Starting phenix.real_space_refine on Mon Mar 18 02:09:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/03_2024/7a6b_11669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/03_2024/7a6b_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_11669/03_2024/7a6b_11669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/03_2024/7a6b_11669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/03_2024/7a6b_11669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/03_2024/7a6b_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-dev-5265/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: 27.94, per 1000 atoms: 0.67 Number of scatterers: 41494 At special positions: 0 Unit cell: (131.364, 131.364, 131.364, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Na 32 11.00 O 11150 8.00 N 6672 7.00 C 23520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.89 Conformation dependent library (CDL) restraints added in 8.5 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: 4.57 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: 11.48 Time building geometry restraints manager: 16.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.400 Construct map_model_manager: 0.040 Extract box with map and model: 23.960 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 104.870 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.510 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.011 TRP 1 93 HIS 0.025 0.008 HIS H 173 PHE 0.041 0.011 PHE I 41 TYR 0.103 0.025 TYR r 137 ARG 0.015 0.005 ARG 6 22 *********************** 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 : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.6095 (m-30) REVERT: A 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6337 (tppt) REVERT: 1 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.6103 (m-30) REVERT: 1 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: K 89 ASP cc_start: 0.6376 (m-30) cc_final: 0.6101 (m-30) REVERT: K 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6340 (tppt) REVERT: a 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.6100 (m-30) REVERT: a 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6339 (tppt) REVERT: B 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6089 (m-30) REVERT: B 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6342 (tppt) REVERT: E 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6088 (m-30) REVERT: E 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: e 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.6096 (m-30) REVERT: e 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6340 (tppt) REVERT: r 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.6100 (m-30) REVERT: r 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6339 (tppt) REVERT: G 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.6103 (m-30) REVERT: G 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6341 (tppt) REVERT: I 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.6095 (m-30) REVERT: I 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: M 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6091 (m-30) REVERT: M 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6338 (tppt) REVERT: O 89 ASP cc_start: 0.6376 (m-30) cc_final: 0.6102 (m-30) REVERT: O 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: Q 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.6103 (m-30) REVERT: Q 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6342 (tppt) REVERT: S 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6091 (m-30) REVERT: S 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: U 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.6086 (m-30) REVERT: U 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: W 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6091 (m-30) REVERT: W 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: Y 89 ASP cc_start: 0.6377 (m-30) cc_final: 0.6102 (m-30) REVERT: Y 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6339 (tppt) REVERT: 2 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.6086 (m-30) REVERT: 2 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6337 (tppt) REVERT: 4 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.6093 (m-30) REVERT: 4 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6341 (tppt) REVERT: F 89 ASP cc_start: 0.6365 (m-30) cc_final: 0.6088 (m-30) REVERT: F 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6339 (tppt) REVERT: H 89 ASP cc_start: 0.6359 (m-30) cc_final: 0.6080 (m-30) REVERT: H 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6340 (tppt) REVERT: P 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.6095 (m-30) REVERT: P 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: X 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.6094 (m-30) REVERT: X 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6343 (tppt) REVERT: 6 89 ASP cc_start: 0.6365 (m-30) cc_final: 0.6090 (m-30) REVERT: 6 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6338 (tppt) outliers start: 72 outliers final: 0 residues processed: 768 average time/residue: 1.3545 time to fit residues: 1258.5066 Evaluate side-chains 546 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 3.241 ------------------------------------------------------------------------------- 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: 6.9990 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: 2.1588 ------------------------------------------------------------------------------- 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 1 60 HIS 1 83 GLN 1 86 GLN 1 98 ASN 1 136 HIS K 60 HIS K 83 GLN K 86 GLN K 98 ASN K 136 HIS a 60 HIS a 83 GLN a 86 GLN a 98 ASN a 136 HIS B 60 HIS B 83 GLN B 86 GLN B 98 ASN E 60 HIS E 83 GLN E 86 GLN E 98 ASN e 60 HIS e 83 GLN e 86 GLN e 98 ASN r 60 HIS r 83 GLN r 86 GLN r 98 ASN r 136 HIS G 60 HIS G 83 GLN G 86 GLN G 98 ASN G 136 HIS I 60 HIS I 83 GLN I 86 GLN I 98 ASN I 136 HIS M 60 HIS M 83 GLN M 86 GLN M 98 ASN M 136 HIS O 60 HIS O 83 GLN O 86 GLN O 98 ASN O 136 HIS Q 60 HIS Q 83 GLN Q 86 GLN Q 98 ASN Q 136 HIS S 60 HIS S 83 GLN S 86 GLN S 98 ASN S 136 HIS U 60 HIS U 83 GLN U 86 GLN U 98 ASN U 136 HIS W 60 HIS W 83 GLN W 86 GLN W 98 ASN W 136 HIS Y 60 HIS Y 75 GLN B Y 83 GLN Y 86 GLN Y 98 ASN Y 136 HIS 2 60 HIS 2 75 GLN B 2 83 GLN 2 86 GLN 2 98 ASN 2 136 HIS 4 60 HIS 4 83 GLN 4 86 GLN 4 98 ASN 4 136 HIS F 60 HIS