Starting phenix.real_space_refine on Sun Mar 24 16:40:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd6_6425/03_2024/3jd6_6425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd6_6425/03_2024/3jd6_6425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd6_6425/03_2024/3jd6_6425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd6_6425/03_2024/3jd6_6425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd6_6425/03_2024/3jd6_6425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd6_6425/03_2024/3jd6_6425.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 144 5.16 5 C 13904 2.51 5 N 3792 2.21 5 O 4032 1.98 5 H 21216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43088 Number of models: 1 Model: "" Number of chains: 16 Chain: "O" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "B" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "F" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "G" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "H" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "I" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "J" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "K" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "L" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "M" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "N" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Chain: "P" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Time building chain proxies: 18.95, per 1000 atoms: 0.44 Number of scatterers: 43088 At special positions: 0 Unit cell: (149.35, 149.35, 91.67, 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 144 16.00 O 4032 8.00 N 3792 7.00 C 13904 6.00 H 21216 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 219 " distance=2.04 Simple disulfide: pdb=" SG CYS O 110 " - pdb=" SG CYS O 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 219 " distance=2.04 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 219 " distance=2.04 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 219 " distance=2.04 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 219 " distance=2.04 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 219 " distance=2.04 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 219 " distance=2.04 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 142 " distance=2.04 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 219 " distance=2.04 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.04 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 219 " distance=2.04 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 142 " distance=2.04 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 219 " distance=2.04 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 142 " distance=2.04 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 219 " distance=2.04 Simple disulfide: pdb=" SG CYS J 110 " - pdb=" SG CYS J 142 " distance=2.04 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 219 " distance=2.04 Simple disulfide: pdb=" SG CYS K 110 " - pdb=" SG CYS K 142 " distance=2.04 Simple disulfide: pdb=" SG CYS L 63 " - pdb=" SG CYS L 219 " distance=2.04 Simple disulfide: pdb=" SG CYS L 110 " - pdb=" SG CYS L 142 " distance=2.04 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 219 " distance=2.04 Simple disulfide: pdb=" SG CYS M 110 " - pdb=" SG CYS M 142 " distance=2.04 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 219 " distance=2.04 Simple disulfide: pdb=" SG CYS N 110 " - pdb=" SG CYS N 142 " distance=2.04 Simple disulfide: pdb=" SG CYS P 63 " - pdb=" SG CYS P 219 " distance=2.04 Simple disulfide: pdb=" SG CYS P 110 " - pdb=" SG CYS P 142 " distance=2.04 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: 35.15 Conformation dependent library (CDL) restraints added in 4.6 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 32 sheets defined 1.8% alpha, 55.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'O' and resid 77 through 79 No H-bonds generated for 'chain 'O' and resid 77 through 79' Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'M' and resid 77 through 79 No H-bonds generated for 'chain 'M' and resid 77 through 79' Processing helix chain 'N' and resid 77 through 79 No H-bonds generated for 'chain 'N' and resid 77 through 79' Processing helix chain 'P' and resid 77 through 79 No H-bonds generated for 'chain 'P' and resid 77 through 79' Processing sheet with id= 1, first strand: chain 'O' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN O 124 " --> pdb=" O ARG O 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG O 200 " --> pdb=" O GLN O 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP O 126 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE O 198 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS O 128 " --> pdb=" O SER O 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER O 196 " --> pdb=" O LYS O 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE O 130 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE O 194 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL O 132 " --> pdb=" O PRO O 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER O 134 " --> pdb=" O LEU O 190 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'O' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN O 124 " --> pdb=" O ARG O 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG O 200 " --> pdb=" O GLN O 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP O 126 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE O 198 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS O 128 " --> pdb=" O SER O 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER O 196 " --> pdb=" O LYS O 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE O 130 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE O 194 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL O 132 " --> pdb=" O PRO O 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER O 134 " --> pdb=" O LEU O 190 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN A 124 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG A 200 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP A 126 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 198 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A 128 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER A 196 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE A 130 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE A 194 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL A 132 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 134 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN A 124 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG A 200 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP A 126 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 198 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A 128 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER A 196 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE A 130 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE A 194 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL A 132 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 134 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN B 124 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG B 200 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP B 126 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 198 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS B 128 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER B 196 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE B 130 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE B 194 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL B 132 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER B 134 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN B 124 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG B 200 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP B 126 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 198 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS B 128 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER B 196 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE B 130 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE B 194 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL B 132 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER B 134 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN C 124 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG C 200 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 126 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE C 198 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C 128 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER C 196 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE C 130 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE C 194 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL C 132 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER C 134 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN C 124 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG C 200 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 126 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE C 198 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C 128 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER C 196 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE C 130 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE C 194 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL C 132 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER C 134 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN D 124 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG D 200 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 126 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE D 198 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D 128 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER D 196 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE D 130 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE D 194 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL D 132 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER D 134 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN D 124 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG D 200 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 126 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE D 198 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D 128 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER D 196 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE D 130 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE D 194 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL D 132 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER D 134 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN E 124 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG E 200 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP E 126 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE E 198 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS E 128 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER E 196 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE E 130 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE E 194 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL E 132 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER E 134 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN E 124 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG E 200 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP E 126 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE E 198 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS E 128 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER E 196 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE E 130 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE E 194 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL E 132 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER E 134 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN F 124 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG F 200 " --> pdb=" O GLN F 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 126 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE F 198 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS F 128 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER F 196 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F 130 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE F 194 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL F 132 " --> pdb=" O PRO F 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER F 134 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN F 124 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG F 200 " --> pdb=" O GLN F 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 126 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE F 198 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS F 128 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER F 196 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F 130 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE F 194 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL F 132 " --> pdb=" O PRO F 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER F 134 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN G 124 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG G 200 " --> pdb=" O GLN G 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP G 126 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE G 198 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 128 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER G 196 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE G 130 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE G 194 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL G 132 " --> pdb=" O PRO G 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER G 134 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN G 124 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG G 200 " --> pdb=" O GLN G 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP G 126 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE G 198 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 128 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER G 196 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE G 130 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE G 194 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL G 132 " --> pdb=" O PRO G 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER G 134 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN H 124 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG H 200 " --> pdb=" O GLN H 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP H 126 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE H 198 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS H 128 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER H 196 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE H 130 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE H 194 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL H 132 " --> pdb=" O PRO H 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER H 134 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN H 124 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG H 200 " --> pdb=" O GLN H 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP H 126 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE H 198 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS H 128 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER H 196 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE H 130 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE H 194 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL H 132 " --> pdb=" O PRO H 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER H 134 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN I 124 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG I 200 " --> pdb=" O GLN I 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP I 126 " --> pdb=" O PHE I 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE I 198 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS I 128 " --> pdb=" O SER I 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER I 196 " --> pdb=" O LYS I 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE I 130 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE I 194 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL I 132 " --> pdb=" O PRO I 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER I 134 " --> pdb=" O LEU I 190 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN I 124 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG I 200 " --> pdb=" O GLN I 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP I 126 " --> pdb=" O PHE I 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE I 198 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS I 128 " --> pdb=" O SER I 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER I 196 " --> pdb=" O LYS I 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE I 130 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE I 194 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL I 132 " --> pdb=" O PRO I 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER I 134 " --> pdb=" O LEU I 190 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN J 124 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG J 200 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP J 126 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE J 198 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS J 128 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER J 196 " --> pdb=" O LYS J 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE J 130 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE J 194 " --> pdb=" O ILE J 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL J 132 " --> pdb=" O PRO J 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER J 134 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN J 124 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG J 200 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP J 126 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE J 198 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS J 128 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER J 196 " --> pdb=" O LYS J 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE J 130 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE J 194 " --> pdb=" O ILE J 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL J 132 " --> pdb=" O PRO J 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER J 134 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN K 124 " --> pdb=" O ARG K 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG K 200 " --> pdb=" O GLN K 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP K 126 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE K 198 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS K 128 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER K 196 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE K 130 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE K 194 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL K 132 " --> pdb=" O PRO K 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER K 134 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN K 124 " --> pdb=" O ARG K 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG K 200 " --> pdb=" O GLN K 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP K 126 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE K 198 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS K 128 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER K 196 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE K 130 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE K 194 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL K 132 " --> pdb=" O PRO K 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER K 134 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN L 124 " --> pdb=" O ARG L 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG L 200 " --> pdb=" O GLN L 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP L 126 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE L 198 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS L 128 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER L 196 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE L 130 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE L 194 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL L 132 " --> pdb=" O PRO L 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER L 134 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN L 124 " --> pdb=" O ARG L 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG L 200 " --> pdb=" O GLN L 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP L 126 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE L 198 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS L 128 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER L 196 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE L 130 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE L 194 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL L 132 " --> pdb=" O PRO L 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER L 134 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN M 124 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG M 200 " --> pdb=" O GLN M 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP M 126 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE M 198 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS M 128 " --> pdb=" O SER M 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER M 196 " --> pdb=" O LYS M 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE M 130 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE M 194 " --> pdb=" O ILE M 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL M 132 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER M 134 " --> pdb=" O LEU M 190 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN M 124 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG M 200 " --> pdb=" O GLN M 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP M 126 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE M 198 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS M 128 " --> pdb=" O SER M 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER M 196 " --> pdb=" O LYS M 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE M 130 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE M 194 " --> pdb=" O ILE M 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL M 132 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER M 134 " --> pdb=" O LEU M 190 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN N 124 " --> pdb=" O ARG N 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG N 200 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP N 126 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE N 198 " --> pdb=" O ASP N 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS N 128 " --> pdb=" O SER N 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER N 196 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE N 130 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE N 194 " --> pdb=" O ILE N 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL N 132 " --> pdb=" O PRO N 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER N 134 " --> pdb=" O LEU N 190 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN N 124 " --> pdb=" O ARG N 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG N 200 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP N 126 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE N 198 " --> pdb=" O ASP N 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS N 128 " --> pdb=" O SER N 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER N 196 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE N 130 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE N 194 " --> pdb=" O ILE N 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL N 132 " --> pdb=" O PRO N 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER N 134 " --> pdb=" O LEU N 190 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN P 124 " --> pdb=" O ARG P 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG P 200 " --> pdb=" O GLN P 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP P 126 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE P 198 " --> pdb=" O ASP P 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS P 128 " --> pdb=" O SER P 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER P 196 " --> pdb=" O LYS P 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE P 130 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE P 194 " --> pdb=" O ILE P 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL P 132 " --> pdb=" O PRO P 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER P 134 " --> pdb=" O LEU P 190 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN P 124 " --> pdb=" O ARG P 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG P 200 " --> pdb=" O GLN P 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP P 126 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE P 198 " --> pdb=" O ASP P 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS P 128 " --> pdb=" O SER P 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER P 196 " --> pdb=" O LYS P 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE P 130 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE P 194 " --> pdb=" O ILE P 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL P 132 " --> pdb=" O PRO P 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER P 134 " --> pdb=" O LEU P 190 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1632 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: 16.12 Time building geometry restraints manager: 36.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 20952 1.13 - 1.30: 3816 1.30 - 1.47: 9288 1.47 - 1.64: 9432 1.64 - 1.81: 176 Bond restraints: 43664 Sorted by residual: bond pdb=" CE2 PHE P 198 " pdb=" HE2 PHE P 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE K 198 " pdb=" HE2 PHE K 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE E 198 " pdb=" HE2 PHE E 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE I 198 " pdb=" HE2 PHE I 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE A 198 " pdb=" HE2 PHE A 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 43659 not shown) Histogram of bond angle deviations from ideal: 93.86 - 102.05: 848 102.05 - 110.25: 37640 110.25 - 118.44: 19072 118.44 - 126.63: 19664 126.63 - 134.83: 1384 Bond angle restraints: 78608 Sorted by residual: angle pdb=" C ILE A 60 " pdb=" CA ILE A 60 " pdb=" CB ILE A 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE P 60 " pdb=" CA ILE P 60 " pdb=" CB ILE P 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE M 60 " pdb=" CA ILE M 60 " pdb=" CB ILE M 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE G 60 " pdb=" CA ILE G 60 " pdb=" CB ILE G 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE E 60 " pdb=" CA ILE E 60 " pdb=" CB ILE E 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 ... (remaining 78603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 19680 24.13 - 48.26: 784 48.26 - 72.39: 96 72.39 - 96.52: 48 96.52 - 120.65: 48 Dihedral angle restraints: 20656 sinusoidal: 11168 harmonic: 9488 Sorted by residual: dihedral pdb=" CA SER A 95 " pdb=" C SER A 95 " pdb=" N TRP A 96 " pdb=" CA TRP A 96 " ideal model delta harmonic sigma weight residual 180.00 59.35 120.65 0 5.00e+00 4.00e-02 5.82e+02 dihedral pdb=" CA SER M 95 " pdb=" C SER M 95 " pdb=" N TRP M 96 " pdb=" CA TRP M 96 " ideal model delta harmonic sigma weight residual 180.00 59.35 120.65 0 5.00e+00 4.00e-02 5.82e+02 dihedral pdb=" CA SER K 95 " pdb=" C SER K 95 " pdb=" N TRP K 96 " pdb=" CA TRP K 96 " ideal model delta harmonic sigma weight residual 180.00 59.35 120.65 0 5.00e+00 4.00e-02 5.82e+02 ... (remaining 20653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2216 0.109 - 0.218: 824 0.218 - 0.327: 128 0.327 - 0.436: 16 0.436 - 0.545: 32 Chirality restraints: 3216 Sorted by residual: chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA ALA E 111 " pdb=" N ALA E 111 " pdb=" C ALA E 111 " pdb=" CB ALA E 111 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA ALA P 111 " pdb=" N ALA P 111 " pdb=" C ALA P 111 " pdb=" CB ALA P 111 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 3213 not shown) Planarity restraints: 6416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 112 " -0.038 2.00e-02 2.50e+03 1.01e-01 4.10e+02 pdb=" CG TRP A 112 " -0.162 2.00e-02 2.50e+03 pdb=" CD1 TRP A 112 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP A 112 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 112 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 112 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 