11669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/12_2022/7a6b_11669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/12_2022/7a6b_11669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/12_2022/7a6b_11669_updated.pdb" } resolution = 1.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 41494 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" 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 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 162": "OE1" <-> "OE2" Residue "6 GLU 167": "OE1" <-> "OE2" Residue "6 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 41494 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1567 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: 1284 Chain: "1" Number of atoms: 1567 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: 1284 Chain: "K" Number of atoms: 1567 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: 1284 Chain: "a" Number of atoms: 1567 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: 1284 Chain: "B" Number of atoms: 1567 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: 1284 Chain: "E" Number of atoms: 1567 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: 1284 Chain: "e" Number of atoms: 1567 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: 1284 Chain: "r" Number of atoms: 1567 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: 1284 Chain: "G" Number of atoms: 1567 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: 1284 Chain: "I" Number of atoms: 1567 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: 1284 Chain: "M" Number of atoms: 1567 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: 1284 Chain: "O" Number of atoms: 1567 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: 1284 Chain: "Q" Number of atoms: 1567 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: 1284 Chain: "S" Number of atoms: 1567 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: 1284 Chain: "U" Number of atoms: 1567 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: 1284 Chain: "W" Number of atoms: 1567 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: 1284 Chain: "Y" Number of atoms: 1567 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: 1284 Chain: "2" Number of atoms: 1567 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: 1284 Chain: "4" Number of atoms: 1567 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: 1284 Chain: "F" Number of atoms: 1567 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: 1284 Chain: "H" Number of atoms: 1567 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: 1284 Chain: "P" Number of atoms: 1567 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: 1284 Chain: "X" Number of atoms: 1567 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: 1284 Chain: "6" Number of atoms: 1567 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: 1284 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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "1" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "K" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "a" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "E" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "e" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "r" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "G" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "I" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "M" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "O" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "Q" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "S" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "U" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "W" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "Y" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "2" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "4" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "H" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "6" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Residues with excluded nonbonded symmetry interactions: 432 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 ALYS A 87 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 87 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N AASN A 109 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 109 " occ=0.50 residue: pdb=" N ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 113 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 ... (remaining 420 not shown) Time building chain proxies: 27.80, per 1000 atoms: 0.67 Number of scatterers: 41494 At special positions: 0 Unit cell: (131.364, 131.364, 131.364, 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 11150 8.00 N 6672 7.00 C 23520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.03 Conformation dependent library (CDL) restraints added in 7.1 seconds 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 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: 1.58 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 2808 hydrogen bonds defined for protein. 8688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 17.