F 83 GLN F 86 GLN F 98 ASN H 60 HIS H 83 GLN H 86 GLN H 98 ASN H 136 HIS P 60 HIS P 83 GLN P 86 GLN P 98 ASN P 136 HIS X 60 HIS X 75 GLN B X 83 GLN X 86 GLN X 98 ASN X 136 HIS 6 60 HIS 6 83 GLN 6 86 GLN 6 98 ASN 6 136 HIS Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 38640 Z= 0.196 Angle : 0.647 5.906 52464 Z= 0.360 Chirality : 0.040 0.156 5400 Planarity : 0.004 0.045 7128 Dihedral : 4.779 18.568 5328 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 2.85 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.11), residues: 5136 helix: 3.11 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.76 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP r 93 HIS 0.013 0.002 HIS K 60 PHE 0.026 0.003 PHE S 41 TYR 0.024 0.003 TYR H 39 ARG 0.010 0.001 ARG 1 63 *********************** 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 624 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5976 (m-30) REVERT: A 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6393 (tppt) REVERT: 1 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5976 (m-30) REVERT: 1 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6392 (tppt) REVERT: K 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: K 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: a 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5975 (m-30) REVERT: a 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: B 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5969 (m-30) REVERT: B 119 LYS cc_start: 0.6891 (ttmm) cc_final: 0.6393 (tppt) REVERT: E 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5969 (m-30) REVERT: E 119 LYS cc_start: 0.6891 (ttmm) cc_final: 0.6394 (tppt) REVERT: e 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5976 (m-30) REVERT: e 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6393 (tppt) REVERT: r 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5975 (m-30) REVERT: r 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: G 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: G 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6392 (tppt) REVERT: I 89 ASP cc_start: 0.6379 (m-30) cc_final: 0.5975 (m-30) REVERT: I 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: M 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5968 (m-30) REVERT: M 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: O 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: O 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: Q 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: Q 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6392 (tppt) REVERT: S 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5968 (m-30) REVERT: S 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: U 89 ASP cc_start: 0.6378 (m-30) cc_final: 0.5975 (m-30) REVERT: U 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: W 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5968 (m-30) REVERT: W 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: Y 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: Y 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6392 (tppt) REVERT: 2 89 ASP cc_start: 0.6378 (m-30) cc_final: 0.5975 (m-30) REVERT: 2 119 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6391 (tppt) REVERT: 4 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: 4 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6393 (tppt) REVERT: F 89 ASP cc_start: 0.6380 (m-30) cc_final: 0.5977 (m-30) REVERT: F 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6394 (tppt) REVERT: H 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5969 (m-30) REVERT: H 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6393 (tppt) REVERT: P 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5976 (m-30) REVERT: P 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6393 (tppt) REVERT: X 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: X 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6392 (tppt) REVERT: 6 89 ASP cc_start: 0.6380 (m-30) cc_final: 0.5974 (m-30) REVERT: 6 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6393 (tppt) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 1.5029 time to fit residues: 1117.0061 Evaluate side-chains 572 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 3.214 ------------------------------------------------------------------------------- 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: 9.9990 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 368 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 1 75 GLN B 1 86 GLN K 75 GLN B K 86 GLN a 75 GLN B a 86 GLN B 75 GLN B B 86 GLN E 75 GLN B E 86 GLN e 75 GLN B e 86 GLN r 75 GLN B r 86 GLN G 75 GLN B G 86 GLN I 75 GLN B I 86 GLN M 75 GLN B M 86 GLN O 75 GLN B O 86 GLN Q 75 GLN B Q 86 GLN S 75 GLN B S 86 GLN U 75 GLN B U 86 GLN W 75 GLN B W 86 GLN Y 86 GLN 2 86 GLN 4 75 GLN B 4 86 GLN F 75 GLN B F 86 GLN H 75 GLN B H 86 GLN P 75 GLN B P 86 GLN X 86 GLN 6 75 GLN B 6 86 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 38640 Z= 0.190 Angle : 0.638 6.093 52464 Z= 0.354 Chirality : 0.038 0.147 5400 Planarity : 0.004 0.048 7128 Dihedral : 4.743 20.746 5328 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.36 % Allowed : 2.46 % Favored : 95.19 % 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: 4.31 (0.11), residues: 5136 helix: 3.28 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.75 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 93 HIS 0.006 0.001 HIS X 57 PHE 0.024 0.003 PHE A 41 TYR 0.022 0.003 TYR Y 39 ARG 0.014 0.001 ARG E 63 *********************** 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 : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6356 (m-30) cc_final: 0.5959 (m-30) REVERT: A 119 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6387 (tppt) REVERT: 1 89 ASP cc_start: 0.6359 (m-30) cc_final: 0.5958 (m-30) REVERT: 1 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6385 (tppt) REVERT: K 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5956 (m-30) REVERT: K 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6388 (tppt) REVERT: a 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5957 (m-30) REVERT: a 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6384 (tppt) REVERT: B 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5952 (m-30) REVERT: B 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6384 (tppt) REVERT: E 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5951 (m-30) REVERT: E 119 LYS cc_start: 0.6886 (ttmm) cc_final: 0.6388 (tppt) REVERT: e 89 ASP cc_start: 0.6356 (m-30) cc_final: 0.5959 (m-30) REVERT: e 119 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6389 (tppt) REVERT: r 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5957 (m-30) REVERT: r 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6384 (tppt) REVERT: G 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5959 (m-30) REVERT: G 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6384 (tppt) REVERT: I 89 ASP cc_start: 0.6353 (m-30) cc_final: 0.5956 (m-30) REVERT: I 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6385 (tppt) REVERT: M 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5950 (m-30) REVERT: M 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6385 (tppt) REVERT: O 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5957 (m-30) REVERT: O 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6385 (tppt) REVERT: Q 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5958 (m-30) REVERT: Q 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6384 (tppt) REVERT: S 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5951 (m-30) REVERT: S 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6385 (tppt) REVERT: U 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5957 (m-30) REVERT: U 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6385 (tppt) REVERT: W 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5951 (m-30) REVERT: W 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6385 (tppt) REVERT: Y 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5957 (m-30) REVERT: Y 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6383 (tppt) REVERT: 2 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5957 (m-30) REVERT: 2 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6383 (tppt) REVERT: 4 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5958 (m-30) REVERT: 4 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6384 (tppt) REVERT: F 89 ASP cc_start: 0.6356 (m-30) cc_final: 0.5959 (m-30) REVERT: F 119 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6387 (tppt) REVERT: H 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5952 (m-30) REVERT: H 119 LYS cc_start: 0.6885 (ttmm) cc_final: 0.6388 (tppt) REVERT: P 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5959 (m-30) REVERT: P 119 LYS cc_start: 0.6886 (ttmm) cc_final: 0.6388 (tppt) REVERT: X 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5958 (m-30) REVERT: X 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6388 (tppt) REVERT: 6 89 ASP cc_start: 0.6357 (m-30) cc_final: 0.5967 (m-30) REVERT: 6 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6385 (tppt) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 1.5612 time to fit residues: 1038.9464 Evaluate side-chains 528 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.295 ------------------------------------------------------------------------------- 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: 0.0980 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 177 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 372 optimal weight: 0.6980 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 86 GLN K 86 GLN a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 86 GLN G 86 GLN I 86 GLN M 86 GLN O 86 GLN Q 86 GLN S 86 GLN U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 86 GLN F 86 GLN H 86 GLN P 86 GLN X 86 GLN 6 86 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 38640 Z= 0.116 Angle : 0.489 4.918 52464 Z= 0.268 Chirality : 0.034 0.135 5400 Planarity : 0.003 0.047 7128 Dihedral : 4.280 18.344 5328 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 2.38 % Favored : 95.24 % 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: 5.18 (0.12), residues: 5136 helix: 3.92 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.87 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP X 93 HIS 0.004 0.001 HIS I 60 PHE 0.015 0.002 PHE I 41 TYR 0.016 0.002 TYR 6 39 ARG 0.008 0.001 ARG P 63 *********************** 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 635 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5893 (m-30) REVERT: A 119 LYS cc_start: 0.6797 (ttmm) cc_final: 0.6305 (tppt) REVERT: 1 89 ASP cc_start: 0.6299 (m-30) cc_final: 0.5894 (m-30) REVERT: 1 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6307 (tppt) REVERT: K 89 ASP cc_start: 0.6300 (m-30) cc_final: 0.5894 (m-30) REVERT: K 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6307 (tppt) REVERT: a 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5891 (m-30) REVERT: a 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6308 (tppt) REVERT: B 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5886 (m-30) REVERT: B 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6307 (tppt) REVERT: E 89 ASP cc_start: 0.6293 (m-30) cc_final: 0.5888 (m-30) REVERT: E 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6308 (tppt) REVERT: e 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5894 (m-30) REVERT: e 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6308 (tppt) REVERT: r 89 ASP cc_start: 0.6298 (m-30) cc_final: 0.5892 (m-30) REVERT: r 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6308 (tppt) REVERT: G 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5892 (m-30) REVERT: G 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6309 (tppt) REVERT: I 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5894 (m-30) REVERT: I 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6309 (tppt) REVERT: M 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5887 (m-30) REVERT: M 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6308 (tppt) REVERT: O 89 ASP cc_start: 0.6298 (m-30) cc_final: 0.5892 (m-30) REVERT: O 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6308 (tppt) REVERT: Q 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5892 (m-30) REVERT: Q 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6309 (tppt) REVERT: S 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5887 (m-30) REVERT: S 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6309 (tppt) REVERT: U 89 ASP cc_start: 0.6294 (m-30) cc_final: 0.5891 (m-30) REVERT: U 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6309 (tppt) REVERT: W 89 ASP cc_start: 0.6292 (m-30) cc_final: 0.5888 (m-30) REVERT: W 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6308 (tppt) REVERT: Y 89 ASP cc_start: 0.6300 (m-30) cc_final: 0.5894 (m-30) REVERT: Y 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6306 (tppt) REVERT: 2 89 ASP cc_start: 0.6295 (m-30) cc_final: 0.5891 (m-30) REVERT: 2 119 LYS cc_start: 0.6798 (ttmm) cc_final: 0.6307 (tppt) REVERT: 4 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5892 (m-30) REVERT: 4 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6309 (tppt) REVERT: F 89 ASP cc_start: 0.6295 (m-30) cc_final: 0.5892 (m-30) REVERT: F 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6307 (tppt) REVERT: H 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5885 (m-30) REVERT: H 119 LYS cc_start: 0.6798 (ttmm) cc_final: 0.6307 (tppt) REVERT: P 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5892 (m-30) REVERT: P 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6309 (tppt) REVERT: X 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5891 (m-30) REVERT: X 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6308 (tppt) REVERT: 6 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5894 (m-30) REVERT: 6 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6308 (tppt) outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 1.3091 time to fit residues: 1011.4808 Evaluate side-chains 568 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 3.262 ------------------------------------------------------------------------------- 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: 6.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 0.0010 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 139 ASN 1 86 GLN 1 139 ASN K 86 GLN K 139 ASN a 86 GLN a 139 ASN B 86 GLN B 139 ASN E 86 GLN E 139 ASN e 86 GLN e 139 ASN r 86 GLN r 139 ASN G 86 GLN G 139 ASN I 86 GLN I 139 ASN M 86 GLN M 139 ASN O 86 GLN O 139 ASN Q 86 GLN Q 139 ASN S 86 GLN S 139 ASN U 86 GLN U 139 ASN W 86 GLN W 139 ASN Y 86 GLN Y 139 ASN 2 86 GLN 2 139 ASN 4 86 GLN 4 139 ASN F 86 GLN F 139 ASN H 86 GLN H 139 ASN P 86 GLN P 139 ASN X 86 GLN X 139 ASN 6 86 GLN 6 139 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 0.020 38640 Z= 0.180 Angle : 0.622 6.771 52464 Z= 0.343 Chirality : 0.038 0.136 5400 Planarity : 0.004 0.019 7128 Dihedral : 4.645 21.307 5328 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 3.08 % Favored : 95.14 % 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: 4.55 (0.11), residues: 5136 helix: 3.47 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.72 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 93 HIS 0.004 0.001 HIS U 128 PHE 0.021 0.003 PHE M 41 TYR 0.020 0.003 TYR a 39 ARG 0.006 0.001 ARG 4 63 *********************** 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 560 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5948 (m-30) REVERT: A 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6378 (tppt) REVERT: 1 89 ASP cc_start: 0.6349 (m-30) cc_final: 0.5948 (m-30) REVERT: 1 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: K 89 ASP cc_start: 0.6349 (m-30) cc_final: 0.5949 (m-30) REVERT: K 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6377 (tppt) REVERT: a 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5949 (m-30) REVERT: a 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6378 (tppt) REVERT: B 89 ASP cc_start: 0.6341 (m-30) cc_final: 0.5942 (m-30) REVERT: B 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6377 (tppt) REVERT: E 89 ASP cc_start: 0.6341 (m-30) cc_final: 0.5942 (m-30) REVERT: E 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6378 (tppt) REVERT: e 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5949 (m-30) REVERT: e 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6379 (tppt) REVERT: r 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5947 (m-30) REVERT: r 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: G 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5946 (m-30) REVERT: G 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: I 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5949 (m-30) REVERT: I 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6378 (tppt) REVERT: M 89 ASP cc_start: 0.6343 (m-30) cc_final: 0.5943 (m-30) REVERT: M 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6377 (tppt) REVERT: O 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5947 (m-30) REVERT: O 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: Q 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5947 (m-30) REVERT: Q 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: S 89 ASP cc_start: 0.6340 (m-30) cc_final: 0.5940 (m-30) REVERT: S 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: U 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5949 (m-30) REVERT: U 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6378 (tppt) REVERT: W 89 ASP cc_start: 0.6342 (m-30) cc_final: 0.5942 (m-30) REVERT: W 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6377 (tppt) REVERT: Y 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5947 (m-30) REVERT: Y 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6375 (tppt) REVERT: 2 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5948 (m-30) REVERT: 2 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: 4 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5947 (m-30) REVERT: 4 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) REVERT: F 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5949 (m-30) REVERT: F 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6379 (tppt) REVERT: H 89 ASP cc_start: 0.6341 (m-30) cc_final: 0.5942 (m-30) REVERT: H 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6378 (tppt) REVERT: P 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5948 (m-30) REVERT: P 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6378 (tppt) REVERT: X 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5948 (m-30) REVERT: X 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6378 (tppt) REVERT: 6 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5947 (m-30) REVERT: 6 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6377 (tppt) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 1.4032 time to fit residues: 944.5673 Evaluate side-chains 508 