Starting phenix.real_space_refine on Mon Nov 20 00:09:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/11_2023/7a6b_11669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/11_2023/7a6b_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_11669/11_2023/7a6b_11669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/11_2023/7a6b_11669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/11_2023/7a6b_11669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/11_2023/7a6b_11669_updated.pdb" } resolution = 1.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 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. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 162": "OE1" <-> "OE2" Residue "6 GLU 167": "OE1" <-> "OE2" Residue "6 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 27.45, per 1000 atoms: 0.66 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: 15.01 Conformation dependent library (CDL) restraints added in 8.7 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: 4.91 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: 11.02 Time building geometry restraints manager: 16.06 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 - 34.98: 22945 34.98 - 69.96: 719 69.96 - 104.93: 72 104.93 - 139.91: 0 139.91 - 174.89: 24 Dihedral angle restraints: 23760 sinusoidal: 9864 harmonic: 13896 Sorted by residual: dihedral pdb=" CB BGLU A 162 " pdb=" CG BGLU A 162 " pdb=" CD BGLU A 162 " pdb=" OE1BGLU A 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.89 -174.89 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU 1 162 " pdb=" CG BGLU 1 162 " pdb=" CD BGLU 1 162 " pdb=" OE1BGLU 1 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.68 -174.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU K 162 " pdb=" CG BGLU K 162 " pdb=" CD BGLU K 162 " pdb=" OE1BGLU K 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.49 -174.49 1 3.00e+01 1.11e-03 2.13e+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 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: 8.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.040 Extract box with map and model: 25.670 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 102.980 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 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= 0.971 Angle : 1.602 9.077 52464 Z= 1.097 Chirality : 0.123 0.437 5400 Planarity : 0.011 0.061 7128 Dihedral : 16.776 174.891 14976 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.17 % Allowed : 3.35 % Favored : 92.49 % 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 : 3.150 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: 1.3645 time to fit residues: 1268.6394 Evaluate side-chains 522 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 3.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0000 ------------------------------------------------------------------------------- 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 H 136 HIS 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: 144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 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 5.750 52464 Z= 0.348 Chirality : 0.039 0.156 5400 Planarity : 0.004 0.043 7128 Dihedral : 4.697 18.451 5328 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 3.15 % Favored : 94.47 % 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 : 3.509 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: 1.4875 time to fit residues: 1153.9965 Evaluate side-chains 538 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 3.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0611 ------------------------------------------------------------------------------- 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: 10.0000 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.6509 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 38640 Z= 0.188 Angle : 0.636 5.998 52464 Z= 0.350 Chirality : 0.038 0.146 5400 Planarity : 0.004 0.043 7128 Dihedral : 4.745 21.847 5328 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 3.08 % Favored : 94.54 % 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: 4.36 (0.11), residues: 5136 helix: 3.31 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.77 (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 : 3.254 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: 1.5085 time to fit residues: 999.1412 Evaluate side-chains 491 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 3.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 0.7980 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.6487 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 38640 Z= 0.147 Angle : 0.553 5.249 52464 Z= 0.303 Chirality : 0.036 0.136 5400 Planarity : 0.003 0.053 7128 Dihedral : 4.463 18.680 5328 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.38 % Allowed : 3.57 % Favored : 94.05 % 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: 4.85 (0.11), residues: 5136 helix: 3.68 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.82 (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 566 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 1.4399 time to fit residues: 981.3301 Evaluate side-chains 494 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 60 HIS 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 60 HIS 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 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: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 38640 Z= 0.177 Angle : 0.615 7.370 52464 Z= 0.337 Chirality : 0.037 0.139 5400 Planarity : 0.004 0.031 7128 Dihedral : 4.660 21.893 5328 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 4.37 % Favored : 93.85 % 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: 3.49 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.72 (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 533 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 3.663 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: 533 average time/residue: 1.5087 time to fit residues: 964.6671 Evaluate side-chains 485 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0224 ------------------------------------------------------------------------------- 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: 5.9990 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 60 HIS 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 60 HIS 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 60 HIS 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 60 HIS 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.1569 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= 0.197 Angle : 0.645 8.406 52464 Z= 0.354 Chirality : 0.038 0.139 5400 Planarity : 0.004 0.027 7128 Dihedral : 4.686 21.959 5328 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 4.24 % Favored : 93.97 % 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: 4.43 (0.11), residues: 5136 helix: 3.39 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.66 (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 528 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.5047 time to fit residues: 952.8736 Evaluate side-chains 466 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 0.0470 chunk 220 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 50.0000 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- 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 60 HIS 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 60 HIS 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 60 HIS 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 60 HIS 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38640 Z= 0.173 Angle : 0.613 8.952 52464 Z= 0.335 Chirality : 0.037 0.138 5400 Planarity : 0.004 0.035 7128 Dihedral : 4.598 20.163 5328 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 4.24 % Favored : 93.97 % 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: 4.59 (0.11), residues: 5136 helix: 3.49 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.74 (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 524 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 3.201 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 outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 1.5084 time to fit residues: 948.4388 Evaluate side-chains 477 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 3.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0260 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 40.0000 chunk 250 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 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 60 HIS 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 60 HIS 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 60 HIS 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 60 HIS 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38640 Z= 0.217 Angle : 0.686 11.066 52464 Z= 0.375 Chirality : 0.039 0.141 5400 Planarity : 0.004 0.055 7128 Dihedral : 4.752 23.232 5328 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 4.24 % Favored : 93.97 % 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: 4.25 (0.11), residues: 5136 helix: 3.26 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.61 (0.22), 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 522 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 3.328 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: 522 average time/residue: 1.5606 time to fit residues: 988.6993 Evaluate side-chains 468 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 3.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0970 chunk 376 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 365 optimal weight: 0.0170 overall best weight: 0.8222 ------------------------------------------------------------------------------- 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 60 HIS 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 60 HIS 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 60 HIS 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 60 HIS 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: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 38640 Z= 0.150 Angle : 0.576 10.696 52464 Z= 0.311 Chirality : 0.035 0.139 5400 Planarity : 0.004 0.102 7128 Dihedral : 4.442 18.816 5328 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 4.34 % Favored : 93.87 % 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: 4.89 (0.11), residues: 5136 helix: 3.72 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.77 (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 526 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 3.163 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: 1.4949 time to fit residues: 945.4107 Evaluate side-chains 499 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3136 > 50: distance: 75 - 93: 5.418 distance: 79 - 100: 6.039 distance: 88 - 93: 6.922 distance: 89 - 116: 6.261 distance: 89 - 127: 8.369 distance: 93 - 94: 5.906 distance: 94 - 95: 4.234 distance: 94 - 97: 12.953 distance: 95 - 96: 3.748 distance: 95 - 100: 10.355 distance: 96 - 138: 11.148 distance: 97 - 98: 11.457 distance: 97 - 99: 7.931 distance: 100 - 101: 4.025 distance: 101 - 102: 7.174 distance: 101 - 104: 8.452 distance: 102 - 103: 4.232 distance: 102 - 108: 8.579 distance: 103 - 147: 16.025 distance: 104 - 105: 6.268 distance: 108 - 109: 4.731 distance: 109 - 110: 7.672 distance: 109 - 112: 9.654 distance: 110 - 111: 8.297 distance: 110 - 116: 10.093 distance: 110 - 127: 15.623 distance: 112 - 113: 8.828 distance: 113 - 114: 5.737 distance: 113 - 115: 11.986 distance: 116 - 117: 7.062 distance: 117 - 118: 7.448 distance: 117 - 120: 6.609 distance: 118 - 119: 5.828 distance: 118 - 138: 5.270 distance: 120 - 121: 8.489 distance: 121 - 122: 12.535 distance: 122 - 123: 12.807 distance: 123 - 124: 7.122 distance: 124 - 125: 12.735 distance: 124 - 126: 9.683 distance: 127 - 128: 3.113 distance: 128 - 129: 6.853 distance: 128 - 131: 15.598 distance: 129 - 130: 7.595 distance: 129 - 138: 20.057 distance: 131 - 132: 6.410 distance: 132 - 133: 7.828 distance: 133 - 134: 4.373 distance: 134 - 135: 7.459 distance: 135 - 136: 9.090 distance: 135 - 137: 9.252 distance: 138 - 139: 8.772 distance: 139 - 140: 13.720 distance: 139 - 142: 19.378 distance: 140 - 141: 7.677 distance: 140 - 147: 11.088 distance: 142 - 143: 22.691 distance: 143 - 144: 8.021 distance: 144 - 145: 14.002 distance: 145 - 146: 4.250 distance: 147 - 148: 8.448 distance: 148 - 149: 7.296 distance: 148 - 151: 6.391 distance: 149 - 150: 13.079 distance: 149 - 155: 12.274 distance: 151 - 152: 15.759 distance: 152 - 153: 11.057 distance: 153 - 154: 11.643 distance: 155 - 156: 8.676 distance: 156 - 157: 19.267 distance: 157 - 158: 16.476 distance: 157 - 159: 19.552 distance: 159 - 160: 17.182 distance: 160 - 161: 37.633 distance: 160 - 163: 20.011 distance: 161 - 162: 28.430 distance: 161 - 164: 17.632 distance: 164 - 165: 25.598 distance: 164 - 170: 10.463 distance: 165 - 166: 25.940 distance: 165 - 168: 25.774 distance: 166 - 167: 20.392 distance: 166 - 171: 7.028 distance: 166 - 180: 13.230 distance: 168 - 169: 19.783 distance: 169 - 170: 30.400 distance: 171 - 172: 13.798 distance: 172 - 173: 8.694 distance: 172 - 175: 11.339 distance: 173 - 174: 13.452 distance: 173 - 189: 21.106 distance: 175 - 176: 6.213 distance: 176 - 177: 8.139 distance: 177 - 178: 6.169 distance: 177 - 179: 8.983 distance: 180 - 181: 11.103 distance: 181 - 182: 4.669 distance: 181 - 184: 13.580 distance: 182 - 183: 11.922 distance: 182 - 195: 4.028 distance: 184 - 185: 14.968 distance: 185 - 186: 6.092 distance: 186 - 187: 16.700 distance: 186 - 188: 26.496