Starting phenix.real_space_refine on Tue Mar 12 02:43:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/03_2024/3j6e_5895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/03_2024/3j6e_5895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/03_2024/3j6e_5895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/03_2024/3j6e_5895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/03_2024/3j6e_5895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/03_2024/3j6e_5895_updated.pdb" } resolution = 4.7 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= 0.468 sd= 1.871 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: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 18 5.21 5 S 414 5.16 5 C 38223 2.51 5 N 10395 2.21 5 O 11880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 251": "OD1" <-> "OD2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 251": "OD1" <-> "OD2" Residue "H PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 330": "OE1" <-> "OE2" Residue "H TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 417": "OE1" <-> "OE2" Residue "H PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 71": "OE1" <-> "OE2" Residue "J PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 251": "OD1" <-> "OD2" Residue "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 330": "OE1" <-> "OE2" Residue "J TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 417": "OE1" <-> "OE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 437": "OD1" <-> "OD2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 207": "OE1" <-> "OE2" Residue "K TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 71": "OE1" <-> "OE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 251": "OD1" <-> "OD2" Residue "L PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 330": "OE1" <-> "OE2" Residue "L TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 417": "OE1" <-> "OE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 437": "OD1" <-> "OD2" Residue "M TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 251": "OD1" <-> "OD2" Residue "N PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 330": "OE1" <-> "OE2" Residue "N TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 417": "OE1" <-> "OE2" Residue "N PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 437": "OD1" <-> "OD2" Residue "O TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 251": "OD1" <-> "OD2" Residue "P PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 330": "OE1" <-> "OE2" Residue "P TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 417": "OE1" <-> "OE2" Residue "P PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 437": "OD1" <-> "OD2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 207": "OE1" <-> "OE2" Residue "Q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 251": "OD1" <-> "OD2" Residue "R PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 330": "OE1" <-> "OE2" Residue "R TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 417": "OE1" <-> "OE2" Residue "R PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 437": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 60984 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "G" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "H" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "I" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "J" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "L" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "M" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "N" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "O" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "P" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "Q" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "R" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 24.02, per 1000 atoms: 0.39 Number of scatterers: 60984 At special positions: 0 Unit cell: (168.78, 88.74, 295.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 414 16.00 P 54 15.00 Mg 18 11.99 O 11880 8.00 N 10395 7.00 C 38223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.38 Conformation dependent library (CDL) restraints added in 8.7 seconds 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 360 helices and 54 sheets defined 48.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.645A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.856A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.544A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.687A pdb=" N VAL A 409 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 4.067A pdb=" N GLY B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 283' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.760A pdb=" N GLU B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 399 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 82 through 85 removed outlier: 3.646A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.856A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.601A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.544A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 278 through 281 No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 382 through 401 Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.687A pdb=" N VAL C 409 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 106 No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.066A pdb=" N GLY D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS D 229 " --> pdb=" O GLY D 225 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 283' Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.760A pdb=" N GLU D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 399 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 415 through 436 Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 72 through 79 Processing helix chain 'E' and resid 82 through 85 removed outlier: 3.645A pdb=" N GLN E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 85' Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.855A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.545A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 278 through 281 No H-bonds generated for 'chain 'E' and resid 278 through 281' Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 325 through 338 Processing helix chain 'E' and resid 382 through 401 Processing helix chain 'E' and resid 405 through 409 removed outlier: 3.686A pdb=" N VAL E 409 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 106 No H-bonds generated for 'chain 'F' and resid 103 through 106' Processing helix chain 'F' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 4.068A pdb=" N GLY F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN F 282 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 283' Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 3.760A pdb=" N GLU F 393 " --> pdb=" O ARG F 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 399 " --> pdb=" O THR F 396 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 409 Processing helix chain 'F' and resid 415 through 436 Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 82 through 85 removed outlier: 3.645A pdb=" N GLN G 85 " --> pdb=" O THR G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 85' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 148 through 160 removed outlier: 3.856A pdb=" N VAL G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 4.544A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 278 through 281 No H-bonds generated for 'chain 'G' and resid 278 through 281' Processing helix chain 'G' and resid 288 through 295 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 382 through 401 Processing helix chain 'G' and resid 405 through 409 removed outlier: 3.686A pdb=" N VAL G 409 " --> pdb=" O HIS G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 436 Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 106 No H-bonds generated for 'chain 'H' and resid 103 through 106' Processing helix chain 'H' and resid 110 through 128 removed outlier: 3.717A pdb=" N LEU H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 160 removed outlier: 4.067A pdb=" N GLY H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 197 removed outlier: 4.126A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS H 229 " --> pdb=" O GLY H 225 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN H 282 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 283' Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 3.761A pdb=" N GLU H 393 " --> pdb=" O ARG H 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE H 399 " --> pdb=" O THR H 396 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 409 Processing helix chain 'H' and resid 415 through 436 Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 72 through 79 Processing helix chain 'I' and resid 82 through 85 removed outlier: 3.645A pdb=" N GLN I 85 " --> pdb=" O THR I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 82 through 85' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 148 through 160 removed outlier: 3.856A pdb=" N VAL I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 4.544A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 278 through 281 No H-bonds generated for 'chain 'I' and resid 278 through 281' Processing helix chain 'I' and resid 288 through 295 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 382 through 401 Processing helix chain 'I' and resid 405 through 409 removed outlier: 3.687A pdb=" N VAL I 409 " --> pdb=" O HIS I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 436 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 106 No H-bonds generated for 'chain 'J' and resid 103 through 106' Processing helix chain 'J' and resid 110 through 128 removed outlier: 3.717A pdb=" N LEU J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.066A pdb=" N GLY J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 215 Processing helix chain 'J' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS J 229 " --> pdb=" O GLY J 225 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR J 239 " --> pdb=" O MET J 235 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS J 241 " --> pdb=" O GLY J 237 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU J 242 " --> pdb=" O VAL J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN J 282 " --> pdb=" O ARG J 278 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR J 283 " --> pdb=" O GLY J 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 278 through 283' Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 338 Processing helix chain 'J' and resid 340 through 342 No H-bonds generated for 'chain 'J' and resid 340 through 342' Processing helix chain 'J' and resid 382 through 401 removed outlier: 3.761A pdb=" N GLU J 393 " --> pdb=" O ARG J 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE J 399 " --> pdb=" O THR J 396 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG J 400 " --> pdb=" O ALA J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 409 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 72 through 79 Processing helix chain 'K' and resid 82 through 85 removed outlier: 3.646A pdb=" N GLN K 85 " --> pdb=" O THR K 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 82 through 85' Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 Processing helix chain 'K' and resid 148 through 160 removed outlier: 3.855A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.601A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 215 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.545A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 278 through 281 No H-bonds generated for 'chain 'K' and resid 278 through 281' Processing helix chain 'K' and resid 288 through 295 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 325 through 338 Processing helix chain 'K' and resid 382 through 401 Processing helix chain 'K' and resid 405 through 409 removed outlier: 3.687A pdb=" N VAL K 409 " --> pdb=" O HIS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 72 through 80 Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 106 No H-bonds generated for 'chain 'L' and resid 103 through 106' Processing helix chain 'L' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.067A pdb=" N GLY L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 Processing helix chain 'L' and resid 224 through 243 removed outlier: 3.716A pdb=" N HIS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR L 239 " --> pdb=" O MET L 235 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS L 241 " --> pdb=" O GLY L 237 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU L 242 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN L 282 " --> pdb=" O ARG L 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR L 283 " --> pdb=" O GLY L 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 278 through 283' Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 338 Processing helix chain 'L' and resid 340 through 342 No H-bonds generated for 'chain 'L' and resid 340 through 342' Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.761A pdb=" N GLU L 393 " --> pdb=" O ARG L 390 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE L 399 " --> pdb=" O THR L 396 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG L 400 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 409 Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'M' and resid 10 through 28 Processing helix chain 'M' and resid 72 through 79 Processing helix chain 'M' and resid 82 through 85 removed outlier: 3.646A pdb=" N GLN M 85 " --> pdb=" O THR M 