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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: 30.0000 chunk 77 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 394 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 60 HIS 1 86 GLN K 60 HIS K 86 GLN a 60 HIS a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 60 HIS r 86 GLN G 60 HIS G 86 GLN I 60 HIS I 86 GLN M 60 HIS M 86 GLN O 60 HIS O 86 GLN Q 60 HIS Q 86 GLN S 86 GLN U 86 GLN W 86 GLN Y 60 HIS Y 86 GLN 2 60 HIS 2 86 GLN 4 86 GLN F 60 HIS F 86 GLN H 60 HIS H 86 GLN P 86 GLN X 86 GLN 6 60 HIS 6 86 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1469 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= 0.221 Angle : 0.678 7.943 52464 Z= 0.376 Chirality : 0.039 0.138 5400 Planarity : 0.005 0.082 7128 Dihedral : 4.804 23.279 5328 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % 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: 4.16 (0.11), residues: 5136 helix: 3.20 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.58 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP a 93 HIS 0.005 0.001 HIS U 60 PHE 0.024 0.004 PHE F 41 TYR 0.024 0.003 TYR 1 39 ARG 0.014 0.001 ARG r 63 *********************** 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 510 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6380 (m-30) cc_final: 0.5989 (m-30) REVERT: A 119 LYS cc_start: 0.6869 (ttmm) cc_final: 0.6371 (tppt) REVERT: 1 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5988 (m-30) REVERT: 1 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6372 (tppt) REVERT: K 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5990 (m-30) REVERT: K 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: a 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5988 (m-30) REVERT: a 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: B 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5982 (m-30) REVERT: B 119 LYS cc_start: 0.6868 (ttmm) cc_final: 0.6371 (tppt) REVERT: E 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5982 (m-30) REVERT: E 119 LYS cc_start: 0.6868 (ttmm) cc_final: 0.6371 (tppt) REVERT: e 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5990 (m-30) REVERT: e 119 LYS cc_start: 0.6869 (ttmm) cc_final: 0.6372 (tppt) REVERT: r 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5988 (m-30) REVERT: r 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: G 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5991 (m-30) REVERT: G 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: I 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5990 (m-30) REVERT: I 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6371 (tppt) REVERT: M 89 ASP cc_start: 0.6377 (m-30) cc_final: 0.5984 (m-30) REVERT: M 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6371 (tppt) REVERT: O 89 ASP cc_start: 0.6384 (m-30) cc_final: 0.5991 (m-30) REVERT: O 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6371 (tppt) REVERT: Q 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5990 (m-30) REVERT: Q 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: S 89 ASP cc_start: 0.6377 (m-30) cc_final: 0.5984 (m-30) REVERT: S 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6371 (tppt) REVERT: U 89 ASP cc_start: 0.6380 (m-30) cc_final: 0.5990 (m-30) REVERT: U 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6371 (tppt) REVERT: W 89 ASP cc_start: 0.6376 (m-30) cc_final: 0.5984 (m-30) REVERT: W 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6371 (tppt) REVERT: Y 89 ASP cc_start: 0.6384 (m-30) cc_final: 0.5991 (m-30) REVERT: Y 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6369 (tppt) REVERT: 2 89 ASP cc_start: 0.6380 (m-30) cc_final: 0.5989 (m-30) REVERT: 2 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: 4 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5990 (m-30) REVERT: 4 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) REVERT: F 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5990 (m-30) REVERT: F 119 LYS cc_start: 0.6869 (ttmm) cc_final: 0.6372 (tppt) REVERT: H 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5983 (m-30) REVERT: H 119 LYS cc_start: 0.6868 (ttmm) cc_final: 0.6372 (tppt) REVERT: P 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.5990 (m-30) REVERT: P 119 LYS cc_start: 0.6868 (ttmm) cc_final: 0.6372 (tppt) REVERT: X 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5988 (m-30) REVERT: X 119 LYS cc_start: 0.6868 (ttmm) cc_final: 0.6372 (tppt) REVERT: 6 89 ASP cc_start: 0.6383 (m-30) cc_final: 0.6000 (m-30) REVERT: 6 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6371 (tppt) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 1.4853 time to fit residues: 903.8594 Evaluate side-chains 508 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 3.170 ------------------------------------------------------------------------------- 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: 0.8980 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 0.0980 chunk 220 optimal weight: 1.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 50.0000 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 60 HIS 1 86 GLN K 60 HIS K 86 GLN a 60 HIS a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 60 HIS r 86 GLN G 60 HIS G 86 GLN I 60 HIS I 86 GLN M 60 HIS M 86 GLN O 86 GLN Q 60 HIS Q 86 GLN S 86 GLN U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 86 GLN F 60 HIS F 86 GLN H 60 HIS H 86 GLN P 86 GLN X 86 GLN 6 60 HIS 6 86 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.1572 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= 0.155 Angle : 0.583 8.929 52464 Z= 0.322 Chirality : 0.036 0.141 5400 Planarity : 0.004 0.035 7128 Dihedral : 4.554 18.533 5328 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % 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: 4.56 (0.11), residues: 5136 helix: 3.49 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.65 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 1 93 HIS 0.008 0.001 HIS A 60 PHE 0.019 0.003 PHE e 41 TYR 0.019 0.002 TYR a 39 ARG 0.010 0.001 ARG K 63 *********************** 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 519 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5953 (m-30) REVERT: A 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: 1 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5962 (m-30) REVERT: 1 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6375 (tppt) REVERT: K 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5943 (m-30) REVERT: K 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: a 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5952 (m-30) REVERT: a 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6375 (tppt) REVERT: B 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5955 (m-30) REVERT: B 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: E 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5955 (m-30) REVERT: E 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: e 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5963 (m-30) REVERT: e 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6377 (tppt) REVERT: r 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5962 (m-30) REVERT: r 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6375 (tppt) REVERT: G 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5943 (m-30) REVERT: G 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6375 (tppt) REVERT: I 89 ASP cc_start: 0.6343 (m-30) cc_final: 0.5942 (m-30) REVERT: I 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6376 (tppt) REVERT: M 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5936 (m-30) REVERT: M 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: O 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5943 (m-30) REVERT: O 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: Q 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5943 (m-30) REVERT: Q 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: S 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5936 (m-30) REVERT: S 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6376 (tppt) REVERT: U 89 ASP cc_start: 0.6343 (m-30) cc_final: 0.5942 (m-30) REVERT: U 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6376 (tppt) REVERT: W 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5936 (m-30) REVERT: W 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: Y 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5943 (m-30) REVERT: Y 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6374 (tppt) REVERT: 2 89 ASP cc_start: 0.6343 (m-30) cc_final: 0.5942 (m-30) REVERT: 2 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: 4 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5952 (m-30) REVERT: 4 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: F 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5963 (m-30) REVERT: F 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6377 (tppt) REVERT: H 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5955 (m-30) REVERT: H 119 LYS cc_start: 0.6875 (ttmm) cc_final: 0.6376 (tppt) REVERT: P 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5962 (m-30) REVERT: P 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: X 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5962 (m-30) REVERT: X 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: 6 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5951 (m-30) REVERT: 6 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6375 (tppt) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 1.5072 time to fit residues: 932.0559 Evaluate side-chains 519 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 3.259 ------------------------------------------------------------------------------- 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: 0.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 250 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 60 HIS 1 86 GLN K 60 HIS K 86 GLN a 60 HIS a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 60 HIS r 86 GLN G 60 HIS G 86 GLN I 60 HIS I 86 GLN M 60 HIS M 86 GLN O 60 HIS O 86 GLN Q 60 HIS Q 86 GLN S 86 GLN U 86 GLN W 86 GLN Y 60 HIS Y 86 GLN 2 60 HIS 2 86 GLN 4 86 GLN F 60 HIS F 86 GLN H 60 HIS H 86 GLN P 86 GLN X 86 GLN 6 60 HIS 6 86 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 38640 Z= 0.169 Angle : 0.609 9.863 52464 Z= 0.336 Chirality : 0.037 0.139 5400 Planarity : 0.004 0.048 7128 Dihedral : 4.606 19.080 5328 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % 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: 4.50 (0.11), residues: 5136 helix: 3.44 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.68 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP O 93 HIS 0.008 0.001 HIS U 60 PHE 0.021 0.003 PHE e 41 TYR 0.019 0.003 TYR Q 39 ARG 0.011 0.001 ARG M 63 *********************** 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 519 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5956 (m-30) REVERT: A 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6369 (tppt) REVERT: 1 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5956 (m-30) REVERT: 1 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6369 (tppt) REVERT: K 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5955 (m-30) REVERT: K 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) REVERT: a 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5955 (m-30) REVERT: a 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) REVERT: B 89 ASP cc_start: 0.6340 (m-30) cc_final: 0.5949 (m-30) REVERT: B 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6369 (tppt) REVERT: E 89 ASP cc_start: 0.6340 (m-30) cc_final: 0.5949 (m-30) REVERT: E 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6369 (tppt) REVERT: e 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5957 (m-30) REVERT: e 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6370 (tppt) REVERT: r 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5955 (m-30) REVERT: r 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) REVERT: G 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5955 (m-30) REVERT: G 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6369 (tppt) REVERT: I 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5955 (m-30) REVERT: I 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6369 (tppt) REVERT: M 89 ASP cc_start: 0.6341 (m-30) cc_final: 0.5949 (m-30) REVERT: M 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) REVERT: O 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5956 (m-30) REVERT: O 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6369 (tppt) REVERT: Q 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5955 (m-30) REVERT: Q 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6369 (tppt) REVERT: S 89 