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8432 1.32 - 1.45: 8657 1.45 - 1.58: 21335 1.58 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 38640 Sorted by residual: bond pdb=" C BSER a 163 " pdb=" O BSER a 163 " ideal model delta sigma weight residual 1.236 1.357 -0.122 1.32e-02 5.74e+03 8.50e+01 bond pdb=" C BSER K 163 " pdb=" O BSER K 163 " ideal model delta sigma weight residual 1.236 1.353 -0.117 1.32e-02 5.74e+03 7.83e+01 bond pdb=" C BSER A 163 " pdb=" O BSER A 163 " ideal model delta sigma weight residual 1.236 1.330 -0.094 1.32e-02 5.74e+03 5.09e+01 bond pdb=" C BSER 1 163 " pdb=" O BSER 1 163 " ideal model delta sigma weight residual 1.236 1.319 -0.083 1.32e-02 5.74e+03 3.96e+01 bond pdb=" C BSER B 163 " pdb=" O BSER B 163 " ideal model delta sigma weight residual 1.236 1.309 -0.074 1.32e-02 5.74e+03 3.11e+01 ... (remaining 38635 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.70: 475 105.70 - 112.81: 17464 112.81 - 119.92: 18193 119.92 - 127.03: 15972 127.03 - 134.13: 360 Bond angle restraints: 52464 Sorted by residual: angle pdb=" CA ASP W 150 " pdb=" CB ASP W 150 " pdb=" CG ASP W 150 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" CA ASP K 150 " pdb=" CB ASP K 150 " pdb=" CG ASP K 150 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" CA ASP 1 150 " pdb=" CB ASP 1 150 " pdb=" CG ASP 1 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP O 150 " pdb=" CB ASP O 150 " pdb=" CG ASP O 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP Q 150 " pdb=" CB ASP Q 150 " pdb=" CG ASP Q 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 ... (remaining 52459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 20885 15.57 - 31.13: 1917 31.13 - 46.70: 622 46.70 - 62.27: 264 62.27 - 77.84: 72 Dihedral angle restraints: 23760 sinusoidal: 9864 harmonic: 13896 Sorted by residual: dihedral pdb=" C TYR P 39 " pdb=" N TYR P 39 " pdb=" CA TYR P 39 " pdb=" CB TYR P 39 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C TYR 2 39 " pdb=" N TYR 2 39 " pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.97e+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 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 23757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2981 0.087 - 0.175: 1560 0.175 - 0.262: 685 0.262 - 0.350: 126 0.350 - 0.437: 48 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA TYR P 39 " pdb=" N TYR P 39 " pdb=" C TYR P 39 " pdb=" CB TYR P 39 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA TYR 2 39 " pdb=" N TYR 2 39 " pdb=" C TYR 2 39 " pdb=" CB TYR 2 39 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 5397 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 137 " 0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR K 137 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR K 137 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR K 137 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR K 137 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR K 137 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR K 137 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR K 137 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR a 137 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 137 " -0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR B 137 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 137 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR B 137 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 137 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 137 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR B 137 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 137 " -0.086 2.00e-02 2.50e+03 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 221 2.49 - 3.10: 35979 3.10 - 3.70: 77464 3.70 - 4.30: 125861 4.30 - 4.90: 187106 Nonbonded interactions: 426631 Sorted by model distance: nonbonded pdb=" OE2 GLU K 101 " pdb=" NH2BARG K 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU G 101 " pdb=" NH2BARG G 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU 1 101 " pdb=" NH2BARG 1 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU U 101 " pdb=" NH2BARG U 156 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU O 101 " pdb=" NH2BARG O 156 " model vdw 1.893 2.520 ... (remaining 426626 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain '2' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'Y' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'a' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'e' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) selection = (chain 'r' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 or resid 300)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 23520 2.51 5 N 6672 2.21 5 O 11150 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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=0.91 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: 8.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.420 Construct map_model_manager: 0.030 Extract box with map and model: 25.320 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.290 Process input model: 101.730 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 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 0.122 38640 Z= 0.970 Angle : 1.602 9.077 52464 Z= 1.097 Chirality : 0.123 0.437 5400 Planarity : 0.011 0.061 7128 Dihedral : 15.345 77.836 14976 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 25.00 % 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: 2.52 (0.11), residues: 5136 helix: 1.91 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.84 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 744 time to evaluate : 3.401 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 outliers start: 72 outliers final: 0 residues processed: 768 average time/residue: 1.2992 time to fit residues: 1215.9549 Evaluate side-chains 522 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 3.