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 82 through 85' Processing helix chain 'M' and resid 89 through 91 No H-bonds generated for 'chain 'M' and resid 89 through 91' Processing helix chain 'M' and resid 103 through 107 Processing helix chain 'M' and resid 111 through 113 No H-bonds generated for 'chain 'M' and resid 111 through 113' Processing helix chain 'M' and resid 115 through 128 Processing helix chain 'M' and resid 148 through 160 removed outlier: 3.855A pdb=" N VAL M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 215 Processing helix chain 'M' and resid 224 through 243 removed outlier: 4.544A pdb=" N SER M 241 " --> pdb=" O SER M 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU M 242 " --> pdb=" O ILE M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 259 Processing helix chain 'M' and resid 278 through 281 No H-bonds generated for 'chain 'M' and resid 278 through 281' Processing helix chain 'M' and resid 288 through 295 Processing helix chain 'M' and resid 298 through 300 No H-bonds generated for 'chain 'M' and resid 298 through 300' Processing helix chain 'M' and resid 325 through 338 Processing helix chain 'M' and resid 382 through 401 Processing helix chain 'M' and resid 405 through 409 removed outlier: 3.686A pdb=" N VAL M 409 " --> pdb=" O HIS M 406 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 436 Processing helix chain 'N' and resid 10 through 28 Processing helix chain 'N' and resid 41 through 47 Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 72 through 80 Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'N' and resid 103 through 106 No H-bonds generated for 'chain 'N' and resid 103 through 106' Processing helix chain 'N' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU N 114 " --> pdb=" O GLU N 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER N 117 " --> pdb=" O GLU N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 160 removed outlier: 4.067A pdb=" N GLY N 150 " --> pdb=" O GLY N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU N 196 " --> pdb=" O HIS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 215 Processing helix chain 'N' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR N 239 " --> pdb=" O MET N 235 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS N 241 " --> pdb=" O GLY N 237 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU N 242 " --> pdb=" O VAL N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 259 Processing helix chain 'N' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN N 282 " --> pdb=" O ARG N 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR N 283 " --> pdb=" O GLY N 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 278 through 283' Processing helix chain 'N' and resid 288 through 296 Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'N' and resid 307 through 309 No H-bonds generated for 'chain 'N' and resid 307 through 309' Processing helix chain 'N' and resid 325 through 338 Processing helix chain 'N' and resid 340 through 342 No H-bonds generated for 'chain 'N' and resid 340 through 342' Processing helix chain 'N' and resid 382 through 401 removed outlier: 3.760A pdb=" N GLU N 393 " --> pdb=" O ARG N 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE N 399 " --> pdb=" O THR N 396 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG N 400 " --> pdb=" O ALA N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 409 Processing helix chain 'N' and resid 415 through 436 Processing helix chain 'O' and resid 10 through 28 Processing helix chain 'O' and resid 72 through 79 Processing helix chain 'O' and resid 82 through 85 removed outlier: 3.645A pdb=" N GLN O 85 " --> pdb=" O THR O 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 85' Processing helix chain 'O' and resid 89 through 91 No H-bonds generated for 'chain 'O' and resid 89 through 91' Processing helix chain 'O' and resid 103 through 107 Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 115 through 128 Processing helix chain 'O' and resid 148 through 160 removed outlier: 3.856A pdb=" N VAL O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 215 Processing helix chain 'O' and resid 224 through 243 removed outlier: 4.544A pdb=" N SER O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU O 242 " --> pdb=" O ILE O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 278 through 281 No H-bonds generated for 'chain 'O' and resid 278 through 281' Processing helix chain 'O' and resid 288 through 295 Processing helix chain 'O' and resid 298 through 300 No H-bonds generated for 'chain 'O' and resid 298 through 300' Processing helix chain 'O' and resid 325 through 338 Processing helix chain 'O' and resid 382 through 401 Processing helix chain 'O' and resid 405 through 409 removed outlier: 3.687A pdb=" N VAL O 409 " --> pdb=" O HIS O 406 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 436 Processing helix chain 'P' and resid 10 through 28 Processing helix chain 'P' and resid 41 through 47 Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 72 through 80 Processing helix chain 'P' and resid 89 through 91 No H-bonds generated for 'chain 'P' and resid 89 through 91' Processing helix chain 'P' and resid 103 through 106 No H-bonds generated for 'chain 'P' and resid 103 through 106' Processing helix chain 'P' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU P 114 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 160 removed outlier: 4.066A pdb=" N GLY P 150 " --> pdb=" O GLY P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 197 removed outlier: 4.127A pdb=" N GLU P 196 " --> pdb=" O HIS P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 215 Processing helix chain 'P' and resid 224 through 243 removed outlier: 3.717A pdb=" N HIS P 229 " --> pdb=" O GLY P 225 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR P 239 " --> pdb=" O MET P 235 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS P 241 " --> pdb=" O GLY P 237 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU P 242 " --> pdb=" O VAL P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 259 Processing helix chain 'P' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN P 282 " --> pdb=" O ARG P 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR P 283 " --> pdb=" O GLY P 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 278 through 283' Processing helix chain 'P' and resid 288 through 296 Processing helix chain 'P' and resid 298 through 300 No H-bonds generated for 'chain 'P' and resid 298 through 300' Processing helix chain 'P' and resid 307 through 309 No H-bonds generated for 'chain 'P' and resid 307 through 309' Processing helix chain 'P' and resid 325 through 338 Processing helix chain 'P' and resid 340 through 342 No H-bonds generated for 'chain 'P' and resid 340 through 342' Processing helix chain 'P' and resid 382 through 401 removed outlier: 3.760A pdb=" N GLU P 393 " --> pdb=" O ARG P 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE P 399 " --> pdb=" O THR P 396 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG P 400 " --> pdb=" O ALA P 397 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 409 Processing helix chain 'P' and resid 415 through 436 Processing helix chain 'Q' and resid 10 through 28 Processing helix chain 'Q' and resid 72 through 79 Processing helix chain 'Q' and resid 82 through 85 removed outlier: 3.646A pdb=" N GLN Q 85 " --> pdb=" O THR Q 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 82 through 85' Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 103 through 107 Processing helix chain 'Q' and resid 111 through 113 No H-bonds generated for 'chain 'Q' and resid 111 through 113' Processing helix chain 'Q' and resid 115 through 128 Processing helix chain 'Q' and resid 148 through 160 removed outlier: 3.856A pdb=" N VAL Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 197 removed outlier: 3.602A pdb=" N THR Q 193 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 215 Processing helix chain 'Q' and resid 224 through 243 removed outlier: 4.543A pdb=" N SER Q 241 " --> pdb=" O SER Q 237 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU Q 242 " --> pdb=" O ILE Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 259 Processing helix chain 'Q' and resid 278 through 281 No H-bonds generated for 'chain 'Q' and resid 278 through 281' Processing helix chain 'Q' and resid 288 through 295 Processing helix chain 'Q' and resid 298 through 300 No H-bonds generated for 'chain 'Q' and resid 298 through 300' Processing helix chain 'Q' and resid 325 through 338 Processing helix chain 'Q' and resid 382 through 401 Processing helix chain 'Q' and resid 405 through 409 removed outlier: 3.686A pdb=" N VAL Q 409 " --> pdb=" O HIS Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'R' and resid 10 through 28 Processing helix chain 'R' and resid 41 through 47 Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 72 through 80 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 103 through 106 No H-bonds generated for 'chain 'R' and resid 103 through 106' Processing helix chain 'R' and resid 110 through 128 removed outlier: 3.718A pdb=" N LEU R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER R 117 " --> pdb=" O GLU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 160 removed outlier: 4.067A pdb=" N GLY R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 197 removed outlier: 4.126A pdb=" N GLU R 196 " --> pdb=" O HIS R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 215 Processing helix chain 'R' and resid 224 through 243 removed outlier: 3.716A pdb=" N HIS R 229 " --> pdb=" O GLY R 225 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR R 239 " --> pdb=" O MET R 235 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 259 Processing helix chain 'R' and resid 278 through 283 removed outlier: 3.830A pdb=" N GLN R 282 " --> pdb=" O ARG R 278 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR R 283 " --> pdb=" O GLY R 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 278 through 283' Processing helix chain 'R' and resid 288 through 296 Processing helix chain 'R' and resid 298 through 300 No H-bonds generated for 'chain 'R' and resid 298 through 300' Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 325 through 338 Processing helix chain 'R' and resid 340 through 342 No H-bonds generated for 'chain 'R' and resid 340 through 342' Processing helix chain 'R' and resid 382 through 401 removed outlier: 3.760A pdb=" N GLU R 393 " --> pdb=" O ARG R 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE R 399 " --> pdb=" O THR R 396 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG R 400 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 409 Processing helix chain 'R' and resid 415 through 436 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= F, first strand: chain 'B' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 5 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE C 135 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 7 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL C 137 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 9 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS C 139 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'C' and resid 269 through 273 Processing sheet with id= J, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= L, first strand: chain 'D' and resid 269 through 273 Processing sheet with id= M, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE E 135 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL E 9 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS E 139 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'E' and resid 269 through 273 Processing sheet with id= P, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 53 through 56 Processing sheet with id= R, first strand: chain 'F' and resid 269 through 273 Processing sheet with id= S, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE G 67 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL G 66 " --> pdb=" O CYS G 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE G 135 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL G 9 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS G 139 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL G 137 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 167 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS G 139 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS G 200 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER G 170 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR G 172 " --> pdb=" O PHE G 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL G 204 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'G' and resid 269 through 273 Processing sheet with id= V, first strand: chain 'H' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 53 through 56 Processing sheet with id= X, first strand: chain 'H' and resid 269 through 273 Processing sheet with id= Y, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE I 135 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL I 9 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS I 139 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL I 137 " --> pdb=" O SER I 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS I 139 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS I 200 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER I 170 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR I 172 " --> pdb=" O PHE I 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL I 204 " --> pdb=" O TYR I 172 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'I' and