ASP cc_start: 0.6340 (m-30) cc_final: 0.5949 (m-30) REVERT: S 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6369 (tppt) REVERT: U 89 ASP cc_start: 0.6344 (m-30) cc_final: 0.5955 (m-30) REVERT: U 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6369 (tppt) REVERT: W 89 ASP cc_start: 0.6340 (m-30) cc_final: 0.5949 (m-30) REVERT: W 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) REVERT: Y 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5955 (m-30) REVERT: Y 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6367 (tppt) REVERT: 2 89 ASP cc_start: 0.6344 (m-30) cc_final: 0.5954 (m-30) REVERT: 2 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) REVERT: 4 89 ASP cc_start: 0.6347 (m-30) cc_final: 0.5954 (m-30) REVERT: 4 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6369 (tppt) REVERT: F 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5956 (m-30) REVERT: F 119 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6370 (tppt) REVERT: H 89 ASP cc_start: 0.6340 (m-30) cc_final: 0.5949 (m-30) REVERT: H 119 LYS cc_start: 0.6868 (ttmm) cc_final: 0.6370 (tppt) REVERT: P 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5956 (m-30) REVERT: P 119 LYS cc_start: 0.6866 (ttmm) cc_final: 0.6369 (tppt) REVERT: X 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5956 (m-30) REVERT: X 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6369 (tppt) REVERT: 6 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5955 (m-30) REVERT: 6 119 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6368 (tppt) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 1.5016 time to fit residues: 928.4845 Evaluate side-chains 519 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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: 2.9990 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 20.0000 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 346 optimal weight: 1.9990 chunk 365 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 60 HIS 1 86 GLN K 60 HIS K 86 GLN a 60 HIS a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 60 HIS r 86 GLN G 60 HIS G 86 GLN I 60 HIS I 86 GLN M 60 HIS M 86 GLN O 60 HIS O 86 GLN Q 60 HIS Q 86 GLN S 86 GLN U 86 GLN W 86 GLN Y 60 HIS Y 86 GLN 2 60 HIS 2 86 GLN 4 86 GLN F 60 HIS F 86 GLN H 60 HIS H 86 GLN P 86 GLN X 86 GLN 6 60 HIS 6 86 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 38640 Z= 0.153 Angle : 0.585 11.286 52464 Z= 0.322 Chirality : 0.036 0.138 5400 Planarity : 0.004 0.072 7128 Dihedral : 4.539 18.762 5328 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 3.10 % Favored : 95.11 % 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: 4.66 (0.11), residues: 5136 helix: 3.55 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 4 93 HIS 0.006 0.001 HIS U 60 PHE 0.018 0.003 PHE B 41 TYR 0.018 0.002 TYR G 39 ARG 0.013 0.001 ARG A 63 *********************** 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 514 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5946 (m-30) REVERT: A 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6373 (tppt) REVERT: 1 89 ASP cc_start: 0.6339 (m-30) cc_final: 0.5946 (m-30) REVERT: 1 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: K 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5946 (m-30) REVERT: K 119 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6373 (tppt) REVERT: a 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5946 (m-30) REVERT: a 119 LYS cc_start: 0.6869 (ttmm) cc_final: 0.6374 (tppt) REVERT: B 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5939 (m-30) REVERT: B 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: E 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5939 (m-30) REVERT: E 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: e 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5947 (m-30) REVERT: e 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: r 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5946 (m-30) REVERT: r 119 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6374 (tppt) REVERT: G 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5945 (m-30) REVERT: G 119 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6373 (tppt) REVERT: I 89 ASP cc_start: 0.6335 (m-30) cc_final: 0.5945 (m-30) REVERT: I 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: M 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5939 (m-30) REVERT: M 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6375 (tppt) REVERT: O 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5946 (m-30) REVERT: O 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6375 (tppt) REVERT: Q 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5944 (m-30) REVERT: Q 119 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6373 (tppt) REVERT: S 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5938 (m-30) REVERT: S 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: U 89 ASP cc_start: 0.6334 (m-30) cc_final: 0.5944 (m-30) REVERT: U 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6376 (tppt) REVERT: W 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5939 (m-30) REVERT: W 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: Y 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5945 (m-30) REVERT: Y 119 LYS cc_start: 0.6872 (ttmm) cc_final: 0.6375 (tppt) REVERT: 2 89 ASP cc_start: 0.6334 (m-30) cc_final: 0.5943 (m-30) REVERT: 2 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6375 (tppt) REVERT: 4 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5944 (m-30) REVERT: 4 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6376 (tppt) REVERT: F 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5946 (m-30) REVERT: F 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: H 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5939 (m-30) REVERT: H 119 LYS cc_start: 0.6874 (ttmm) cc_final: 0.6376 (tppt) REVERT: P 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5945 (m-30) REVERT: P 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6376 (tppt) REVERT: X 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5945 (m-30) REVERT: X 119 LYS cc_start: 0.6873 (ttmm) cc_final: 0.6375 (tppt) REVERT: 6 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5945 (m-30) REVERT: 6 119 LYS cc_start: 0.6871 (ttmm) cc_final: 0.6374 (tppt) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 1.5479 