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1515 ------------------------------------------------------------------------------- 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: 7.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN A 86 GLN A 98 ASN A 125 ASN 1 60 HIS 1 83 GLN 1 86 GLN 1 98 ASN 1 125 ASN 1 136 HIS K 60 HIS K 75 GLN B K 83 GLN K 86 GLN K 98 ASN K 125 ASN K 136 HIS a 60 HIS a 83 GLN a 86 GLN a 98 ASN a 125 ASN a 136 HIS B 60 HIS B 75 GLN B B 83 GLN B 86 GLN B 98 ASN B 125 ASN E 60 HIS E 83 GLN E 86 GLN E 98 ASN E 125 ASN e 60 HIS e 83 GLN e 86 GLN e 98 ASN e 125 ASN r 60 HIS r 83 GLN r 86 GLN r 98 ASN r 125 ASN r 136 HIS G 60 HIS G 83 GLN G 86 GLN G 98 ASN G 125 ASN G 136 HIS I 60 HIS I 83 GLN I 86 GLN I 98 ASN I 125 ASN I 136 HIS M 60 HIS M 83 GLN M 86 GLN M 98 ASN M 125 ASN M 136 HIS O 60 HIS O 75 GLN B O 83 GLN O 86 GLN O 98 ASN O 125 ASN O 136 HIS Q 60 HIS Q 83 GLN Q 86 GLN Q 98 ASN Q 125 ASN Q 136 HIS S 60 HIS S 83 GLN S 86 GLN S 98 ASN S 125 ASN S 136 HIS U 60 HIS U 83 GLN U 86 GLN U 98 ASN U 125 ASN U 136 HIS W 60 HIS W 83 GLN W 86 GLN W 98 ASN W 125 ASN W 136 HIS Y 60 HIS Y 83 GLN Y 86 GLN Y 98 ASN Y 125 ASN Y 136 HIS 2 60 HIS 2 83 GLN 2 86 GLN 2 98 ASN 2 125 ASN 2 136 HIS 4 60 HIS 4 83 GLN 4 86 GLN 4 98 ASN 4 125 ASN 4 136 HIS F 60 HIS F 75 GLN B F 83 GLN F 86 GLN F 98 ASN F 125 ASN H 60 HIS H 83 GLN H 86 GLN H 98 ASN H 125 ASN P 60 HIS P 83 GLN P 86 GLN P 98 ASN P 125 ASN P 136 HIS X 60 HIS X 75 GLN B X 83 GLN X 86 GLN X 98 ASN X 125 ASN X 136 HIS 6 60 HIS 6 83 GLN 6 86 GLN 6 98 ASN 6 125 ASN 6 136 HIS Total number of N/Q/H flips: 143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 38640 Z= 0.188 Angle : 0.630 5.747 52464 Z= 0.348 Chirality : 0.039 0.156 5400 Planarity : 0.004 0.043 7128 Dihedral : 4.695 18.465 5328 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.11), residues: 5136 helix: 3.21 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.77 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 1.3654 time to fit residues: 1067.3979 Evaluate side-chains 533 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 3.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1648 ------------------------------------------------------------------------------- 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: 10.0000 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 368 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 297 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B A 86 GLN A 125 ASN 1 75 GLN B 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 75 GLN B a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 75 GLN B E 86 GLN E 125 ASN e 75 GLN B e 86 GLN e 125 ASN r 75 GLN B r 86 GLN r 125 ASN G 75 GLN B G 86 GLN G 125 ASN I 75 GLN B I 86 GLN I 125 ASN M 75 GLN B M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 75 GLN B Q 86 GLN Q 125 ASN S 75 GLN B S 86 GLN S 125 ASN U 75 GLN B U 86 GLN U 125 ASN W 75 GLN B W 86 GLN W 125 ASN Y 75 GLN B Y 86 GLN Y 125 ASN 2 75 GLN B 2 86 GLN 2 125 ASN 4 75 GLN B 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 75 GLN B H 86 GLN H 125 ASN P 75 GLN B P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 75 GLN B 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 38640 Z= 0.163 Angle : 0.591 5.591 52464 Z= 0.325 Chirality : 0.037 0.144 5400 Planarity : 0.004 0.054 7128 Dihedral : 4.627 18.923 5328 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.57 (0.11), residues: 5136 helix: 3.46 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.84 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 1.4042 time to fit residues: 933.4607 Evaluate side-chains 503 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1855 ------------------------------------------------------------------------------- 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: 4.9990 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 38640 Z= 0.171 Angle : 0.602 5.606 52464 Z= 0.331 Chirality : 0.037 0.140 5400 Planarity : 0.004 0.044 7128 Dihedral : 4.621 19.660 5328 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.58 (0.11), residues: 5136 helix: 3.48 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.81 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 3.360 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 outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 1.3839 time to fit residues: 915.0917 Evaluate side-chains 503 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1942 ------------------------------------------------------------------------------- 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: 9.9990 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 38640 Z= 0.256 Angle : 0.722 6.926 52464 Z= 0.398 Chirality : 0.040 0.144 5400 Planarity : 0.005 0.051 7128 Dihedral : 4.892 26.263 5328 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.05 (0.11), residues: 5136 helix: 3.11 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.59 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 1.3887 time to fit residues: 925.5061 Evaluate side-chains 481 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1976 ------------------------------------------------------------------------------- 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: 6.9990 chunk 355 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 38640 Z= 0.226 Angle : 0.693 7.722 52464 Z= 0.380 Chirality : 0.039 0.143 5400 Planarity : 0.004 0.026 7128 Dihedral : 4.791 23.289 5328 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.09 (0.11), residues: 5136 helix: 3.15 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.56 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 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: 0 outliers final: 0 residues processed: 551 average time/residue: 1.4286 time to fit residues: 946.1258 Evaluate side-chains 483 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 3.