resid 269 through 273 Processing sheet with id= AB, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 67 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE J 66 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS J 6 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL J 68 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL J 5 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE J 135 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE J 7 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU J 137 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA J 9 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS J 139 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU J 137 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN J 167 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS J 139 " --> pdb=" O ASN J 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU J 200 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER J 170 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 53 through 56 Processing sheet with id= AD, first strand: chain 'J' and resid 269 through 273 Processing sheet with id= AE, first strand: chain 'K' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE K 5 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE K 135 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE K 7 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL K 137 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL K 9 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS K 139 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AG, first strand: chain 'K' and resid 269 through 273 Processing sheet with id= AH, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU L 67 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE L 66 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS L 6 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL L 68 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL L 5 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE L 135 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE L 7 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU L 137 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA L 9 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS L 139 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU L 137 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN L 167 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS L 139 " --> pdb=" O ASN L 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU L 200 " --> pdb=" O THR L 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER L 170 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 53 through 56 Processing sheet with id= AJ, first strand: chain 'L' and resid 269 through 273 Processing sheet with id= AK, first strand: chain 'M' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE M 93 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE M 67 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL M 66 " --> pdb=" O CYS M 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER M 6 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL M 68 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS M 8 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE M 5 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE M 135 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE M 7 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL M 137 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL M 9 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS M 139 " --> pdb=" O VAL M 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER M 165 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL M 137 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU M 167 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS M 139 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE M 169 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS M 200 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER M 170 " --> pdb=" O CYS M 200 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE M 202 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR M 172 " --> pdb=" O PHE M 202 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL M 204 " --> pdb=" O TYR M 172 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 53 through 55 Processing sheet with id= AM, first strand: chain 'M' and resid 269 through 273 Processing sheet with id= AN, first strand: chain 'N' and resid 92 through 94 removed outlier: 8.160A pdb=" N VAL N 93 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU N 67 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE N 66 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS N 6 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL N 68 " --> pdb=" O HIS N 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN N 8 " --> pdb=" O VAL N 68 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL N 5 " --> pdb=" O GLN N 133 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE N 135 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE N 7 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU N 137 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA N 9 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS N 139 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE N 165 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU N 137 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN N 167 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS N 139 " --> pdb=" O ASN N 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE N 169 " --> pdb=" O HIS N 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU N 200 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER N 170 " --> pdb=" O GLU N 200 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR N 202 " --> pdb=" O SER N 170 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 53 through 56 Processing sheet with id= AP, first strand: chain 'N' and resid 269 through 273 Processing sheet with id= AQ, first strand: chain 'O' and resid 92 through 94 removed outlier: 7.981A pdb=" N ILE O 93 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE O 67 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL O 66 " --> pdb=" O CYS O 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER O 6 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL O 68 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS O 8 " --> pdb=" O VAL O 68 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE O 5 " --> pdb=" O GLN O 133 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE O 135 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE O 7 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL O 137 " --> pdb=" O ILE O 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL O 9 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS O 139 " --> pdb=" O VAL O 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER O 165 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL O 137 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU O 167 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS O 139 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE O 169 " --> pdb=" O HIS O 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS O 200 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER O 170 " --> pdb=" O CYS O 200 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE O 202 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR O 172 " --> pdb=" O PHE O 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL O 204 " --> pdb=" O TYR O 172 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 53 through 55 Processing sheet with id= AS, first strand: chain 'O' and resid 269 through 273 Processing sheet with id= AT, first strand: chain 'P' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL P 93 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU P 67 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE P 66 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS P 6 " --> pdb=" O ILE P 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL P 68 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN P 8 " --> pdb=" O VAL P 68 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL P 5 " --> pdb=" O GLN P 133 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE P 135 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE P 7 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU P 137 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA P 9 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS P 139 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE P 165 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU P 137 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN P 167 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS P 139 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE P 169 " --> pdb=" O HIS P 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU P 200 " --> pdb=" O THR P 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER P 170 " --> pdb=" O GLU P 200 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR P 202 " --> pdb=" O SER P 170 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'P' and resid 53 through 56 Processing sheet with id= AV, first strand: chain 'P' and resid 269 through 273 Processing sheet with id= AW, first strand: chain 'Q' and resid 92 through 94 removed outlier: 7.980A pdb=" N ILE Q 93 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE Q 67 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL Q 66 " --> pdb=" O CYS Q 4 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER Q 6 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL Q 68 " --> pdb=" O SER Q 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS Q 8 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE Q 5 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE Q 135 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE Q 7 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL Q 137 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL Q 9 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS Q 139 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER Q 165 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL Q 137 " --> pdb=" O SER Q 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU Q 167 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS Q 139 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE Q 169 " --> pdb=" O HIS Q 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS Q 200 " --> pdb=" O GLU Q 168 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER Q 170 " --> pdb=" O CYS Q 200 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE Q 202 " --> pdb=" O SER Q 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR Q 172 " --> pdb=" O PHE Q 202 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL Q 204 " --> pdb=" O TYR Q 172 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 53 through 55 Processing sheet with id= AY, first strand: chain 'Q' and resid 269 through 273 Processing sheet with id= AZ, first strand: chain 'R' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL R 93 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU R 67 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE R 66 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS R 6 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL R 68 " --> pdb=" O HIS R 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN R 8 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL R 5 " --> pdb=" O GLN R 133 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE R 135 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE R 7 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU R 137 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA R 9 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS R 139 " --> pdb=" O ALA R 9 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE R 165 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU R 137 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN R 167 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS R 139 " --> pdb=" O ASN R 167 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE R 169 " --> pdb=" O HIS R 139 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU R 200 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER R 170 " --> pdb=" O GLU R 200 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR R 202 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'R' and resid 53 through 56 Processing sheet with id= BB, first strand: chain 'R' and resid 269 through 273 2637 hydrogen bonds defined for protein. 6939 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: 22.09 Time building geometry restraints manager: 22.