time to fit residues: 943.7874 Evaluate side-chains 514 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 6.9990 chunk 236 optimal weight: 0.0170 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 0.9980 chunk 374 optimal weight: 0.0970 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 60 HIS 1 86 GLN K 60 HIS K 86 GLN a 60 HIS a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 60 HIS r 86 GLN G 60 HIS G 86 GLN I 60 HIS I 86 GLN M 60 HIS M 86 GLN O 60 HIS O 86 GLN Q 60 HIS Q 86 GLN S 86 GLN U 86 GLN W 86 GLN Y 60 HIS Y 86 GLN 2 60 HIS 2 86 GLN 4 86 GLN F 60 HIS F 86 GLN H 60 HIS H 86 GLN P 86 GLN X 86 GLN 6 60 HIS 6 86 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 38640 Z= 0.123 Angle : 0.521 12.795 52464 Z= 0.285 Chirality : 0.035 0.140 5400 Planarity : 0.004 0.121 7128 Dihedral : 4.333 18.528 5328 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 3.12 % Favored : 95.09 % 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: 5.08 (0.12), residues: 5136 helix: 3.85 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.79 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP O 93 HIS 0.007 0.001 HIS E 60 PHE 0.015 0.002 PHE E 41 TYR 0.016 0.002 TYR G 39 ARG 0.011 0.001 ARG U 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6295 (m-30) cc_final: 0.5904 (m-30) REVERT: A 119 LYS cc_start: 0.6795 (ttmm) cc_final: 0.6301 (tppt) REVERT: 1 89 ASP cc_start: 0.6298 (m-30) cc_final: 0.5904 (m-30) REVERT: 1 119 LYS cc_start: 0.6788 (ttmm) cc_final: 0.6296 (tppt) REVERT: K 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5905 (m-30) REVERT: K 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: a 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5904 (m-30) REVERT: a 119 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6300 (tppt) REVERT: B 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5898 (m-30) REVERT: B 119 LYS cc_start: 0.6790 (ttmm) cc_final: 0.6299 (tppt) REVERT: E 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5898 (m-30) REVERT: E 119 LYS cc_start: 0.6790 (ttmm) cc_final: 0.6299 (tppt) REVERT: e 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5905 (m-30) REVERT: e 119 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6300 (tppt) REVERT: r 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5904 (m-30) REVERT: r 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: G 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5905 (m-30) REVERT: G 119 LYS cc_start: 0.6794 (ttmm) cc_final: 0.6300 (tppt) REVERT: I 89 ASP cc_start: 0.6294 (m-30) cc_final: 0.5904 (m-30) REVERT: I 119 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6300 (tppt) REVERT: M 89 ASP cc_start: 0.6289 (m-30) cc_final: 0.5898 (m-30) REVERT: M 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: O 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5905 (m-30) REVERT: O 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: Q 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5905 (m-30) REVERT: Q 119 LYS cc_start: 0.6795 (ttmm) cc_final: 0.6301 (tppt) REVERT: S 89 ASP cc_start: 0.6289 (m-30) cc_final: 0.5898 (m-30) REVERT: S 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6300 (tppt) REVERT: U 89 ASP cc_start: 0.6294 (m-30) cc_final: 0.5904 (m-30) REVERT: U 119 LYS cc_start: 0.6794 (ttmm) cc_final: 0.6301 (tppt) REVERT: W 89 ASP cc_start: 0.6289 (m-30) cc_final: 0.5898 (m-30) REVERT: W 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: Y 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5905 (m-30) REVERT: Y 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6301 (tppt) REVERT: 2 89 ASP cc_start: 0.6294 (m-30) cc_final: 0.5904 (m-30) REVERT: 2 119 LYS cc_start: 0.6788 (ttmm) cc_final: 0.6298 (tppt) REVERT: 4 89 ASP cc_start: 0.6297 (m-30) cc_final: 0.5906 (m-30) REVERT: 4 119 LYS cc_start: 0.6795 (ttmm) cc_final: 0.6301 (tppt) REVERT: F 89 ASP cc_start: 0.6295 (m-30) cc_final: 0.5905 (m-30) REVERT: F 119 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6300 (tppt) REVERT: H 89 ASP cc_start: 0.6291 (m-30) cc_final: 0.5900 (m-30) REVERT: H 119 LYS cc_start: 0.6796 (ttmm) cc_final: 0.6302 (tppt) REVERT: P 89 ASP cc_start: 0.6298 (m-30) cc_final: 0.5907 (m-30) REVERT: P 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: X 89 ASP cc_start: 0.6298 (m-30) cc_final: 0.5904 (m-30) REVERT: X 119 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6299 (tppt) REVERT: 6 89 ASP cc_start: 0.6296 (m-30) cc_final: 0.5905 (m-30) REVERT: 6 119 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6300 (tppt) outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 1.3876 time to fit residues: 977.0001 Evaluate side-chains 561 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 139 ASN 1 60 HIS 1 86 GLN 1 139 ASN K 60 HIS K 86 GLN K 139 ASN a 60 HIS a 86 GLN a 139 ASN B 86 GLN B 139 ASN E 86 GLN E 139 ASN e 86 GLN e 139 ASN r 60 HIS r 86 GLN r 139 ASN G 60 HIS G 86 GLN G 139 ASN I 60 HIS I 86 GLN I 139 ASN M 60 HIS M 86 GLN M 139 ASN O 60 HIS O 86 GLN O 139 ASN Q 60 HIS Q 86 GLN Q 139 ASN S 86 GLN S 139 ASN U 86 GLN U 139 ASN W 86 GLN W 139 ASN Y 60 HIS Y 86 GLN Y 139 ASN 2 60 HIS 2 86 GLN 2 139 ASN 4 60 HIS 4 86 GLN 4 139 ASN F 60 HIS F 86 GLN F 139 ASN H 60 HIS H 86 GLN H 139 ASN P 86 GLN P 139 ASN X 86 GLN X 139 ASN 6 60 HIS 6 86 GLN 6 139 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.161217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.132806 restraints weight = 177983.084| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.63 r_work: 0.3021 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.2774 rms_B_bonded: 2.83 restraints_weight: 0.1250 r_work: 0.2730 rms_B_bonded: 3.83 restraints_weight: 0.0625 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 38640 Z= 0.146 Angle : 0.574 13.451 52464 Z= 0.315 Chirality : 0.036 0.135 5400 Planarity : 0.005 0.127 7128 Dihedral : 4.476 18.984 5328 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 3.10 % Favored : 95.11 % 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: 4.84 (0.11), residues: 5136 helix: 3.68 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.76 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP W 93 HIS 0.005 0.001 HIS A 60 PHE 0.017 0.003 PHE Y 41 TYR 0.017 0.002 TYR I 39 ARG 0.016 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19089.18 seconds wall clock time: 331 minutes 56.95 seconds (19916.95 seconds total)