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1788 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 chunk 393 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 38640 Z= 0.165 Angle : 0.605 7.834 52464 Z= 0.330 Chirality : 0.036 0.142 5400 Planarity : 0.004 0.062 7128 Dihedral : 4.563 18.813 5328 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.11), residues: 5136 helix: 3.52 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.70 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 1.3590 time to fit residues: 866.1056 Evaluate side-chains 478 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 3.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 50.0000 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 38640 Z= 0.165 Angle : 0.611 9.412 52464 Z= 0.331 Chirality : 0.036 0.138 5400 Planarity : 0.004 0.082 7128 Dihedral : 4.551 19.049 5328 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.11), residues: 5136 helix: 3.59 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.80 (0.23), residues: 960 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 1.3927 time to fit residues: 891.9193 Evaluate side-chains 504 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2094 ------------------------------------------------------------------------------- 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: 9.9990 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 287 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 86 GLN B 125 ASN E 86 GLN E 125 ASN e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 86 GLN P 125 ASN X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 38640 Z= 0.216 Angle : 0.697 11.408 52464 Z= 0.381 Chirality : 0.039 0.140 5400 Planarity : 0.006 0.140 7128 Dihedral : 4.790 23.881 5328 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.11), residues: 5136 helix: 3.27 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.63 (0.22), residues: 960 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 3.563 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 outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 1.4004 time to fit residues: 926.8987 Evaluate side-chains 489 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 3.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1962 ------------------------------------------------------------------------------- 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: 9.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 60 HIS B 86 GLN B 125 ASN E 60 HIS E 86 GLN E 125 ASN e 60 HIS e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 60 HIS S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 60 HIS W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 60 HIS P 86 GLN P 125 ASN X 60 HIS X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 38640 Z= 0.200 Angle : 0.667 12.244 52464 Z= 0.364 Chirality : 0.038 0.140 5400 Planarity : 0.005 0.104 7128 Dihedral : 4.730 22.778 5328 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.32 (0.11), residues: 5136 helix: 3.31 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.64 (0.22), residues: 960 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 534 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 534 average time/residue: 1.3846 time to fit residues: 890.0675 Evaluate side-chains 479 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 332 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 86 GLN A 125 ASN 1 86 GLN 1 125 ASN K 86 GLN K 125 ASN a 86 GLN a 125 ASN B 60 HIS B 86 GLN B 125 ASN E 60 HIS E 86 GLN E 125 ASN e 60 HIS e 86 GLN e 125 ASN r 86 GLN r 125 ASN G 86 GLN G 125 ASN I 86 GLN I 125 ASN M 86 GLN M 125 ASN O 86 GLN O 125 ASN Q 86 GLN Q 125 ASN S 60 HIS S 86 GLN S 125 ASN U 60 HIS U 86 GLN U 125 ASN W 60 HIS W 86 GLN W 125 ASN Y 86 GLN Y 125 ASN 2 86 GLN 2 125 ASN 4 60 HIS 4 86 GLN 4 125 ASN F 86 GLN F 125 ASN H 86 GLN H 125 ASN P 60 HIS P 86 GLN P 125 ASN X 60 HIS X 86 GLN X 125 ASN 6 86 GLN 6 125 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.158250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.129627 restraints weight = 174494.537| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.57 r_work: 0.2982 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.2726 rms_B_bonded: 2.74 restraints_weight: 0.1250 r_work: 0.2679 rms_B_bonded: 3.74 restraints_weight: 0.0625 r_work: 0.2656 rms_B_bonded: 4.92 restraints_weight: 0.0312 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 38640 Z= 0.209 Angle : 0.699 15.525 52464 Z= 0.380 Chirality : 0.038 0.140 5400 Planarity : 0.006 0.139 7128 Dihedral : 4.764 23.128 5328 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.24 (0.11), residues: 5136 helix: 3.25 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.62 (0.22), residues: 960 =============================================================================== Job complete usr+sys time: 18523.34 seconds wall clock time: 321 minutes 33.07 seconds (19293.07 seconds total)