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 10970 1.30 - 1.43: 17265 1.43 - 1.56: 33235 1.56 - 1.68: 171 1.68 - 1.81: 657 Bond restraints: 62298 Sorted by residual: bond pdb=" CA THR K 349 " pdb=" C THR K 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.10e+02 bond pdb=" CA THR C 349 " pdb=" C THR C 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.10e+02 bond pdb=" CA THR E 349 " pdb=" C THR E 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.09e+02 bond pdb=" CA THR I 349 " pdb=" C THR I 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.09e+02 bond pdb=" CA THR O 349 " pdb=" C THR O 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.08e+02 ... (remaining 62293 not shown) Histogram of bond angle deviations from ideal: 89.64 - 100.91: 727 100.91 - 112.18: 28122 112.18 - 123.44: 48942 123.44 - 134.71: 6827 134.71 - 145.98: 27 Bond angle restraints: 84645 Sorted by residual: angle pdb=" CA ARG M 339 " pdb=" C ARG M 339 " pdb=" N THR M 340 " ideal model delta sigma weight residual 115.21 93.87 21.34 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG I 339 " pdb=" C ARG I 339 " pdb=" N THR I 340 " ideal model delta sigma weight residual 115.21 93.87 21.34 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG O 339 " pdb=" C ARG O 339 " pdb=" N THR O 340 " ideal model delta sigma weight residual 115.21 93.87 21.34 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG G 339 " pdb=" C ARG G 339 " pdb=" N THR G 340 " ideal model delta sigma weight residual 115.21 93.88 21.33 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG C 339 " pdb=" C ARG C 339 " pdb=" N THR C 340 " ideal model delta sigma weight residual 115.21 93.88 21.33 1.33e+00 5.65e-01 2.57e+02 ... (remaining 84640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.15: 36475 33.15 - 66.30: 533 66.30 - 99.45: 135 99.45 - 132.60: 18 132.60 - 165.75: 18 Dihedral angle restraints: 37179 sinusoidal: 15012 harmonic: 22167 Sorted by residual: dihedral pdb=" C PHE N 83 " pdb=" N PHE N 83 " pdb=" CA PHE N 83 " pdb=" CB PHE N 83 " ideal model delta harmonic sigma weight residual -122.60 -143.51 20.91 0 2.50e+00 1.60e-01 7.00e+01 dihedral pdb=" C PHE R 83 " pdb=" N PHE R 83 " pdb=" CA PHE R 83 " pdb=" CB PHE R 83 " ideal model delta harmonic sigma weight residual -122.60 -143.49 20.89 0 2.50e+00 1.60e-01 6.98e+01 dihedral pdb=" C PHE F 83 " pdb=" N PHE F 83 " pdb=" CA PHE F 83 " pdb=" CB PHE F 83 " ideal model delta harmonic sigma weight residual -122.60 -143.48 20.88 0 2.50e+00 1.60e-01 6.98e+01 ... (remaining 37176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 8210 0.193 - 0.386: 853 0.386 - 0.579: 108 0.579 - 0.772: 36 0.772 - 0.965: 9 Chirality restraints: 9216 Sorted by residual: chirality pdb=" CA PHE N 83 " pdb=" N PHE N 83 " pdb=" C PHE N 83 " pdb=" CB PHE N 83 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA PHE F 83 " pdb=" N PHE F 83 " pdb=" C PHE F 83 " pdb=" CB PHE F 83 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA PHE H 83 " pdb=" N PHE H 83 " pdb=" C PHE H 83 " pdb=" CB PHE H 83 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 ... (remaining 9213 not shown) Planarity restraints: 11043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 437 " 0.040 2.00e-02 2.50e+03 8.19e-02 6.70e+01 pdb=" C ASP R 437 " -0.142 2.00e-02 2.50e+03 pdb=" O ASP R 437 " 0.052 2.00e-02 2.50e+03 pdb=" OXT ASP R 437 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 437 " 0.040 2.00e-02 2.50e+03 8.18e-02 6.69e+01 pdb=" C ASP F 437 " -0.141 2.00e-02 2.50e+03 pdb=" O ASP F 437 " 0.052 2.00e-02 2.50e+03 pdb=" OXT ASP F 437 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP J 437 " 0.040 2.00e-02 2.50e+03 8.18e-02 6.69e+01 pdb=" C ASP J 437 " -0.141 2.00e-02 2.50e+03 pdb=" O ASP J 437 " 0.052 2.00e-02 2.50e+03 pdb=" OXT ASP J 437 " 0.049 2.00e-02 2.50e+03 ... (remaining 11040 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 45 2.21 - 2.88: 27789 2.88 - 3.56: 93981 3.56 - 4.23: 162554 4.23 - 4.90: 266500 Nonbonded interactions: 550869 Sorted by model distance: nonbonded pdb="MG MG E 502 " pdb=" O HOH E 604 " model vdw 1.539 2.170 nonbonded pdb="MG MG Q 502 " pdb=" O HOH Q 604 " model vdw 1.539 2.170 nonbonded pdb="MG MG C 502 " pdb=" O HOH C 604 " model vdw 1.540 2.170 nonbonded pdb="MG MG M 502 " pdb=" O HOH M 604 " model vdw 1.540 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH A 604 " model vdw 1.540 2.170 ... (remaining 550864 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } 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: 0.070 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: 0.060 Extract box with map and model: 3.370 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 129.420 Find NCS groups from input model: 3.870 Set up NCS constraints: 0.550 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: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 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 : 0.021 0.253 62298 Z= 1.365 Angle : 2.598 27.047 84645 Z= 1.704 Chirality : 0.134 0.965 9216 Planarity : 0.008 0.082 11043 Dihedral : 13.517 165.753 22977 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.42 % Favored : 96.23 % Rotamer: Outliers : 0.28 % Allowed : 0.41 % Favored : 99.31 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.09), residues: 7632 helix: -0.52 (0.07), residues: 3510 sheet: 1.04 (0.13), residues: 1197 loop : -0.83 (0.11), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.007 TRP R 103 HIS 0.012 0.002 HIS Q 139 PHE 0.019 0.004 PHE N 267 TYR 0.053 0.007 TYR N 61 ARG 0.008 0.001 ARG P 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2736 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2718 time to evaluate : 5.532 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: A 14 VAL cc_start: 0.9005 (t) cc_final: 0.8744 (p) REVERT: A 24 TYR cc_start: 0.8333 (m-80) cc_final: 0.8093 (m-80) REVERT: A 74 VAL cc_start: 0.8038 (t) cc_final: 0.7748 (t) REVERT: A 75 ILE cc_start: 0.9048 (mm) cc_final: 0.8684 (mm) REVERT: A 118 VAL cc_start: 0.9402 (t) cc_final: 0.9072 (t) REVERT: A 167 LEU cc_start: 0.8545 (mt) cc_final: 0.8199 (mt) REVERT: A 188 ILE cc_start: 0.8618 (mt) cc_final: 0.8191 (mm) REVERT: A 207 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.4331 (mp0) REVERT: A 217 LEU cc_start: 0.8701 (mt) cc_final: 0.8473 (tp) REVERT: A 224 TYR cc_start: 0.6543 (m-80) cc_final: 0.5789 (m-10) REVERT: A 302 MET cc_start: 0.8237 (mmt) cc_final: 0.7438 (mpp) REVERT: A 315 CYS cc_start: 0.8097 (t) cc_final: 0.7861 (m) REVERT: A 344 VAL cc_start: 0.8043 (t) cc_final: 0.7499 (t) REVERT: A 378 LEU cc_start: 0.8334 (mt) cc_final: 0.7956 (mp) REVERT: A 384 ILE cc_start: 0.7868 (tt) cc_final: 0.6936 (tp) REVERT: A 391 LEU cc_start: 0.8639 (mt) cc_final: 0.8338 (mt) REVERT: A 413 MET cc_start: 0.7468 (mmm) cc_final: 0.6950 (mmp) REVERT: B 5 VAL cc_start: 0.9244 (t) cc_final: 0.8703 (t) REVERT: B 14 ASN cc_start: 0.8673 (m-40) cc_final: 0.8165 (m-40) REVERT: B 44 LEU cc_start: 0.8278 (mt) cc_final: 0.7911 (mt) REVERT: B 122 VAL cc_start: 0.9484 (t) cc_final: 0.9079 (t) REVERT: B 153 LEU cc_start: 0.8290 (tp) cc_final: 0.7716 (tp) REVERT: B 213 CYS cc_start: 0.8380 (m) cc_final: 0.8097 (m) REVERT: B 222 PRO cc_start: 0.8067 (Cg_exo) cc_final: 0.7751 (Cg_endo) REVERT: B 230 LEU cc_start: 0.9268 (mt) cc_final: 0.8684 (tt) REVERT: B 326 LYS cc_start: 0.7146 (tptp) cc_final: 0.6178 (ttpp) REVERT: B 378 ILE cc_start: 0.8391 (mt) cc_final: 0.8065 (mt) REVERT: B 391 ILE cc_start: 0.8744 (mt) cc_final: 0.8523 (mt) REVERT: B 413 MET cc_start: 0.7482 (mmm) cc_final: 0.7226 (mmt) REVERT: B 417 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7307 (tt0) REVERT: C 24 TYR cc_start: 0.8288 (m-80) cc_final: 0.7905 (m-80) REVERT: C 137 VAL cc_start: 0.7615 (t) cc_final: 0.7129 (t) REVERT: C 155 GLU cc_start: 0.6963 (tp30) cc_final: 0.6675 (tp30) REVERT: C 167 LEU cc_start: 0.7349 (mt) cc_final: 0.5806 (mt) REVERT: C 171 ILE cc_start: 0.9288 (mm) cc_final: 0.9043 (mm) REVERT: C 217 LEU cc_start: 0.8418 (mt) cc_final: 0.7929 (tt) REVERT: C 318 LEU cc_start: 0.8017 (mt) cc_final: 0.7692 (mm) REVERT: C 391 LEU cc_start: 0.8264 (mt) cc_final: 0.7942 (mt) REVERT: D 14 ASN cc_start: 0.8684 (m-40) cc_final: 0.8324 (m-40) REVERT: D 24 ILE cc_start: 0.8943 (mm) cc_final: 0.8490 (mm) REVERT: D 44 LEU cc_start: 0.7606 (mt) cc_final: 0.7141 (mp) REVERT: D 53 TYR cc_start: 0.5790 (m-80) cc_final: 0.5588 (m-80) REVERT: D 120 ASP cc_start: 0.5817 (m-30) cc_final: 0.5420 (m-30) REVERT: D 235 MET cc_start: 0.7347 (mtp) cc_final: 0.7138 (ttm) REVERT: D 248 LEU cc_start: 0.7637 (mt) cc_final: 0.7426 (mp) REVERT: D 283 TYR cc_start: 0.6231 (m-80) cc_final: 0.5809 (m-80) REVERT: D 378 ILE cc_start: 0.7902 (mt) cc_final: 0.7424 (mt) REVERT: D 398 MET cc_start: 0.7104 (mtp) cc_final: 0.4353 (mtp) REVERT: E 24 TYR cc_start: 0.7826 (m-80) cc_final: 0.7235 (m-10) REVERT: E 80 THR cc_start: 0.7552 (p) cc_final: 0.7296 (t) REVERT: E 157 LEU cc_start: 0.8540 (mt) cc_final: 0.8200 (mt) REVERT: E 167 LEU cc_start: 0.7529 (mt) cc_final: 0.6707 (mt) REVERT: E 171 ILE cc_start: 0.8528 (mm) cc_final: 0.8140 (mm) REVERT: E 209 ILE cc_start: 0.9499 (mt) cc_final: 0.9261 (mp) REVERT: E 227 LEU cc_start: 0.9380 (mt) cc_final: 0.9134 (mt) REVERT: E 302 MET cc_start: 0.8486 (mmt) cc_final: 0.7629 (mpp) REVERT: E 352 LYS cc_start: 0.8200 (tttp) cc_final: 0.7706 (ttpt) REVERT: E 378 LEU cc_start: 0.8586 (mt) cc_final: 0.7355 (mp) REVERT: E 413 MET cc_start: 0.7920 (mmm) cc_final: 0.7285 (mmp) REVERT: F 14 ASN cc_start: 0.8518 (m-40) cc_final: 0.8218 (m110) REVERT: F 24 ILE cc_start: 0.9209 (mm) cc_final: 0.8550 (mm) REVERT: F 53 TYR cc_start: 0.5198 (m-80) cc_final: 0.4957 (m-80) REVERT: F 72 PRO cc_start: 0.8061 (Cg_exo) cc_final: 0.7547 (Cg_endo) REVERT: F 115 VAL cc_start: 0.9338 (t) cc_final: 0.8981 (p) REVERT: F 119 LEU cc_start: 0.8759 (tp) cc_final: 0.8333 (tp) REVERT: F 122 VAL cc_start: 0.9573 (t) cc_final: 0.9235 (t) REVERT: F 192 HIS cc_start: 0.8292 (t-170) cc_final: 0.8081 (t-90) REVERT: F 209 LEU cc_start: 0.8346 (mt) cc_final: 0.6878 (mt) REVERT: F 230 LEU cc_start: 0.9194 (mt) cc_final: 0.8969 (mt) REVERT: F 305 CYS cc_start: 0.6448 (t) cc_final: 0.5557 (t) REVERT: F 335 VAL cc_start: 0.7401 (t) cc_final: 0.6113 (t) REVERT: F 351 VAL cc_start: 0.8422 (t) cc_final: 0.7267 (t) REVERT: F 413 MET cc_start: 0.7059 (mmm) cc_final: 0.6776 (mmt) REVERT: G 14 VAL cc_start: 0.8430 (t) cc_final: 0.7668 (p) REVERT: G 16 ILE cc_start: 0.9245 (mt) cc_final: 0.8942 (tp) REVERT: G 75 ILE cc_start: 0.7997 (mm) cc_final: 0.6496 (mm) REVERT: G 115 ILE cc_start: 0.8574 (tp) cc_final: 0.8251 (tp) REVERT: G 118 VAL cc_start: 0.9238 (t) cc_final: 0.8898 (t) REVERT: G 129 CYS cc_start: 0.6655 (m) cc_final: 0.6270 (t) REVERT: G 132 LEU cc_start: 0.8207 (tp) cc_final: 0.7951 (tp) REVERT: G 137 VAL cc_start: 0.8091 (t) cc_final: 0.7516 (t) REVERT: G 153 LEU cc_start: 0.8753 (tp) cc_final: 0.8457 (tt) REVERT: G 167 LEU cc_start: 0.7620 (mt) cc_final: 0.6790 (mt) REVERT: G 195 LEU cc_start: 0.7785 (tp) cc_final: 0.7057 (tt) REVERT: G 207 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: G 218 ASP cc_start: 0.6492 (m-30) cc_final: 0.6073 (m-30) REVERT: G 267 PHE cc_start: 0.7518 (m-80) cc_final: 0.6915 (m-80) REVERT: G 295 CYS cc_start: 0.9347 (m) cc_final: 0.8867 (m) REVERT: G 316 CYS cc_start: 0.8497 (t) cc_final: 0.6608 (m) REVERT: G 378 LEU cc_start: 0.7961 (mt) cc_final: 0.7581 (mp) REVERT: G 384 ILE cc_start: 0.6140 (tt) cc_final: 0.5857 (pt) REVERT: H 5 VAL cc_start: 0.8572 (t) cc_final: 0.8367 (t) REVERT: H 14 ASN cc_start: 0.8778 (m-40) cc_final: 0.7906 (t0) REVERT: H 122 VAL cc_start: 0.9377 (t) cc_final: 0.8809 (t) REVERT: H 209 LEU cc_start: 0.8081 (mt) cc_final: 0.6194 (tp) REVERT: H 242 LEU cc_start: 0.7547 (tp) cc_final: 0.7245 (tp) REVERT: H 248 LEU cc_start: 0.6848 (mt) cc_final: 0.6038 (mp) REVERT: H 332 MET cc_start: 0.7472 (mmm) cc_final: 0.6914 (mmm) REVERT: H 391 ILE cc_start: 0.9095 (mt) cc_final: 0.8774 (mm) REVERT: I 22 GLU cc_start: 0.5877 (tt0) cc_final: 0.5637 (tt0) REVERT: I 119 LEU cc_start: 0.7008 (tp) cc_final: 0.6655 (mt) REVERT: I 120 ASP cc_start: 0.5264 (t70) cc_final: 0.4414 (t0) REVERT: I 122 ILE cc_start: 0.9052 (mt) cc_final: 0.8750 (mt) REVERT: I 132 LEU cc_start: 0.7904 (tp) cc_final: 0.7456 (tp) REVERT: I 181 VAL cc_start: 0.7900 (m) cc_final: 0.7605 (p) REVERT: I 186 ASN cc_start: 0.8025 (m-40) cc_final: 0.7684 (t0) REVERT: I 212 ILE cc_start: 0.8375 (mt) cc_final: 0.8160 (mt) REVERT: I 224 TYR cc_start: 0.7424 (m-80) cc_final: 0.7076 (m-80) REVERT: I 286 LEU cc_start: 0.8676 (mt) cc_final: 0.8322 (mt) REVERT: I 378 LEU cc_start: 0.8802 (mt) cc_final: 0.8528 (mp) REVERT: I 395 PHE cc_start: 0.7750 (t80) cc_final: 0.7546 (t80) REVERT: J 14 ASN cc_start: 0.8643 (m-40) cc_final: 0.7925 (t0) REVERT: J 62 VAL cc_start: 0.8153 (t) cc_final: 0.7877 (p) REVERT: J 72 PRO cc_start: 0.8852 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: J 119 LEU cc_start: 0.9030 (tp) cc_final: 0.8662 (tp) REVERT: J 122 VAL cc_start: 0.9090 (t) cc_final: 0.8835 (t) REVERT: J 209 LEU cc_start: 0.8014 (mt) cc_final: 0.7029 (mt) REVERT: J 266 HIS cc_start: 0.7185 (p-80) cc_final: 0.6720 (p-80) REVERT: J 295 MET cc_start: 0.8061 (mtm) cc_final: 0.7706 (ptm) REVERT: J 332 MET cc_start: 0.7396 (mmm) cc_final: 0.7069 (mmt) REVERT: J 376 THR cc_start: 0.8250 (m) cc_final: 0.7739 (p) REVERT: K 56 THR cc_start: 0.3881 (p) cc_final: 0.3277 (p) REVERT: K 75 ILE cc_start: 0.7526 (mm) cc_final: 0.6222 (mm) REVERT: K 207 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: K 219 ILE cc_start: 0.8555 (mt) cc_final: 0.8300 (mm) REVERT: K 295 CYS cc_start: 0.9092 (m) cc_final: 0.8822 (m) REVERT: K 377 MET cc_start: 0.7921 (ttt) cc_final: 0.7691 (tmm) REVERT: K 378 LEU cc_start: 0.8591 (mt) cc_final: 0.8225 (mt) REVERT: L 14 ASN cc_start: 0.8519 (m-40) cc_final: 0.7581 (t0) REVERT: L 242 LEU cc_start: 0.7534 (tp) cc_final: 0.6840 (tp) REVERT: L 248 LEU cc_start: 0.7271 (mt) cc_final: 0.6933 (mp) REVERT: L 300 ASN cc_start: 0.6582 (m-40) cc_final: 0.6189 (m-40) REVERT: M 66 VAL cc_start: 0.7848 (t) cc_final: 0.7601 (t) REVERT: M 75 ILE cc_start: 0.8601 (mm) cc_final: 0.8297 (mm) REVERT: M 119 LEU cc_start: 0.8671 (tp) cc_final: 0.8399 (tp) REVERT: M 121 ARG cc_start: 0.8141 (mmp-170) cc_final: 0.7921 (mmp80) REVERT: M 132 LEU cc_start: 0.8045 (tp) cc_final: 0.7712 (tp) REVERT: M 167 LEU cc_start: 0.7610 (mt) cc_final: 0.7125 (mp) REVERT: M 212 ILE cc_start: 0.8100 (mt) cc_final: 0.6736 (mt) REVERT: M 316 CYS cc_start: 0.6300 (t) cc_final: 0.5982 (t) REVERT: M 357 TYR cc_start: 0.6117 (m-80) cc_final: 0.5548 (m-80) REVERT: M 384 ILE cc_start: 0.8451 (tt) cc_final: 0.6597 (tp) REVERT: M 391 LEU cc_start: 0.6667 (mt) cc_final: 0.6357 (mm) REVERT: N 4 ILE cc_start: 0.8967 (mt) cc_final: 0.8625 (mm) REVERT: N 14 ASN cc_start: 0.8019 (m-40) cc_final: 0.6916 (m-40) REVERT: N 24 ILE cc_start: 0.9436 (mm) cc_final: 0.9057 (mm) REVERT: N 220 THR cc_start: 0.6854 (p) cc_final: 0.6188 (p) REVERT: N 235 MET cc_start: 0.7425 (mtp) cc_final: 0.6748 (ttt) REVERT: N 244 PHE cc_start: 0.6849 (m-80) cc_final: 0.6648 (m-10) REVERT: N 301 MET cc_start: 0.7149 (mmp) cc_final: 0.6743 (mmm) REVERT: N 398 MET cc_start: 0.5945 (mtp) cc_final: 0.3968 (mtp) REVERT: N 405 LEU cc_start: 0.8138 (tp) cc_final: 0.7853 (tp) REVERT: O 6 SER cc_start: 0.7974 (t) cc_final: 0.7599 (p) REVERT: O 14 VAL cc_start: 0.8997 (t) cc_final: 0.8737 (p) REVERT: O 23 LEU cc_start: 0.9077 (tp) cc_final: 0.8625 (mm) REVERT: O 60 LYS cc_start: 0.8066 (mmtt) cc_final: 0.6424 (mmmt) REVERT: O 75 ILE cc_start: 0.8596 (mm) cc_final: 0.8337 (mm) REVERT: O 138 PHE cc_start: 0.7242 (m-80) cc_final: 0.6941 (m-80) REVERT: O 171 ILE cc_start: 0.7881 (mm) cc_final: 0.7637 (mm) REVERT: O 303 VAL cc_start: 0.8882 (t) cc_final: 0.8672 (p) REVERT: O 343 PHE cc_start: 0.6626 (m-80) cc_final: 0.6199 (m-80) REVERT: O 384 ILE cc_start: 0.8385 (tt) cc_final: 0.7344 (tp) REVERT: O 391 LEU cc_start: 0.7074 (mt) cc_final: 0.6668 (mm) REVERT: P 4 ILE cc_start: 0.8875 (mt) cc_final: 0.8660 (mm) REVERT: P 14 ASN cc_start: 0.8077 (m-40) cc_final: 0.7407 (m-40) REVERT: P 24 ILE cc_start: 0.9604 (mm) cc_final: 0.9076 (mm) REVERT: P 107 HIS cc_start: 0.7083 (t70) cc_final: 0.6769 (t-90) REVERT: P 192 HIS cc_start: 0.7519 (t-170) cc_final: 0.6331 (t-90) REVERT: P 288 VAL cc_start: 0.9004 (t) cc_final: 0.8460 (t) REVERT: P 301 MET cc_start: 0.6161 (mmp) cc_final: 0.5194 (mmp) REVERT: P 306 ASP cc_start: 0.4149 (t0) cc_final: 0.2553 (t70) REVERT: P 377 PHE cc_start: 0.6493 (t80) cc_final: 0.5607 (t80) REVERT: P 384 ILE cc_start: 0.8083 (mt) cc_final: 0.7659 (tp) REVERT: P 391 ILE cc_start: 0.8111 (mt) cc_final: 0.7880 (mt) REVERT: Q 5 ILE cc_start: 0.7809 (mt) cc_final: 0.7375 (mm) REVERT: Q 6 SER cc_start: 0.7647 (t) cc_final: 0.7397 (p) REVERT: Q 23 LEU cc_start: 0.8985 (tp) cc_final: 0.8707 (mm) REVERT: Q 66 VAL cc_start: 0.7655 (t) cc_final: 0.7098 (t) REVERT: Q 132 LEU cc_start: 0.7764 (tp) cc_final: 0.7228 (tt) REVERT: Q 167 LEU cc_start: 0.7531 (mt) cc_final: 0.7192 (mt) REVERT: Q 302 MET cc_start: 0.7850 (mmt) cc_final: 0.6973 (mpp) REVERT: Q 303 VAL cc_start: 0.9070 (t) cc_final: 0.8550 (p) REVERT: Q 355 ILE cc_start: 0.9091 (mt) cc_final: 0.8807 (tp) REVERT: Q 384 ILE cc_start: 0.8724 (tt) cc_final: 0.6861 (tp) REVERT: Q 391 LEU cc_start: 0.6330 (mt) cc_final: 0.5818 (mt) REVERT: R 24 ILE cc_start: 0.9570 (mm) cc_final: 0.8587 (tp) REVERT: R 86 ILE cc_start: 0.7893 (tt) cc_final: 0.7658 (tt) REVERT: R 103 TRP cc_start: 0.5760 (t60) cc_final: 0.4529 (t60) REVERT: R 199 ASP cc_start: 0.7082 (m-30) cc_final: 0.6513 (m-30) REVERT: R 221 THR cc_start: 0.5261 (p) cc_final: 0.4692 (p) REVERT: R 378 ILE cc_start: 0.7390 (mt) cc_final: 0.6857 (mt) REVERT: R 380 ASN cc_start: 0.6343 (t0) cc_final: 0.6136 (t0) outliers start: 18 outliers final: 2 residues processed: 2730 average time/residue: 0.6473 time to fit residues: 2862.6564 Evaluate side-chains 1432 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1427 time to evaluate : 5.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 5.9990 chunk 573 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 386 optimal weight: 6.9990 chunk 306 optimal weight: 30.0000 chunk 592 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 360 optimal weight: 7.9990 chunk 441 optimal weight: 6.9990 chunk 686 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 91 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 133 GLN B 136 GLN B 192 HIS B 331 GLN C 11 GLN C 28 HIS C 91 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 133 GLN D 192 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 31 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 133 GLN F 206 ASN F 281 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 HIS G 285 GLN H 37 HIS H 102 ASN H 133 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS J 6 HIS J 37 HIS ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN J 192 HIS ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 HIS ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 339 ASN ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS L 102 ASN L 133 GLN L 192 HIS L 331 GLN L 337 ASN M 15 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN N 229 HIS ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 301 GLN P 15 GLN ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN P 331 GLN Q 15 GLN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 ASN R 101 ASN R 102 ASN R 192 HIS R 339 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 62298 Z= 0.250 Angle : 0.702 9.714 84645 Z= 0.374 Chirality : 0.046 0.228 9216 Planarity : 0.006 0.130 11043 Dihedral : 12.361 165.617 8784 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.15 % Allowed : 2.75 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 7632 helix: 0.43 (0.08), residues: 3519 sheet: 1.44 (0.15), residues: 1089 loop : 0.01 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP M 388 HIS 0.021 0.002 HIS H 28 PHE 0.035 0.002 PHE B 296 TYR 0.026 0.002 TYR I 24 ARG 0.017 0.001 ARG D 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1906 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1896 time to evaluate : 5.391 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: A 16 ILE cc_start: 0.9199 (mt) cc_final: 0.8848 (mt) REVERT: A 66 VAL cc_start: 0.7621 (t) cc_final: 0.7234 (t) REVERT: A 118 VAL cc_start: 0.8974 (t) cc_final: 0.8583 (t) REVERT: A 122 ILE cc_start: 0.8988 (mt) cc_final: 0.8638 (mt) REVERT: A 209 ILE cc_start: 0.9108 (mp) cc_final: 0.7504 (mp) REVERT: A 210 TYR cc_start: 0.8713 (m-80) cc_final: 0.8123 (m-80) REVERT: A 221 ARG cc_start: 0.7391 (mmt180) cc_final: 0.6117 (mmt180) REVERT: A 227 LEU cc_start: 0.8846 (mt) cc_final: 0.8573 (mt) REVERT: A 315 CYS cc_start: 0.7743 (t) cc_final: 0.7484 (m) REVERT: A 322 ASP cc_start: 0.6071 (t0) cc_final: 0.5760 (m-30) REVERT: A 344 VAL cc_start: 0.8138 (t) cc_final: 0.7785 (t) REVERT: A 378 LEU cc_start: 0.8267 (mt) cc_final: 0.7697 (mp) REVERT: B 5 VAL cc_start: 0.8703 (t) cc_final: 0.8320 (t) REVERT: B 6 HIS cc_start: 0.7947 (t70) cc_final: 0.7329 (t70) REVERT: B 37 HIS cc_start: 0.5152 (t-170) cc_final: 0.4925 (t-170) REVERT: B 44 LEU cc_start: 0.7850 (mt) cc_final: 0.7594 (mt) REVERT: B 53 TYR cc_start: 0.5803 (m-10) cc_final: 0.5174 (m-10) REVERT: B 69 ASP cc_start: 0.7554 (t0) cc_final: 0.7294 (t0) REVERT: B 115 VAL cc_start: 0.8756 (t) cc_final: 0.8307 (t) REVERT: B 120 ASP cc_start: 0.7217 (t0) cc_final: 0.6966 (t70) REVERT: B 227 LEU cc_start: 0.9139 (mt) cc_final: 0.8654 (mt) REVERT: B 230 LEU cc_start: 0.9317 (mt) cc_final: 0.9091 (tt) REVERT: B 291 LEU cc_start: 0.9175 (mm) cc_final: 0.8634 (tp) REVERT: B 325 MET cc_start: 0.6476 (mmm) cc_final: 0.6275 (mmm) REVERT: B 327 GLU cc_start: 0.6863 (pt0) cc_final: 0.6632 (pt0) REVERT: B 356 CYS cc_start: 0.7986 (p) cc_final: 0.7366 (t) REVERT: B 372 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8546 (tttt) REVERT: B 399 PHE cc_start: 0.7250 (t80) cc_final: 0.6838 (t80) REVERT: C 77 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7772 (mt-10) REVERT: C 118 VAL cc_start: 0.9153 (t) cc_final: 0.8717 (t) REVERT: C 132 LEU cc_start: 0.7860 (tp) cc_final: 0.7413 (mp) REVERT: C 153 LEU cc_start: 0.8497 (tp) cc_final: 0.8212 (tp) REVERT: C 217 LEU cc_start: 0.8374 (mt) cc_final: 0.8158 (mt) REVERT: C 291 ILE cc_start: 0.8493 (mt) cc_final: 0.8154 (tt) REVERT: C 377 MET cc_start: 0.8532 (tmm) cc_final: 0.8116 (tmm) REVERT: C 384 ILE cc_start: 0.8226 (tp) cc_final: 0.7919 (tt) REVERT: D 14 ASN cc_start: 0.8612 (m-40) cc_final: 0.7800 (m-40) REVERT: D 49 ILE cc_start: 0.8480 (tp) cc_final: 0.8226 (tp) REVERT: D 115 VAL cc_start: 0.8846 (t) cc_final: 0.8409 (t) REVERT: D 210 TYR cc_start: 0.6624 (m-80) cc_final: 0.6143 (m-80) REVERT: D 291 LEU cc_start: 0.8817 (mm) cc_final: 0.8463 (mm) REVERT: D 301 MET cc_start: 0.6299 (mmm) cc_final: 0.5925 (mmm) REVERT: D 323 MET cc_start: 0.7339 (mtm) cc_final: 0.6992 (mpp) REVERT: D 325 MET cc_start: 0.6311 (mmm) cc_final: 0.5281 (mmt) REVERT: D 425 MET cc_start: 0.6856 (tpp) cc_final: 0.6611 (mmm) REVERT: D 432 TYR cc_start: 0.6945 (m-80) cc_final: 0.5874 (m-10) REVERT: E 24 TYR cc_start: 0.7134 (m-80) cc_final: 0.6715 (m-10) REVERT: E 221 ARG cc_start: 0.7107 (mmt180) cc_final: 0.6496 (mmt180) REVERT: E 227 LEU cc_start: 0.8800 (mt) cc_final: 0.8231 (mt) REVERT: E 377 MET cc_start: 0.8127 (tmm) cc_final: 0.7476 (tmm) REVERT: E 378 LEU cc_start: 0.8229 (mt) cc_final: 0.7620 (mp) REVERT: E 380 ASN cc_start: 0.7861 (t0) cc_final: 0.7417 (t0) REVERT: F 14 ASN cc_start: 0.8302 (m-40) cc_final: 0.7774 (m-40) REVERT: F 24 ILE cc_start: 0.9147 (mm) cc_final: 0.8885 (mm) REVERT: F 79 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.8110 (ptp-170) REVERT: F 115 VAL cc_start: 0.9525 (t) cc_final: 0.8545 (t) REVERT: F 127 GLU cc_start: 0.7741 (pp20) cc_final: 0.6858 (pp20) REVERT: F 239 THR cc_start: 0.8991 (p) cc_final: 0.8612 (m) REVERT: F 257 VAL cc_start: 0.9031 (t) cc_final: 0.8752 (p) REVERT: F 259 MET cc_start: 0.6344 (mmm) cc_final: 0.6033 (mmm) REVERT: F 268 PHE cc_start: 0.7366 (m-80) cc_final: 0.6898 (m-80) REVERT: F 291 LEU cc_start: 0.8931 (mm) cc_final: 0.8590 (tp) REVERT: F 327 GLU cc_start: 0.7168 (pt0) cc_final: 0.6253 (pt0) REVERT: F 328 VAL cc_start: 0.8824 (t) cc_final: 0.8334 (p) REVERT: F 332 MET cc_start: 0.7723 (ttp) cc_final: 0.7379 (tmm) REVERT: F 351 VAL cc_start: 0.7867 (t) cc_final: 0.7664 (t) REVERT: F 373 MET cc_start: 0.8020 (pmm) cc_final: 0.7666 (pmm) REVERT: F 398 MET cc_start: 0.7102 (mtm) cc_final: 0.5689 (mtt) REVERT: F 422 GLU cc_start: 0.7398 (tp30) cc_final: 0.7084 (tp30) REVERT: G 25 CYS cc_start: 0.7242 (m) cc_final: 0.6885 (m) REVERT: G 169 PHE cc_start: 0.6484 (m-80) cc_final: 0.6271 (m-80) REVERT: G 181 VAL cc_start: 0.6997 (m) cc_final: 0.6509 (m) REVERT: G 252 LEU cc_start: 0.7069 (pp) cc_final: 0.6337 (pp) REVERT: G 291 ILE cc_start: 0.9052 (mt) cc_final: 0.8149 (tt) REVERT: G 295 CYS cc_start: 0.8673 (m) cc_final: 0.8423 (m) REVERT: G 315 CYS cc_start: 0.7370 (t) cc_final: 0.5196 (t) REVERT: G 317 LEU cc_start: 0.7503 (mt) cc_final: 0.7270 (mt) REVERT: G 378 LEU cc_start: 0.8001 (mt) cc_final: 0.7250 (mp) REVERT: H 14 ASN cc_start: 0.8444 (m-40) cc_final: 0.8045 (m110) REVERT: H 19 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7651 (mmmm) REVERT: H 62 VAL cc_start: 0.8093 (m) cc_final: 0.7862 (m) REVERT: H 124 LYS cc_start: 0.9072 (pptt) cc_final: 0.8809 (tttp) REVERT: H 259 MET cc_start: 0.7108 (mmm) cc_final: 0.6660 (mmm) REVERT: H 267 PHE cc_start: 0.6925 (m-80) cc_final: 0.6678 (m-80) REVERT: H 332 MET cc_start: 0.7559 (mmm) cc_final: 0.7137 (mmm) REVERT: I 24 TYR cc_start: 0.8112 (m-80) cc_final: 0.7583 (m-80) REVERT: I 26 LEU cc_start: 0.8691 (mt) cc_final: 0.8426 (mt) REVERT: I 122 ILE cc_start: 0.8576 (mt) cc_final: 0.8315 (mt) REVERT: I 171 ILE cc_start: 0.8051 (mm) cc_final: 0.7830 (mm) REVERT: I 218 ASP cc_start: 0.5384 (m-30) cc_final: 0.5147 (m-30) REVERT: I 328 VAL cc_start: 0.8245 (t) cc_final: 0.8043 (t) REVERT: I 346 TRP cc_start: 0.5950 (m-10) cc_final: 0.5734 (m-10) REVERT: I 384 ILE cc_start: 0.7221 (tp) cc_final: 0.6313 (tp) REVERT: J 14 ASN cc_start: 0.8166 (m-40) cc_final: 0.7770 (t0) REVERT: J 69 ASP cc_start: 0.6591 (t0) cc_final: 0.6007 (t70) REVERT: J 120 ASP cc_start: 0.7129 (t0) cc_final: 0.6727 (t70) REVERT: J 203 CYS cc_start: 0.8347 (m) cc_final: 0.7996 (m) REVERT: J 209 LEU cc_start: 0.7333 (mt) cc_final: 0.7076 (mt) REVERT: J 227 LEU cc_start: 0.9168 (mt) cc_final: 0.8140 (mp) REVERT: J 277 SER cc_start: 0.5509 (t) cc_final: 0.3552 (p) REVERT: J 305 CYS cc_start: 0.5902 (t) cc_final: 0.5616 (t) REVERT: J 376 THR cc_start: 0.8690 (m) cc_final: 0.8206 (p) REVERT: K 291 ILE cc_start: 0.8848 (mt) cc_final: 0.7901 (tt) REVERT: K 295 CYS cc_start: 0.8754 (m) cc_final: 0.8464 (m) REVERT: K 315 CYS cc_start: 0.7431 (t) cc_final: 0.7218 (t) REVERT: K 334 THR cc_start: 0.8120 (m) cc_final: 0.7790 (p) REVERT: K 335 ILE cc_start: 0.7040 (mm) cc_final: 0.6814 (mm) REVERT: K 341 ILE cc_start: 0.7059 (pt) cc_final: 0.6050 (pt) REVERT: K 377 MET cc_start: 0.7244 (ttt) cc_final: 0.6574 (tmm) REVERT: K 398 MET cc_start: 0.8146 (mmm) cc_final: 0.7731 (mmp) REVERT: L 14 ASN cc_start: 0.8419 (m-40) cc_final: 0.7115 (t0) REVERT: L 19 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8691 (mmmm) REVERT: L 21 TRP cc_start: 0.7114 (m100) cc_final: 0.6669 (m100) REVERT: L 87 PHE cc_start: 0.7468 (m-10) cc_final: 0.7145 (m-80) REVERT: L 115 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8189 (p) REVERT: L 125 GLU cc_start: 0.4507 (tp30) cc_final: 0.4242 (tp30) REVERT: L 267 PHE cc_start: 0.7051 (m-80) cc_final: 0.6316 (m-10) REVERT: L 275 LEU cc_start: 0.7490 (pt) cc_final: 0.6916 (pt) REVERT: M 21 TRP cc_start: 0.7863 (m100) cc_final: 0.7662 (m100) REVERT: M 25 CYS cc_start: 0.8167 (t) cc_final: 0.7023 (t) REVERT: M 75 ILE cc_start: 0.8514 (mm) cc_final: 0.7997 (tp) REVERT: M 122 ILE cc_start: 0.8943 (mt) cc_final: 0.8659 (mt) REVERT: M 132 LEU cc_start: 0.6954 (tp) cc_final: 0.6753 (tp) REVERT: M 167 LEU cc_start: 0.7401 (mt) cc_final: 0.7130 (mt) REVERT: M 212 ILE cc_start: 0.7577 (mt) cc_final: 0.7280 (tt) REVERT: M 213 CYS cc_start: 0.6105 (t) cc_final: 0.5501 (t) REVERT: M 228 ASN cc_start: 0.8348 (m-40) cc_final: 0.8143 (m-40) REVERT: M 334 THR cc_start: 0.8065 (m) cc_final: 0.7802 (p) REVERT: M 355 ILE cc_start: 0.9306 (mt) cc_final: 0.8888 (tp) REVERT: M 377 MET cc_start: 0.7634 (tmm) cc_final: 0.7143 (tmm) REVERT: M 398 MET cc_start: 0.6602 (mmm) cc_final: 0.6314 (mmm) REVERT: N 14 ASN cc_start: 0.8282 (m-40) cc_final: 0.7388 (m-40) REVERT: N 24 ILE cc_start: 0.9215 (mm) cc_final: 0.8621 (mm) REVERT: N 119 LEU cc_start: 0.8149 (tp) cc_final: 0.5570 (tp) REVERT: N 123 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7307 (mtt-85) REVERT: N 169 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: N 209 LEU cc_start: 0.8197 (tp) cc_final: 0.7920 (tp) REVERT: N 242 LEU cc_start: 0.7170 (tp) cc_final: 0.6965 (tt) REVERT: N 268 PHE cc_start: 0.5992 (m-80) cc_final: 0.5215 (m-80) REVERT: N 300 ASN cc_start: 0.7934 (m-40) cc_final: 0.7365 (t0) REVERT: N 398 MET cc_start: 0.6763 (mtp) cc_final: 0.6284 (mtm) REVERT: N 432 TYR cc_start: 0.6544 (m-10) cc_final: 0.6044 (m-80) REVERT: O 6 SER cc_start: 0.7564 (t) cc_final: 0.7324 (t) REVERT: O 23 LEU cc_start: 0.8801 (tp) cc_final: 0.8485 (tt) REVERT: O 28 HIS cc_start: 0.6227 (m-70) cc_final: 0.5284 (m-70) REVERT: O 138 PHE cc_start: 0.7056 (m-80) cc_final: 0.6854 (m-80) REVERT: O 154 MET cc_start: 0.7197 (ttp) cc_final: 0.6710 (ppp) REVERT: O 172 TYR cc_start: 0.6797 (t80) cc_final: 0.6446 (t80) REVERT: O 216 ASN cc_start: 0.6952 (m-40) cc_final: 0.6675 (m-40) REVERT: O 377 MET cc_start: 0.8138 (tmm) cc_final: 0.7750 (tmm) REVERT: O 384 ILE cc_start: 0.8067 (tt) cc_final: 0.6698 (tp) REVERT: O 391 LEU cc_start: 0.6345 (mt) cc_final: 0.6069 (mt) REVERT: P 14 ASN cc_start: 0.8119 (m-40) cc_final: 0.7581 (m-40) REVERT: P 118 VAL cc_start: 0.7760 (t) cc_final: 0.7363 (t) REVERT: P 154 ILE cc_start: 0.9170 (tp) cc_final: 0.8780 (tp) REVERT: P 235 MET cc_start: 0.8261 (mtp) cc_final: 0.8034 (mtp) REVERT: P 300 ASN cc_start: 0.8682 (m110) cc_final: 0.8219 (t0) REVERT: P 306 ASP cc_start: 0.5048 (t0) cc_final: 0.4272 (t0) REVERT: P 325 MET cc_start: 0.7227 (mmm) cc_final: 0.6187 (mmm) REVERT: P 332 MET cc_start: 0.6483 (mmt) cc_final: 0.5381 (mmt) REVERT: P 413 MET cc_start: 0.8115 (mmm) cc_final: 0.7638 (mmm) REVERT: Q 23 LEU cc_start: 0.8838 (tp) cc_final: 0.8178 (mm) REVERT: Q 24 TYR cc_start: 0.7869 (m-10) cc_final: 0.7533 (m-10) REVERT: Q 25 CYS cc_start: 0.7766 (m) cc_final: 0.7482 (m) REVERT: Q 191 THR cc_start: 0.8002 (p) cc_final: 0.7717 (p) REVERT: Q 203 MET cc_start: 0.6597 (mtm) cc_final: 0.5906 (mtt) REVERT: Q 217 LEU cc_start: 0.8351 (mm) cc_final: 0.8090 (mm) REVERT: Q 271 THR cc_start: 0.5690 (m) cc_final: 0.4938 (p) REVERT: Q 302 MET cc_start: 0.7658 (mmt) cc_final: 0.7325 (mpp) REVERT: Q 303 VAL cc_start: 0.8894 (t) cc_final: 0.8631 (p) REVERT: Q 318 LEU cc_start: 0.6488 (mt) cc_final: 0.6048 (mt) REVERT: Q 376 CYS cc_start: 0.7272 (t) cc_final: 0.6995 (t) REVERT: Q 377 MET cc_start: 0.7930 (tmm) cc_final: 0.6667 (tmm) REVERT: Q 434 GLU cc_start: 0.6755 (tp30) cc_final: 0.6479 (tp30) REVERT: R 5 VAL cc_start: 0.7841 (t) cc_final: 0.7410 (t) REVERT: R 6 HIS cc_start: 0.8848 (t-90) cc_final: 0.8413 (t-90) REVERT: R 20 PHE cc_start: 0.8673 (t80) cc_final: 0.8364 (t80) REVERT: R 24 ILE cc_start: 0.9260 (mm) cc_final: 0.8877 (mm) REVERT: R 123 ARG cc_start: 0.7784 (ptp-110) cc_final: 0.7438 (ptp-170) REVERT: R 235 MET cc_start: 0.8201 (mtp) cc_final: 0.7656 (mtm) REVERT: R 244 PHE cc_start: 0.7293 (m-80) cc_final: 0.7010 (m-10) REVERT: R 378 ILE cc_start: 0.7648 (mt) cc_final: 0.6902 (mt) outliers start: 10 outliers final: 1 residues processed: 1904 average time/residue: 0.6244 time to fit residues: 1983.9930 Evaluate side-chains 1254 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1251 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 50.0000 chunk 213 optimal weight: 0.0970 chunk 571 optimal weight: 50.0000 chunk 467 optimal weight: 30.0000 chunk 189 optimal weight: 4.9990 chunk 687 optimal weight: 30.0000 chunk 742 optimal weight: 40.0000 chunk 612 optimal weight: 1.9990 chunk 682 optimal weight: 50.0000 chunk 234 optimal weight: 50.0000 chunk 551 optimal weight: 40.0000 overall best weight: 13.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 193 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN F 15 GLN F 133 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN F 206 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN J 6 HIS ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS J 193 GLN J 337 ASN ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 GLN L 6 HIS ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS L 193 GLN L 249 ASN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS O 228 ASN O 372 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 HIS ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN R 309 HIS ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 62298 Z= 0.296 Angle : 0.693 12.383 84645 Z= 0.368 Chirality : 0.045 0.191 9216 Planarity : 0.006 0.080 11043 Dihedral : 11.832 173.651 8784 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 7632 helix: 0.30 (0.08), residues: 3528 sheet: 1.17 (0.14), residues: 1224 loop : 0.15 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP Q 388 HIS 0.014 0.002 HIS H 28 PHE 0.024 0.002 PHE F 268 TYR 0.030 0.002 TYR A 24 ARG 0.013 0.001 ARG J 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1540 time to evaluate : 5.435 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: A 21 TRP cc_start: 0.8656 (m100) cc_final: 0.7991 (m100) REVERT: A 24 TYR cc_start: 0.8334 (m-80) cc_final: 0.7564 (m-80) REVERT: A 164 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7878 (tppt) REVERT: A 210 TYR cc_start: 0.8124 (m-80) cc_final: 0.7072 (m-80) REVERT: A 227 LEU cc_start: 0.9262 (mt) cc_final: 0.9054 (mp) REVERT: A 373 ARG cc_start: 0.8461 (ptt180) cc_final: 0.8211 (ptt180) REVERT: A 378 LEU cc_start: 0.8229 (mt) cc_final: 0.7867 (mp) REVERT: A 425 MET cc_start: 0.9109 (mmm) cc_final: 0.8616 (tpt) REVERT: B 166 MET cc_start: 0.5842 (mmp) cc_final: 0.5261 (mmm) REVERT: B 177 VAL cc_start: 0.7793 (t) cc_final: 0.6585 (p) REVERT: B 235 MET cc_start: 0.8572 (mtt) cc_final: 0.8230 (ttt) REVERT: B 259 MET cc_start: 0.7564 (mmp) cc_final: 0.6924 (mmm) REVERT: B 268 PHE cc_start: 0.8702 (m-80) cc_final: 0.8011 (m-80) REVERT: B 302 MET cc_start: 0.7015 (mmt) cc_final: 0.6540 (mtp) REVERT: B 327 GLU cc_start: 0.7312 (pt0) cc_final: 0.7108 (pt0) REVERT: B 332 MET cc_start: 0.7500 (tmm) cc_final: 0.7253 (tmm) REVERT: B 346 TRP cc_start: 0.5246 (m100) cc_final: 0.5000 (m100) REVERT: B 356 CYS cc_start: 0.8205 (p) cc_final: 0.6778 (t) REVERT: B 372 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8808 (tttt) REVERT: B 399 PHE cc_start: 0.7697 (t80) cc_final: 0.7200 (t80) REVERT: C 117 LEU cc_start: 0.7030 (tp) cc_final: 0.6604 (tp) REVERT: C 118 VAL cc_start: 0.9050 (t) cc_final: 0.8539 (t) REVERT: C 217 LEU cc_start: 0.8294 (mt) cc_final: 0.8031 (tt) REVERT: C 291 ILE cc_start: 0.9143 (mt) cc_final: 0.8470 (tt) REVERT: C 302 MET cc_start: 0.8783 (mmp) cc_final: 0.8539 (mmt) REVERT: C 378 LEU cc_start: 0.8215 (tt) cc_final: 0.7822 (tt) REVERT: C 395 PHE cc_start: 0.8403 (t80) cc_final: 0.8095 (t80) REVERT: C 417 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: D 14 ASN cc_start: 0.8164 (m-40) cc_final: 0.7591 (m-40) REVERT: D 16 ILE cc_start: 0.8593 (mt) cc_final: 0.8376 (mt) REVERT: D 21 TRP cc_start: 0.7795 (m100) cc_final: 0.7312 (m100) REVERT: D 163 ASP cc_start: 0.6289 (p0) cc_final: 0.5914 (p0) REVERT: D 210 TYR cc_start: 0.6907 (m-80) cc_final: 0.6572 (m-80) REVERT: D 219 LEU cc_start: 0.8741 (tp) cc_final: 0.8536 (tp) REVERT: D 288 VAL cc_start: 0.8927 (t) cc_final: 0.8586 (t) REVERT: D 295 MET cc_start: 0.8785 (tpp) cc_final: 0.8430 (tmm) REVERT: D 328 VAL cc_start: 0.8598 (t) cc_final: 0.8216 (t) REVERT: D 349 ASN cc_start: 0.7685 (m110) cc_final: 0.7100 (m110) REVERT: E 24 TYR cc_start: 0.7241 (m-80) cc_final: 0.6695 (m-10) REVERT: E 116 ASP cc_start: 0.8232 (p0) cc_final: 0.7933 (p0) REVERT: E 377 MET cc_start: 0.8120 (tmm) cc_final: 0.7561 (tmm) REVERT: E 378 LEU cc_start: 0.7940 (mt) cc_final: 0.7300 (mp) REVERT: E 380 ASN cc_start: 0.7844 (t0) cc_final: 0.7611 (t0) REVERT: E 422 ARG cc_start: 0.6819 (ttp80) cc_final: 0.6338 (ttp80) REVERT: F 14 ASN cc_start: 0.8467 (m-40) cc_final: 0.7980 (m-40) REVERT: F 24 ILE cc_start: 0.8858 (mm) cc_final: 0.7986 (mm) REVERT: F 53 TYR cc_start: 0.4346 (m-80) cc_final: 0.4101 (m-80) REVERT: F 115 VAL cc_start: 0.9055 (t) cc_final: 0.8817 (t) REVERT: F 120 ASP cc_start: 0.6538 (t70) cc_final: 0.6026 (t70) REVERT: F 235 MET cc_start: 0.7749 (mtt) cc_final: 0.7380 (ttm) REVERT: F 288 VAL cc_start: 0.9123 (t) cc_final: 0.8901 (t) REVERT: F 327 GLU cc_start: 0.7251 (pt0) cc_final: 0.6835 (pt0) REVERT: F 373 MET cc_start: 0.8336 (pmm) cc_final: 0.8070 (pmm) REVERT: F 425 MET cc_start: 0.5921 (tmm) cc_final: 0.5156 (tmm) REVERT: G 36 MET cc_start: 0.4676 (ttt) cc_final: 0.3786 (tmm) REVERT: G 129 CYS cc_start: 0.7681 (t) cc_final: 0.7303 (t) REVERT: G 291 ILE cc_start: 0.9247 (mt) cc_final: 0.8133 (tt) REVERT: G 315 CYS cc_start: 0.7482 (t) cc_final: 0.6450 (t) REVERT: G 378 LEU cc_start: 0.7975 (mt) cc_final: 0.7504 (mp) REVERT: H 124 LYS cc_start: 0.8890 (pptt) cc_final: 0.7953 (tttt) REVERT: H 166 MET cc_start: 0.5740 (mtp) cc_final: 0.5329 (mtm) REVERT: H 209 LEU cc_start: 0.8530 (mt) cc_final: 0.8092 (mt) REVERT: H 234 THR cc_start: 0.8697 (p) cc_final: 0.8405 (p) REVERT: H 259 MET cc_start: 0.7328 (mmm) cc_final: 0.6947 (mmm) REVERT: H 292 THR cc_start: 0.8132 (p) cc_final: 0.7767 (p) REVERT: H 295 MET cc_start: 0.8364 (ppp) cc_final: 0.7944 (ppp) REVERT: H 297 ASP cc_start: 0.7675 (t0) cc_final: 0.6899 (t0) REVERT: H 323 MET cc_start: 0.6472 (mpp) cc_final: 0.6032 (mpp) REVERT: H 332 MET cc_start: 0.7065 (mmm) cc_final: 0.6662 (mmm) REVERT: I 286 LEU cc_start: 0.8522 (mt) cc_final: 0.7931 (mt) REVERT: I 291 ILE cc_start: 0.8714 (mm) cc_final: 0.7993 (tt) REVERT: I 302 MET cc_start: 0.7526 (mpp) cc_final: 0.7273 (mpp) REVERT: I 347 CYS cc_start: 0.7806 (t) cc_final: 0.7497 (t) REVERT: I 380 ASN cc_start: 0.7845 (t0) cc_final: 0.7398 (t0) REVERT: I 435 VAL cc_start: 0.8898 (m) cc_final: 0.8641 (m) REVERT: J 8 GLN cc_start: 0.5979 (tt0) cc_final: 0.5484 (tt0) REVERT: J 122 VAL cc_start: 0.9194 (t) cc_final: 0.8907 (t) REVERT: J 209 LEU cc_start: 0.7720 (mt) cc_final: 0.7064 (mt) REVERT: J 227 LEU cc_start: 0.8875 (mt) cc_final: 0.8629 (mp) REVERT: J 231 VAL cc_start: 0.9275 (t) cc_final: 0.9032 (p) REVERT: J 235 MET cc_start: 0.8571 (mtp) cc_final: 0.7772 (mtm) REVERT: J 241 CYS cc_start: 0.8457 (t) cc_final: 0.8181 (t) REVERT: J 259 MET cc_start: 0.7914 (mmm) cc_final: 0.7680 (mmm) REVERT: J 277 SER cc_start: 0.6368 (t) cc_final: 0.4768 (t) REVERT: J 305 CYS cc_start: 0.6659 (t) cc_final: 0.5982 (t) REVERT: J 384 ILE cc_start: 0.8822 (mt) cc_final: 0.8358 (mt) REVERT: K 209 ILE cc_start: 0.8897 (mp) cc_final: 0.8657 (tt) REVERT: K 291 ILE cc_start: 0.9199 (mt) cc_final: 0.8299 (tt) REVERT: K 295 CYS cc_start: 0.8931 (m) cc_final: 0.8535 (m) REVERT: K 334 THR cc_start: 0.8369 (m) cc_final: 0.7960 (p) REVERT: K 377 MET cc_start: 0.7780 (ttt) cc_final: 0.6882 (tmm) REVERT: L 14 ASN cc_start: 0.8405 (m-40) cc_final: 0.7286 (t0) REVERT: L 231 VAL cc_start: 0.8582 (t) cc_final: 0.8257 (t) REVERT: L 332 MET cc_start: 0.7277 (mmm) cc_final: 0.6956 (mmt) REVERT: M 21 TRP cc_start: 0.8196 (m100) cc_final: 0.7865 (m100) REVERT: M 75 ILE cc_start: 0.8396 (mm) cc_final: 0.8077 (tt) REVERT: M 122 ILE cc_start: 0.8748 (mt) cc_final: 0.8484 (mt) REVERT: M 212 ILE cc_start: 0.7515 (mt) cc_final: 0.7189 (tt) REVERT: M 334 THR cc_start: 0.7937 (m) cc_final: 0.7529 (p) REVERT: M 377 MET cc_start: 0.7805 (tmm) cc_final: 0.7176 (tmm) REVERT: M 401 LYS cc_start: 0.8623 (tptt) cc_final: 0.8346 (tptt) REVERT: M 434 GLU cc_start: 0.6712 (pp20) cc_final: 0.6265 (tm-30) REVERT: N 6 HIS cc_start: 0.7345 (t-90) cc_final: 0.6569 (t-90) REVERT: N 14 ASN cc_start: 0.8397 (m-40) cc_final: 0.7425 (m-40) REVERT: N 16 ILE cc_start: 0.8458 (mt) cc_final: 0.8189 (mt) REVERT: N 119 LEU cc_start: 0.7881 (tp) cc_final: 0.6039 (tp) REVERT: N 242 LEU cc_start: 0.7593 (tp) cc_final: 0.7197 (tt) REVERT: N 259 MET cc_start: 0.7587 (mmp) cc_final: 0.7338 (mmm) REVERT: N 268 PHE cc_start: 0.6309 (m-80) cc_final: 0.5318 (m-80) REVERT: N 295 MET cc_start: 0.8450 (ttt) cc_final: 0.7695 (tmm) REVERT: N 332 MET cc_start: 0.6330 (mmt) cc_final: 0.6081 (mmt) REVERT: N 391 ILE cc_start: 0.8092 (mm) cc_final: 0.7730 (mm) REVERT: N 398 MET cc_start: 0.6892 (mtp) cc_final: 0.6210 (mtt) REVERT: N 432 TYR cc_start: 0.6435 (m-10) cc_final: 0.5783 (m-80) REVERT: O 6 SER cc_start: 0.7852 (t) cc_final: 0.7592 (t) REVERT: O 28 HIS cc_start: 0.6378 (m-70) cc_final: 0.5810 (m90) REVERT: O 75 ILE cc_start: 0.8270 (mm) cc_final: 0.8021 (tt) REVERT: O 230 LEU cc_start: 0.8811 (tp) cc_final: 0.8542 (mm) REVERT: O 243 ARG cc_start: 0.7665 (tmm160) cc_final: 0.6161 (tmt170) REVERT: O 295 CYS cc_start: 0.9132 (m) cc_final: 0.8604 (m) REVERT: O 391 LEU cc_start: 0.6907 (mt) cc_final: 0.6662 (mm) REVERT: O 398 MET cc_start: 0.3937 (mmp) cc_final: 0.3658 (mmp) REVERT: P 14 ASN cc_start: 0.8219 (m-40) cc_final: 0.7775 (m-40) REVERT: P 202 TYR cc_start: 0.6435 (m-80) cc_final: 0.6066 (m-10) REVERT: P 266 HIS cc_start: 0.8026 (p-80) cc_final: 0.7606 (p90) REVERT: P 268 PHE cc_start: 0.6711 (m-80) cc_final: 0.5302 (m-80) REVERT: P 295 MET cc_start: 0.7876 (ppp) cc_final: 0.7583 (ppp) REVERT: P 323 MET cc_start: 0.7535 (mpp) cc_final: 0.7316 (mpp) REVERT: P 325 MET cc_start: 0.6830 (mmm) cc_final: 0.5837 (mmm) REVERT: P 332 MET cc_start: 0.5712 (mmt) cc_final: 0.5141 (mmt) REVERT: P 398 MET cc_start: 0.5850 (mmp) cc_final: 0.5418 (mmp) REVERT: P 416 MET cc_start: 0.6908 (mmm) cc_final: 0.6528 (mmm) REVERT: P 428 LEU cc_start: 0.8832 (mt) cc_final: 0.8388 (mt) REVERT: Q 23 LEU cc_start: 0.8781 (tp) cc_final: 0.8560 (tt) REVERT: Q 25 CYS cc_start: 0.7932 (m) cc_final: 0.7111 (m) REVERT: Q 191 THR cc_start: 0.7694 (p) cc_final: 0.7415 (p) REVERT: Q 215 ARG cc_start: 0.6280 (ttp-110) cc_final: 0.5863 (ttp-110) REVERT: Q 217 LEU cc_start: 0.8285 (mm) cc_final: 0.7958 (mm) REVERT: Q 271 THR cc_start: 0.5684 (m) cc_final: 0.4518 (p) REVERT: Q 302 MET cc_start: 0.7919 (mmt) cc_final: 0.7339 (mpp) REVERT: Q 318 LEU cc_start: 0.6909 (mt) cc_final: 0.6692 (mt) REVERT: Q 376 CYS cc_start: 0.8069 (t) cc_final: 0.7809 (t) REVERT: Q 377 MET cc_start: 0.8126 (tmm) cc_final: 0.6897 (tmm) REVERT: R 6 HIS cc_start: 0.8654 (t-90) cc_final: 0.8246 (t-90) REVERT: R 14 ASN cc_start: 0.7750 (m110) cc_final: 0.7225 (m110) REVERT: R 116 ASP cc_start: 0.7603 (p0) cc_final: 0.7257 (p0) REVERT: R 295 MET cc_start: 0.8434 (ttt) cc_final: 0.7313 (tmm) REVERT: R 306 ASP cc_start: 0.4329 (t0) cc_final: 0.4019 (t0) REVERT: R 323 MET cc_start: 0.8589 (mpp) cc_final: 0.8225 (mpp) REVERT: R 380 ASN cc_start: 0.6658 (t0) cc_final: 0.6092 (t0) REVERT: R 425 MET cc_start: 0.8312 (tmm) cc_final: 0.7709 (tmm) outliers start: 16 outliers final: 5 residues processed: 1554 average time/residue: 0.5905 time to fit residues: 1536.0811 Evaluate side-chains 1106 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1100 time to evaluate : 5.