112 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 112 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 112 " 0.117 2.00e-02 2.50e+03 pdb=" CH2 TRP A 112 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 112 " 0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP A 112 " 0.147 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 112 " 0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 112 " 0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP A 112 " -0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 112 " 0.038 2.00e-02 2.50e+03 1.01e-01 4.10e+02 pdb=" CG TRP P 112 " 0.162 2.00e-02 2.50e+03 pdb=" CD1 TRP P 112 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP P 112 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP P 112 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP P 112 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP P 112 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 112 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 112 " -0.117 2.00e-02 2.50e+03 pdb=" CH2 TRP P 112 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP P 112 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP P 112 " -0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP P 112 " -0.147 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 112 " -0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 112 " -0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP P 112 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 112 " -0.038 2.00e-02 2.50e+03 1.01e-01 4.10e+02 pdb=" CG TRP C 112 " -0.162 2.00e-02 2.50e+03 pdb=" CD1 TRP C 112 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP C 112 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP C 112 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 112 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 112 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 112 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 112 " 0.117 2.00e-02 2.50e+03 pdb=" CH2 TRP C 112 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP C 112 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP C 112 " 0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP C 112 " 0.147 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 112 " 0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 112 " 0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP C 112 " -0.239 2.00e-02 2.50e+03 ... (remaining 6413 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.35: 24 1.35 - 2.16: 4968 2.16 - 2.98: 110488 2.98 - 3.79: 184896 3.79 - 4.60: 307560 Warning: very small nonbonded interaction distances. Nonbonded interactions: 607936 Sorted by model distance: nonbonded pdb=" HE3 TRP O 147 " pdb=" HE3 TRP H 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP B 147 " pdb=" HE3 TRP N 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP D 147 " pdb=" HE3 TRP L 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP F 147 " pdb=" HE3 TRP J 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP E 147 " pdb=" HE3 TRP K 147 " model vdw 0.540 2.100 ... (remaining 607931 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.650 Extract box with map and model: 3.630 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 134.780 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.260 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4494 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 : 0.026 0.112 22448 Z= 1.737 Angle : 2.697 14.259 30480 Z= 1.911 Chirality : 0.119 0.545 3216 Planarity : 0.017 0.109 3888 Dihedral : 14.706 120.648 8288 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.33 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.13), residues: 2640 helix: None (None), residues: 0 sheet: -0.77 (0.16), residues: 656 loop : -2.80 (0.11), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.008 TRP P 112 HIS 0.001 0.000 HIS H 66 PHE 0.061 0.007 PHE A 198 TYR 0.001 0.000 TYR G 89 ARG 0.003 0.000 ARG L 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1040 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1040 average time/residue: 0.8520 time to fit residues: 1310.8666 Evaluate side-chains 628 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 628 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 162 ASN O 172 ASN O 179 ASN O 187 GLN A 162 ASN A 179 ASN A 187 GLN B 162 ASN B 179 ASN B 187 GLN C 162 ASN C 179 ASN C 187 GLN D 162 ASN D 179 ASN D 187 GLN E 162 ASN E 179 ASN E 187 GLN F 162 ASN F 179 ASN F 187 GLN G 162 ASN G 179 ASN G 187 GLN H 162 ASN H 172 ASN H 179 ASN H 187 GLN I 162 ASN I 179 ASN I 187 GLN J 162 ASN J 179 ASN J 187 GLN K 162 ASN K 179 ASN K 187 GLN L 162 ASN L 179 ASN L 187 GLN M 162 ASN M 179 ASN M 187 GLN N 162 ASN N 179 ASN N 187 GLN P 162 ASN P 179 ASN P 187 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4757 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22448 Z= 0.282 Angle : 0.839 8.296 30480 Z= 0.464 Chirality : 0.049 0.155 3216 Planarity : 0.006 0.060 3888 Dihedral : 9.856 66.241 2960 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.50 % Favored : 91.89 % Rotamer: Outliers : 1.32 % Allowed : 3.62 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % 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: -2.72 (0.14), residues: 2640 helix: -4.94 (0.15), residues: 96 sheet: 0.32 (0.20), residues: 576 loop : -2.54 (0.11), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 147 HIS 0.002 0.001 HIS O 66 PHE 0.031 0.003 PHE J 198 TYR 0.011 0.001 TYR C 155 ARG 0.002 0.001 ARG M 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 778 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 810 average time/residue: 0.8547 time to fit residues: 1040.5936 Evaluate side-chains 576 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 552 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 172 ASN B 172 ASN D 172 ASN F 172 ASN H 172 ASN J 172 ASN L 172 ASN N 172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4941 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22448 Z= 0.261 Angle : 0.737 5.942 30480 Z= 0.409 Chirality : 0.046 0.136 3216 Planarity : 0.004 0.028 3888 Dihedral : 8.441 53.787 2960 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % 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: -2.24 (0.15), residues: 2640 helix: -4.98 (0.14), residues: 96 sheet: 0.14 (0.19), residues: 736 loop : -2.16 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 122 HIS 0.003 0.001 HIS F 66 PHE 0.009 0.002 PHE I 198 TYR 0.011 0.001 TYR D 155 ARG 0.005 0.001 ARG F 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.8094 time to fit residues: 803.2534 Evaluate side-chains 470 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 156 optimal weight: 30.0000 chunk 233 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 172 ASN O 188 ASN B 172 ASN B 188 ASN D 172 ASN D 188 ASN F 172 ASN F 188 ASN H 172 ASN H 188 ASN J 172 ASN J 188 ASN L 172 ASN L 188 ASN N 172 ASN N 188 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22448 Z= 0.256 Angle : 0.687 6.066 30480 Z= 0.378 Chirality : 0.044 0.151 3216 Planarity : 0.004 0.030 3888 Dihedral : 7.536 45.457 2960 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.27 % 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: -2.07 (0.15), residues: 2640 helix: -4.78 (0.14), residues: 96 sheet: 0.62 (0.20), residues: 736 loop : -2.23 (0.12), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 147 HIS 0.004 0.002 HIS N 207 PHE 0.008 0.002 PHE H 176 TYR 0.011 0.001 TYR H 155 ARG 0.004 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.8248 time to fit residues: 749.2511 Evaluate side-chains 488 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 211 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 121 GLN A 121 GLN B 121 GLN B 172 ASN C 121 GLN D 121 GLN D 172 ASN E 121 GLN F 121 GLN F 172 ASN G 121 GLN H 121 GLN I 121 GLN J 121 GLN J 172 ASN K 121 GLN L 121 GLN L 172 ASN M 121 GLN N 121 GLN N 172 ASN P 121 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.8953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22448 Z= 0.313 Angle : 0.703 4.601 30480 Z= 0.385 Chirality : 0.043 0.191 3216 Planarity : 0.005 0.030 3888 Dihedral : 7.145 42.567 2960 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.22 (0.15), residues: 2640 helix: -4.14 (0.25), residues: 96 sheet: 0.84 (0.20), residues: 688 loop : -2.46 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 122 HIS 0.004 0.003 HIS D 66 PHE 0.013 0.002 PHE M 176 TYR 0.015 0.002 TYR G 155 ARG 0.005 0.001 ARG P 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.9049 time to fit residues: 653.4873 Evaluate side-chains 402 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 40.0000 chunk 222 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 154 GLN B 154 GLN B 172 ASN D 154 GLN D 172 ASN F 154 GLN F 172 ASN H 154 GLN J 154 GLN J 172 ASN L 154 GLN L 172 ASN N 154 GLN N 172 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.9418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22448 Z= 0.264 Angle : 0.631 4.615 30480 Z= 0.349 Chirality : 0.042 0.133 3216 Planarity : 0.004 0.030 3888 Dihedral : 6.715 34.997 2960 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.31 (0.15), residues: 2640 helix: -3.99 (0.28), residues: 96 sheet: 0.70 (0.19), residues: 688 loop : -2.51 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 122 HIS 0.003 0.002 HIS P 207 PHE 0.014 0.001 PHE I 176 TYR 0.011 0.002 TYR G 155 ARG 0.002 0.001 ARG O 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.9028 time to fit residues: 609.9517 Evaluate side-chains 382 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN D 172 ASN F 172 ASN J 172 ASN L 172 ASN N 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.9822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22448 Z= 0.214 Angle : 0.616 5.866 30480 Z= 0.338 Chirality : 0.042 0.128 3216 Planarity : 0.004 0.030 3888 Dihedral : 6.543 32.368 2960 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.71 % Favored : 86.29 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.34 (0.15), residues: 2640 helix: -3.84 (0.32), residues: 96 sheet: 0.41 (0.18), residues: 848 loop : -2.66 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 122 HIS 0.003 0.001 HIS G 66 PHE 0.007 0.001 PHE K 176 TYR 0.012 0.001 TYR H 166 ARG 0.008 0.000 ARG H 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.9337 time to fit residues: 623.4999 Evaluate side-chains 382 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 147 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 40.0000 chunk 121 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 overall best weight: 7.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 172 ASN B 172 ASN D 172 ASN F 172 ASN H 172 ASN J 172 ASN L 172 ASN N 172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 moved from start: 1.0166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22448 Z= 0.210 Angle : 0.592 4.338 30480 Z= 0.327 Chirality : 0.043 0.130 3216 Planarity : 0.004 0.061 3888 Dihedral : 6.377 28.816 2960 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.23 (0.16), residues: 2640 helix: -3.70 (0.35), residues: 96 sheet: 0.49 (0.18), residues: 848 loop : -2.60 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 122 HIS 0.003 0.001 HIS P 207 PHE 0.016 0.001 PHE O 176 TYR 0.009 0.001 TYR G 155 ARG 0.021 0.001 ARG H 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.9587 time to fit residues: 580.6637 Evaluate side-chains 344 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN D 172 ASN F 172 ASN J 172 ASN L 172 ASN N 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 1.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22448 Z= 0.247 Angle : 0.599 4.349 30480 Z= 0.331 Chirality : 0.043 0.137 3216 Planarity : 0.004 0.040 3888 Dihedral : 6.316 26.438 2960 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.35 (0.15), residues: 2640 helix: -3.81 (0.33), residues: 96 sheet: 0.76 (0.19), residues: 688 loop : -2.58 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 122 HIS 0.004 0.002 HIS G 207 PHE 0.010 0.002 PHE I 176 TYR 0.010 0.001 TYR F 89 ARG 0.011 0.001 ARG H 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.9520 time to fit residues: 511.7742 Evaluate side-chains 296 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 30.0000 chunk 148 optimal weight: 0.7980 chunk 115 optimal weight: 30.0000 chunk 169 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 234 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN D 172 ASN F 172 ASN J 172 ASN L 172 ASN N 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 moved from start: 1.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22448 Z= 0.147 Angle : 0.553 4.303 30480 Z= 0.302 Chirality : 0.044 0.135 3216 Planarity : 0.004 0.037 3888 Dihedral : 5.886 23.124 2960 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.22 (0.15), residues: 2640 helix: -4.04 (0.28), residues: 96 sheet: 0.80 (0.19), residues: 688 loop : -2.45 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 122 HIS 0.001 0.001 HIS G 66 PHE 0.007 0.001 PHE C 198 TYR 0.009 0.001 TYR J 155 ARG 0.006 0.000 ARG H 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.9737 time to fit residues: 571.7453 Evaluate side-chains 342 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 208 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 178 optimal weight: 0.6980 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 172 ASN P 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.063883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.051793 restraints weight = 364926.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.054714 restraints weight = 198843.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.056891 restraints weight = 123552.512| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 1.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22448 Z= 0.186 Angle : 0.542 3.926 30480 Z= 0.297 Chirality : 0.043 0.134 3216 Planarity : 0.004 0.036 3888 Dihedral : 5.851 22.723 2960 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.22 (0.15), residues: 2640 helix: -3.89 (0.31), residues: 96 sheet: 0.91 (0.19), residues: 688 loop : -2.51 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 122 HIS 0.003 0.001 HIS G 66 PHE 0.010 0.001 PHE L 198 TYR 0.011 0.001 TYR C 165 ARG 0.007 0.000 ARG H 174 =============================================================================== Job complete usr+sys time: 11387.12 seconds wall clock time: 200 minutes 42.93 seconds (12042.93 seconds total)