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 4.9990 chunk 517 optimal weight: 50.0000 chunk 356 optimal weight: 0.0000 chunk 76 optimal weight: 30.0000 chunk 328 optimal weight: 7.9990 chunk 461 optimal weight: 10.0000 chunk 690 optimal weight: 50.0000 chunk 730 optimal weight: 7.9990 chunk 360 optimal weight: 20.0000 chunk 654 optimal weight: 50.0000 chunk 196 optimal weight: 4.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 192 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 133 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 206 ASN F 281 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 107 HIS H 249 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN J 337 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 GLN M 91 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN N 294 GLN ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 266 HIS O 372 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 331 GLN P 337 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 301 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 101 ASN ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 309 HIS R 337 ASN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 62298 Z= 0.189 Angle : 0.600 9.541 84645 Z= 0.311 Chirality : 0.044 0.219 9216 Planarity : 0.005 0.064 11043 Dihedral : 11.492 167.743 8784 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.09 % Allowed : 2.17 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 7632 helix: 0.50 (0.08), residues: 3519 sheet: 1.32 (0.14), residues: 1251 loop : 0.20 (0.12), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP F 21 HIS 0.011 0.001 HIS O 283 PHE 0.018 0.002 PHE H 169 TYR 0.031 0.002 TYR H 108 ARG 0.012 0.001 ARG Q 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1502 time to evaluate : 6.375 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: A 21 TRP cc_start: 0.8617 (m100) cc_final: 0.8134 (m100) REVERT: A 22 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: A 24 TYR cc_start: 0.8278 (m-80) cc_final: 0.7630 (m-80) REVERT: A 210 TYR cc_start: 0.8122 (m-80) cc_final: 0.7757 (m-80) REVERT: A 243 ARG cc_start: 0.6004 (tmt170) cc_final: 0.4782 (tmt170) REVERT: A 361 THR cc_start: 0.8407 (m) cc_final: 0.8194 (m) REVERT: A 420 GLU cc_start: 0.8055 (pt0) cc_final: 0.7678 (pt0) REVERT: B 41 ASP cc_start: 0.6819 (p0) cc_final: 0.6454 (m-30) REVERT: B 166 MET cc_start: 0.5207 (mmp) cc_final: 0.4992 (mmm) REVERT: B 235 MET cc_start: 0.8636 (mtt) cc_final: 0.8117 (ttm) REVERT: B 259 MET cc_start: 0.7452 (mmp) cc_final: 0.6936 (mmm) REVERT: B 268 PHE cc_start: 0.8434 (m-10) cc_final: 0.8065 (m-80) REVERT: B 291 LEU cc_start: 0.9053 (mm) cc_final: 0.8678 (tp) REVERT: B 372 LYS cc_start: 0.9047 (mmpt) cc_final: 0.8799 (tttt) REVERT: B 399 PHE cc_start: 0.7403 (t80) cc_final: 0.6975 (t80) REVERT: C 118 VAL cc_start: 0.9099 (t) cc_final: 0.8208 (t) REVERT: C 291 ILE cc_start: 0.9080 (mt) cc_final: 0.8311 (tt) REVERT: C 339 ARG cc_start: 0.6041 (mmt180) cc_final: 0.5776 (tpp-160) REVERT: C 377 MET cc_start: 0.8202 (tmm) cc_final: 0.7982 (tmm) REVERT: C 395 PHE cc_start: 0.8038 (t80) cc_final: 0.7707 (t80) REVERT: D 14 ASN cc_start: 0.8224 (m-40) cc_final: 0.7738 (m-40) REVERT: D 55 GLU cc_start: 0.6634 (tp30) cc_final: 0.6255 (tm-30) REVERT: D 163 ASP cc_start: 0.6477 (p0) cc_final: 0.6002 (p0) REVERT: D 210 TYR cc_start: 0.6721 (m-80) cc_final: 0.6306 (m-80) REVERT: D 295 MET cc_start: 0.8116 (tpp) cc_final: 0.7359 (tmm) REVERT: D 335 VAL cc_start: 0.6812 (t) cc_final: 0.6593 (t) REVERT: D 398 MET cc_start: 0.5106 (mtt) cc_final: 0.4806 (mtt) REVERT: E 24 TYR cc_start: 0.7070 (m-10) cc_final: 0.6515 (m-10) REVERT: E 217 LEU cc_start: 0.9046 (tt) cc_final: 0.8836 (tt) REVERT: E 224 TYR cc_start: 0.6076 (m-10) cc_final: 0.5704 (m-10) REVERT: E 334 THR cc_start: 0.7948 (p) cc_final: 0.7733 (p) REVERT: E 337 THR cc_start: 0.6256 (p) cc_final: 0.5937 (p) REVERT: E 377 MET cc_start: 0.8155 (tmm) cc_final: 0.7611 (tmm) REVERT: E 378 LEU cc_start: 0.8071 (mt) cc_final: 0.7544 (mt) REVERT: E 397 LEU cc_start: 0.6641 (mm) cc_final: 0.6416 (mm) REVERT: E 422 ARG cc_start: 0.6804 (ttp80) cc_final: 0.6454 (ttp80) REVERT: F 14 ASN cc_start: 0.8349 (m-40) cc_final: 0.7908 (m-40) REVERT: F 79 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.8072 (ptp-170) REVERT: F 115 VAL cc_start: 0.9202 (t) cc_final: 0.8995 (t) REVERT: F 116 ASP cc_start: 0.8446 (p0) cc_final: 0.8197 (p0) REVERT: F 120 ASP cc_start: 0.6049 (t70) cc_final: 0.5639 (t70) REVERT: F 235 MET cc_start: 0.7647 (mtt) cc_final: 0.7068 (ttm) REVERT: F 269 MET cc_start: 0.7768 (tpp) cc_final: 0.7442 (tpp) REVERT: F 291 LEU cc_start: 0.9060 (mm) cc_final: 0.8824 (mm) REVERT: F 327 GLU cc_start: 0.7952 (pt0) cc_final: 0.6631 (pt0) REVERT: F 328 VAL cc_start: 0.8543 (t) cc_final: 0.7785 (p) REVERT: F 411 GLU cc_start: 0.6393 (mm-30) cc_final: 0.6068 (mt-10) REVERT: G 132 LEU cc_start: 0.8407 (tp) cc_final: 0.8150 (tp) REVERT: G 220 GLU cc_start: 0.8404 (pm20) cc_final: 0.8154 (pm20) REVERT: G 291 ILE cc_start: 0.9294 (mt) cc_final: 0.8177 (tt) REVERT: G 378 LEU cc_start: 0.7877 (mt) cc_final: 0.7611 (mp) REVERT: H 124 LYS cc_start: 0.8735 (pptt) cc_final: 0.7934 (tttt) REVERT: H 209 LEU cc_start: 0.8167 (mt) cc_final: 0.7935 (mt) REVERT: H 297 ASP cc_start: 0.7711 (t0) cc_final: 0.7154 (t0) REVERT: H 301 MET cc_start: 0.7483 (mmp) cc_final: 0.7223 (mmt) REVERT: H 332 MET cc_start: 0.6893 (mmm) cc_final: 0.6349 (mmm) REVERT: I 7 ILE cc_start: 0.8919 (mp) cc_final: 0.8706 (mp) REVERT: I 75 ILE cc_start: 0.6773 (mm) cc_final: 0.6218 (tt) REVERT: I 116 ASP cc_start: 0.7890 (p0) cc_final: 0.7599 (p0) REVERT: I 191 THR cc_start: 0.8002 (p) cc_final: 0.7651 (p) REVERT: I 244 PHE cc_start: 0.5619 (t80) cc_final: 0.5338 (t80) REVERT: I 286 LEU cc_start: 0.8486 (mt) cc_final: 0.7986 (mt) REVERT: I 291 ILE cc_start: 0.8713 (mm) cc_final: 0.7892 (tt) REVERT: I 302 MET cc_start: 0.7461 (mpp) cc_final: 0.7063 (mpp) REVERT: I 378 LEU cc_start: 0.8797 (mt) cc_final: 0.8321 (mp) REVERT: I 380 ASN cc_start: 0.7427 (t0) cc_final: 0.7005 (t0) REVERT: I 386 GLU cc_start: 0.7600 (mp0) cc_final: 0.7310 (mp0) REVERT: I 435 VAL cc_start: 0.8562 (m) cc_final: 0.8079 (m) REVERT: J 115 VAL cc_start: 0.7732 (t) cc_final: 0.7514 (t) REVERT: J 120 ASP cc_start: 0.7428 (t70) cc_final: 0.7167 (t70) REVERT: J 209 LEU cc_start: 0.7697 (mt) cc_final: 0.6951 (mt) REVERT: J 227 LEU cc_start: 0.8948 (mt) cc_final: 0.8175 (mp) REVERT: J 231 VAL cc_start: 0.9177 (t) cc_final: 0.8770 (p) REVERT: J 235 MET cc_start: 0.8460 (mtp) cc_final: 0.7741 (mtm) REVERT: J 259 MET cc_start: 0.7673 (mmm) cc_final: 0.6964 (mmm) REVERT: J 267 PHE cc_start: 0.6953 (m-10) cc_final: 0.6624 (m-10) REVERT: J 277 SER cc_start: 0.6581 (t) cc_final: 0.3828 (t) REVERT: J 305 CYS cc_start: 0.6503 (t) cc_final: 0.5862 (t) REVERT: J 384 ILE cc_start: 0.8805 (mt) cc_final: 0.8520 (pt) REVERT: K 209 ILE cc_start: 0.8881 (mp) cc_final: 0.8267 (mp) REVERT: K 295 CYS cc_start: 0.9023 (m) cc_final: 0.8168 (m) REVERT: K 334 THR cc_start: 0.8244 (m) cc_final: 0.7986 (p) REVERT: K 335 ILE cc_start: 0.7068 (mm) cc_final: 0.6793 (mm) REVERT: K 377 MET cc_start: 0.7645 (ttt) cc_final: 0.6670 (tmm) REVERT: K 378 LEU cc_start: 0.8677 (mt) cc_final: 0.8448 (mt) REVERT: L 19 LYS cc_start: 0.9073 (mmpt) cc_final: 0.8695 (mmmm) REVERT: L 21 TRP cc_start: 0.7870 (m100) cc_final: 0.7607 (m100) REVERT: L 267 PHE cc_start: 0.7006 (m-80) cc_final: 0.6423 (m-10) REVERT: L 269 MET cc_start: 0.7339 (mtm) cc_final: 0.6872 (mtm) REVERT: M 75 ILE cc_start: 0.8353 (mm) cc_final: 0.7957 (tt) REVERT: M 191 THR cc_start: 0.7474 (p) cc_final: 0.7127 (p) REVERT: M 205 ASP cc_start: 0.5984 (t0) cc_final: 0.5455 (t0) REVERT: M 212 ILE cc_start: 0.7297 (mt) cc_final: 0.6464 (tt) REVERT: M 216 ASN cc_start: 0.7526 (m110) cc_final: 0.6340 (m110) REVERT: M 286 LEU cc_start: 0.7802 (mt) cc_final: 0.7585 (mm) REVERT: M 334 THR cc_start: 0.7746 (m) cc_final: 0.7245 (p) REVERT: M 377 MET cc_start: 0.7611 (tmm) cc_final: 0.7017 (tmm) REVERT: M 401 LYS cc_start: 0.8571 (tptt) cc_final: 0.8251 (tptt) REVERT: M 434 GLU cc_start: 0.6606 (pp20) cc_final: 0.6111 (tm-30) REVERT: N 6 HIS cc_start: 0.7051 (t-90) cc_final: 0.6788 (t-90) REVERT: N 14 ASN cc_start: 0.8045 (m-40) cc_final: 0.7234 (m-40) REVERT: N 47 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6894 (mt-10) REVERT: N 122 VAL cc_start: 0.8487 (t) cc_final: 0.7998 (t) REVERT: N 124 LYS cc_start: 0.9103 (pptt) cc_final: 0.8793 (pptt) REVERT: N 217 LEU cc_start: 0.6978 (tp) cc_final: 0.6649 (tp) REVERT: N 259 MET cc_start: 0.7639 (mmp) cc_final: 0.7253 (mmm) REVERT: N 268 PHE cc_start: 0.6202 (m-80) cc_final: 0.5195 (m-80) REVERT: N 295 MET cc_start: 0.7984 (ttt) cc_final: 0.7480 (tmm) REVERT: N 398 MET cc_start: 0.6933 (mtp) cc_final: 0.6487 (mtt) REVERT: N 432 TYR cc_start: 0.6043 (m-10) cc_final: 0.5369 (m-80) REVERT: O 6 SER cc_start: 0.7581 (t) cc_final: 0.7251 (t) REVERT: O 75 ILE cc_start: 0.8329 (mm) cc_final: 0.7891 (tt) REVERT: O 113 GLU cc_start: 0.7946 (mp0) cc_final: 0.7712 (mm-30) REVERT: O 203 MET cc_start: 0.6308 (ttt) cc_final: 0.5543 (ttt) REVERT: O 217 LEU cc_start: 0.7808 (mt) cc_final: 0.7349 (mm) REVERT: O 230 LEU cc_start: 0.8904 (tp) cc_final: 0.8389 (mm) REVERT: O 243 ARG cc_start: 0.7742 (tmm160) cc_final: 0.6039 (tpt170) REVERT: O 305 CYS cc_start: 0.6941 (m) cc_final: 0.6008 (m) REVERT: O 384 ILE cc_start: 0.8490 (tt) cc_final: 0.7684 (tp) REVERT: O 425 MET cc_start: 0.7858 (mmp) cc_final: 0.7074 (mmm) REVERT: P 53 TYR cc_start: 0.5839 (m-10) cc_final: 0.5417 (m-10) REVERT: P 75 MET cc_start: 0.8625 (mmm) cc_final: 0.8372 (mmm) REVERT: P 120 ASP cc_start: 0.7056 (t70) cc_final: 0.6635 (t70) REVERT: P 259 MET cc_start: 0.7730 (mmp) cc_final: 0.7433 (mmm) REVERT: P 266 HIS cc_start: 0.8022 (p-80) cc_final: 0.7508 (p90) REVERT: P 268 PHE cc_start: 0.6446 (m-80) cc_final: 0.4875 (m-80) REVERT: P 295 MET cc_start: 0.7916 (ppp) cc_final: 0.7540 (ppp) REVERT: P 301 MET cc_start: 0.6995 (mmp) cc_final: 0.6774 (mmp) REVERT: P 377 PHE cc_start: 0.6140 (t80) cc_final: 0.5638 (t80) REVERT: P 398 MET cc_start: 0.5622 (mmp) cc_final: 0.4978 (mmp) REVERT: P 416 MET cc_start: 0.7540 (mmm) cc_final: 0.7313 (mmm) REVERT: Q 25 CYS cc_start: 0.7815 (m) cc_final: 0.7396 (m) REVERT: Q 154 MET cc_start: 0.7152 (ppp) cc_final: 0.6495 (ppp) REVERT: Q 318 LEU cc_start: 0.6773 (mt) cc_final: 0.6444 (mt) REVERT: Q 377 MET cc_start: 0.7419 (tmm) cc_final: 0.6898 (tmm) REVERT: Q 425 MET cc_start: 0.7442 (mmp) cc_final: 0.6313 (mmm) REVERT: R 5 VAL cc_start: 0.7694 (t) cc_final: 0.7417 (t) REVERT: R 6 HIS cc_start: 0.8488 (t-90) cc_final: 0.6657 (t-90) REVERT: R 14 ASN cc_start: 0.7738 (m110) cc_final: 0.7122 (m-40) REVERT: R 24 ILE cc_start: 0.8616 (mm) cc_final: 0.8311 (mm) REVERT: R 295 MET cc_start: 0.8425 (ttt) cc_final: 0.7849 (mmm) REVERT: R 380 ASN cc_start: 0.6578 (t0) cc_final: 0.6130 (t0) outliers start: 6 outliers final: 3 residues processed: 1508 average time/residue: 0.5823 time to fit residues: 1477.7030 Evaluate side-chains 1092 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1088 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 40.0000 chunk 414 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 544 optimal weight: 50.0000 chunk 301 optimal weight: 30.0000 chunk 623 optimal weight: 40.0000 chunk 505 optimal weight: 40.0000 chunk 0 optimal weight: 60.0000 chunk 373 optimal weight: 0.7980 chunk 655 optimal weight: 40.0000 chunk 184 optimal weight: 50.0000 overall best weight: 23.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 342 GLN B 15 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 309 HIS B 433 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS C 342 GLN D 337 ASN D 339 ASN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN F 133 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 HIS F 281 GLN F 339 ASN F 380 ASN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 342 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS J 249 ASN ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 342 GLN L 11 GLN L 15 GLN ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 ASN M 31 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 342 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 372 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 197 ASN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS Q 266 HIS ** Q 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN R 15 GLN ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 GLN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 385 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 62298 Z= 0.429 Angle : 0.821 16.553 84645 Z= 0.433 Chirality : 0.048 0.291 9216 Planarity : 0.006 0.101 11043 Dihedral : 12.146 179.516 8784 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 30.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.01 (0.09), residues: 7632 helix: -0.07 (0.08), residues: 3438 sheet: 0.80 (0.14), residues: 1269 loop : -0.02 (0.12), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP R 21 HIS 0.016 0.003 HIS R 6 PHE 0.042 0.003 PHE I 351 TYR 0.045 0.003 TYR C 224 ARG 0.022 0.001 ARG N 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1276 time to evaluate : 5.884 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: A 21 TRP cc_start: 0.8532 (m100) cc_final: 0.8169 (m100) REVERT: A 24 TYR cc_start: 0.8173 (m-80) cc_final: 0.7743 (m-80) REVERT: A 132 LEU cc_start: 0.8150 (tp) cc_final: 0.7730 (tp) REVERT: A 164 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7955 (tppt) REVERT: A 224 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 302 MET cc_start: 0.8942 (tpp) cc_final: 0.8742 (tpp) REVERT: A 351 PHE cc_start: 0.7185 (m-80) cc_final: 0.6874 (m-80) REVERT: B 41 ASP cc_start: 0.6795 (p0) cc_final: 0.5952 (m-30) REVERT: B 44 LEU cc_start: 0.8840 (mt) cc_final: 0.8273 (mp) REVERT: B 116 ASP cc_start: 0.8779 (p0) cc_final: 0.8398 (p0) REVERT: B 183 GLU cc_start: 0.7604 (tt0) cc_final: 0.7295 (tt0) REVERT: B 235 MET cc_start: 0.8230 (mtt) cc_final: 0.7528 (mtt) REVERT: B 242 LEU cc_start: 0.7626 (tp) cc_final: 0.7397 (tp) REVERT: B 259 MET cc_start: 0.8113 (mmp) cc_final: 0.7245 (mmm) REVERT: B 305 CYS cc_start: 0.8446 (m) cc_final: 0.7479 (t) REVERT: B 351 VAL cc_start: 0.7566 (t) cc_final: 0.7263 (t) REVERT: B 399 PHE cc_start: 0.7609 (t80) cc_final: 0.7201 (t80) REVERT: C 217 LEU cc_start: 0.8207 (tp) cc_final: 0.7991 (tp) REVERT: C 291 ILE cc_start: 0.9229 (mt) cc_final: 0.8636 (tt) REVERT: C 360 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8414 (Cg_endo) REVERT: C 413 MET cc_start: 0.8239 (mmp) cc_final: 0.8027 (mmp) REVERT: D 14 ASN cc_start: 0.8358 (m-40) cc_final: 0.7741 (m-40) REVERT: D 302 MET cc_start: 0.6342 (mtm) cc_final: 0.5955 (mtm) REVERT: E 21 TRP cc_start: 0.8331 (m100) cc_final: 0.7076 (m100) REVERT: E 377 MET cc_start: 0.8218 (tmm) cc_final: 0.7839 (tmm) REVERT: E 378 LEU cc_start: 0.7897 (mt) cc_final: 0.7541 (mp) REVERT: E 413 MET cc_start: 0.7992 (mmp) cc_final: 0.7719 (mmp) REVERT: E 422 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6199 (ttp80) REVERT: F 14 ASN cc_start: 0.8699 (m-40) cc_final: 0.8145 (m-40) REVERT: F 120 ASP cc_start: 0.6120 (t70) cc_final: 0.5708 (t70) REVERT: F 177 VAL cc_start: 0.8219 (t) cc_final: 0.7163 (p) REVERT: F 235 MET cc_start: 0.7853 (mtt) cc_final: 0.7333 (ttm) REVERT: F 327 GLU cc_start: 0.6514 (pt0) cc_final: 0.6228 (pt0) REVERT: F 373 MET cc_start: 0.8598 (pmm) cc_final: 0.8265 (pmm) REVERT: F 395 PHE cc_start: 0.7846 (t80) cc_final: 0.6964 (t80) REVERT: F 422 GLU cc_start: 0.7053 (tp30) cc_final: 0.6398 (tp30) REVERT: G 120 ASP cc_start: 0.8129 (p0) cc_final: 0.7928 (p0) REVERT: G 132 LEU cc_start: 0.8691 (tp) cc_final: 0.8265 (tp) REVERT: G 291 ILE cc_start: 0.9365 (mt) cc_final: 0.9081 (mt) REVERT: G 378 LEU cc_start: 0.8141 (mt) cc_final: 0.7491 (mp) REVERT: H 124 LYS cc_start: 0.8850 (pptt) cc_final: 0.8113 (tttp) REVERT: H 166 MET cc_start: 0.4819 (mtp) cc_final: 0.4530 (mtm) REVERT: H 235 MET cc_start: 0.7905 (mmm) cc_final: 0.7537 (mmt) REVERT: H 286 LEU cc_start: 0.8110 (pt) cc_final: 0.6850 (pt) REVERT: H 292 THR cc_start: 0.8311 (p) cc_final: 0.7804 (p) REVERT: H 295 MET cc_start: 0.8263 (ppp) cc_final: 0.7968 (ppp) REVERT: H 332 MET cc_start: 0.7232 (mmm) cc_final: 0.6900 (mmm) REVERT: H 425 MET cc_start: 0.7405 (mmt) cc_final: 0.6873 (mmt) REVERT: I 116 ASP cc_start: 0.8507 (p0) cc_final: 0.8164 (p0) REVERT: I 132 LEU cc_start: 0.8213 (tp) cc_final: 0.7927 (tp) REVERT: I 190 THR cc_start: 0.8080 (m) cc_final: 0.5575 (m) REVERT: I 234 ILE cc_start: 0.8887 (mt) cc_final: 0.8618 (mt) REVERT: J 123 ARG cc_start: 0.7786 (ptp-170) cc_final: 0.7444 (ptp-170) REVERT: J 218 LYS cc_start: 0.4509 (mttt) cc_final: 0.3107 (mtmt) REVERT: J 227 LEU cc_start: 0.8877 (mt) cc_final: 0.8408 (mp) REVERT: J 231 VAL cc_start: 0.9384 (t) cc_final: 0.8875 (p) REVERT: J 235 MET cc_start: 0.8064 (mtp) cc_final: 0.7320 (mtm) REVERT: J 241 CYS cc_start: 0.8765 (t) cc_final: 0.8517 (t) REVERT: J 278 ARG cc_start: 0.7226 (mtm-85) cc_final: 0.6980 (tpt90) REVERT: J 302 MET cc_start: 0.7883 (tpt) cc_final: 0.7619 (tpt) REVERT: J 373 MET cc_start: 0.8483 (mmp) cc_final: 0.7799 (mtt) REVERT: K 116 ASP cc_start: 0.7456 (p0) cc_final: 0.7232 (p0) REVERT: K 117 LEU cc_start: 0.8326 (tp) cc_final: 0.8044 (tp) REVERT: K 132 LEU cc_start: 0.8582 (tp) cc_final: 0.8164 (tp) REVERT: K 163 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8334 (ptmm) REVERT: K 295 CYS cc_start: 0.8889 (m) cc_final: 0.8655 (m) REVERT: L 21 TRP cc_start: 0.8025 (m100) cc_final: 0.7672 (m100) REVERT: L 231 VAL cc_start: 0.8606 (t) cc_final: 0.8330 (p) REVERT: L 242 LEU cc_start: 0.8119 (tp) cc_final: 0.7835 (tt) REVERT: L 269 MET cc_start: 0.7910 (mtm) cc_final: 0.7632 (mtt) REVERT: L 301 MET cc_start: 0.7901 (tpt) cc_final: 0.7397 (tpt) REVERT: M 21 TRP cc_start: 0.8431 (m100) cc_final: 0.7906 (m100) REVERT: M 25 CYS cc_start: 0.8050 (t) cc_final: 0.7844 (t) REVERT: M 75 ILE cc_start: 0.8401 (mm) cc_final: 0.8000 (tt) REVERT: M 213 CYS cc_start: 0.6455 (t) cc_final: 0.6182 (t) REVERT: M 275 VAL cc_start: 0.8177 (m) cc_final: 0.7913 (m) REVERT: M 305 CYS cc_start: 0.7743 (m) cc_final: 0.7477 (m) REVERT: M 334 THR cc_start: 0.7348 (m) cc_final: 0.6370 (p) REVERT: M 398 MET cc_start: 0.6112 (mtm) cc_final: 0.5541 (mmt) REVERT: N 6 HIS cc_start: 0.7583 (t-90) cc_final: 0.6548 (t70) REVERT: N 14 ASN cc_start: 0.8171 (m-40) cc_final: 0.7421 (m-40) REVERT: N 119 LEU cc_start: 0.8131 (tp) cc_final: 0.7776 (tp) REVERT: N 129 CYS cc_start: 0.8668 (m) cc_final: 0.8384 (m) REVERT: N 231 VAL cc_start: 0.9178 (t) cc_final: 0.8816 (p) REVERT: N 268 PHE cc_start: 0.7058 (m-80) cc_final: 0.5931 (m-10) REVERT: N 295 MET cc_start: 0.8144 (ttt) cc_final: 0.7925 (tmm) REVERT: N 332 MET cc_start: 0.6737 (mmt) cc_final: 0.6419 (mmt) REVERT: O 75 ILE cc_start: 0.8078 (mm) cc_final: 0.7798 (tt) REVERT: O 154 MET cc_start: 0.7221 (tmm) cc_final: 0.6479 (tmm) REVERT: O 203 MET cc_start: 0.6553 (ttt) cc_final: 0.5868 (ttt) REVERT: O 230 LEU cc_start: 0.9114 (tp) cc_final: 0.8535 (mm) REVERT: P 53 TYR cc_start: 0.6506 (m-10) cc_final: 0.6235 (m-10) REVERT: P 86 ILE cc_start: 0.9024 (tt) cc_final: 0.8814 (tp) REVERT: P 266 HIS cc_start: 0.7863 (p-80) cc_final: 0.7541 (p-80) REVERT: P 327 GLU cc_start: 0.7344 (pt0) cc_final: 0.7055 (pt0) REVERT: P 332 MET cc_start: 0.5518 (mmt) cc_final: 0.5139 (mmt) REVERT: Q 25 CYS cc_start: 0.8097 (m) cc_final: 0.7791 (m) REVERT: Q 154 MET cc_start: 0.7462 (ppp) cc_final: 0.7246 (ppp) REVERT: Q 191 THR cc_start: 0.7832 (p) cc_final: 0.7479 (p) REVERT: Q 203 MET cc_start: 0.7398 (mtm) cc_final: 0.7033 (mtt) REVERT: Q 217 LEU cc_start: 0.8600 (mm) cc_final: 0.8035 (mm) REVERT: Q 313 MET cc_start: 0.2394 (mmt) cc_final: 0.1972 (mmt) REVERT: Q 318 LEU cc_start: 0.6700 (mt) cc_final: 0.6489 (mt) REVERT: R 5 VAL cc_start: 0.6276 (t) cc_final: 0.5966 (t) REVERT: R 119 LEU cc_start: 0.8350 (mt) cc_final: 0.8059 (mt) REVERT: R 295 MET cc_start: 0.8451 (ttt) cc_final: 0.8144 (tmm) REVERT: R 301 MET cc_start: 0.6809 (ptp) cc_final: 0.6212 (mtm) outliers start: 5 outliers final: 1 residues processed: 1280 average time/residue: 0.5724 time to fit residues: 1241.2984 Evaluate side-chains 965 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 963 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 50.0000 chunk 658 optimal weight: 3.9990 chunk 144 optimal weight: 40.0000 chunk 429 optimal weight: 30.0000 chunk 180 optimal weight: 30.0000 chunk 731 optimal weight: 30.0000 chunk 607 optimal weight: 8.9990 chunk 338 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 309 HIS B 433 GLN C 176 GLN C 206 ASN C 226 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN E 11 GLN ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS E 226 ASN E 309 HIS ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 339 ASN F 380 ASN H 6 HIS H 197 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN H 337 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 GLN L 334 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN M 380 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 HIS ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 331 GLN P 337 ASN P 339 ASN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 192 HIS R 337 ASN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 62298 Z= 0.208 Angle : 0.624 13.858 84645 Z= 0.323 Chirality : 0.044 0.183 9216 Planarity : 0.005 0.052 11043 Dihedral : 11.603 177.333 8784 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.17 % Allowed : 1.62 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.10), residues: 7632 helix: 0.29 (0.08), residues: 3483 sheet: 0.88 (0.14), residues: 1251 loop : -0.13 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP R 21 HIS 0.009 0.001 HIS E 61 PHE 0.031 0.002 PHE P 268 TYR 0.050 0.002 TYR C 224 ARG 0.009 0.001 ARG O 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1351 time to evaluate : 5.477 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: A 21 TRP cc_start: 0.8509 (m100) cc_final: 0.8186 (m100) REVERT: A 24 TYR cc_start: 0.7723 (m-80) cc_final: 0.7397 (m-80) REVERT: A 118 VAL cc_start: 0.9111 (t) cc_final: 0.8787 (t) REVERT: A 132 LEU cc_start: 0.7545 (tp) cc_final: 0.6462 (mp) REVERT: A 214 ARG cc_start: 0.7050 (ptm-80) cc_final: 0.5966 (ptm-80) REVERT: A 221 ARG cc_start: 0.7188 (mmt180) cc_final: 0.6441 (mmt180) REVERT: A 433 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 14 ASN cc_start: 0.8467 (m-40) cc_final: 0.8163 (m-40) REVERT: B 41 ASP cc_start: 0.6913 (p0) cc_final: 0.6595 (m-30) REVERT: B 44 LEU cc_start: 0.8642 (mt) cc_final: 0.8258 (mt) REVERT: B 53 TYR cc_start: 0.5782 (m-10) cc_final: 0.5351 (m-10) REVERT: B 122 VAL cc_start: 0.9334 (t) cc_final: 0.8994 (t) REVERT: B 136 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 235 MET cc_start: 0.8306 (mtt) cc_final: 0.7706 (ttt) REVERT: B 259 MET cc_start: 0.8114 (mmp) cc_final: 0.7268 (mmm) REVERT: B 268 PHE cc_start: 0.8261 (m-80) cc_final: 0.7800 (m-80) REVERT: B 281 GLN cc_start: 0.6751 (mt0) cc_final: 0.6533 (mt0) REVERT: B 302 MET cc_start: 0.6762 (mtp) cc_final: 0.6147 (mtp) REVERT: B 328 VAL cc_start: 0.8017 (t) cc_final: 0.7767 (t) REVERT: B 346 TRP cc_start: 0.5034 (m100) cc_final: 0.4758 (m100) REVERT: B 399 PHE cc_start: 0.7395 (t80) cc_final: 0.7039 (t80) REVERT: C 206 ASN cc_start: 0.7169 (OUTLIER) cc_final: 0.6918 (p0) REVERT: C 395 PHE cc_start: 0.8387 (t80) cc_final: 0.8139 (t80) REVERT: D 14 ASN cc_start: 0.8296 (m-40) cc_final: 0.7602 (m-40) REVERT: D 259 MET cc_start: 0.7042 (mmm) cc_final: 0.6715 (mmm) REVERT: D 332 MET cc_start: 0.7421 (ttt) cc_final: 0.7178 (ttt) REVERT: E 120 ASP cc_start: 0.6234 (t70) cc_final: 0.6007 (t70) REVERT: E 221 ARG cc_start: 0.7259 (mmt180) cc_final: 0.5845 (mmm160) REVERT: E 334 THR cc_start: 0.7898 (p) cc_final: 0.7676 (p) REVERT: E 377 MET cc_start: 0.8091 (tmm) cc_final: 0.7489 (tmm) REVERT: E 378 LEU cc_start: 0.8247 (mt) cc_final: 0.7640 (mt) REVERT: E 425 MET cc_start: 0.8531 (tpp) cc_final: 0.8331 (tpp) REVERT: F 5 VAL cc_start: 0.8445 (t) cc_final: 0.8143 (t) REVERT: F 14 ASN cc_start: 0.8681 (m-40) cc_final: 0.8276 (m-40) REVERT: F 24 ILE cc_start: 0.8896 (mm) cc_final: 0.8582 (mm) REVERT: F 116 ASP cc_start: 0.8582 (p0) cc_final: 0.8271 (p0) REVERT: F 120 ASP cc_start: 0.6321 (t70) cc_final: 0.5815 (t70) REVERT: F 235 MET cc_start: 0.7912 (mtt) cc_final: 0.7290 (ttm) REVERT: F 254 LYS cc_start: 0.7377 (mtpp) cc_final: 0.7083 (mttt) REVERT: F 327 GLU cc_start: 0.7151 (pt0) cc_final: 0.5967 (pt0) REVERT: F 373 MET cc_start: 0.8583 (pmm) cc_final: 0.8167 (pmm) REVERT: F 395 PHE cc_start: 0.7746 (t80) cc_final: 0.6870 (t80) REVERT: F 416 MET cc_start: 0.3555 (tpt) cc_final: 0.2903 (tpt) REVERT: F 422 GLU cc_start: 0.6944 (tp30) cc_final: 0.6096 (tp30) REVERT: G 291 ILE cc_start: 0.9322 (mt) cc_final: 0.9027 (mt) REVERT: G 378 LEU cc_start: 0.8231 (mt) cc_final: 0.7476 (mp) REVERT: H 124 LYS cc_start: 0.8817 (pptt) cc_final: 0.7361 (tttp) REVERT: H 149 MET cc_start: 0.5662 (ppp) cc_final: 0.5111 (ppp) REVERT: H 234 THR cc_start: 0.8570 (p) cc_final: 0.8181 (p) REVERT: H 235 MET cc_start: 0.7977 (mmm) cc_final: 0.7423 (mmt) REVERT: H 295 MET cc_start: 0.8436 (ppp) cc_final: 0.8019 (ppp) REVERT: H 332 MET cc_start: 0.6946 (mmm) cc_final: 0.6558 (mmm) REVERT: H 425 MET cc_start: 0.7070 (mmt) cc_final: 0.6666 (mmt) REVERT: I 103 TYR cc_start: 0.6723 (t80) cc_final: 0.6396 (t80) REVERT: I 132 LEU cc_start: 0.7853 (tp) cc_final: 0.7603 (tp) REVERT: I 190 THR cc_start: 0.7458 (m) cc_final: 0.4621 (m) REVERT: I 234 ILE cc_start: 0.8967 (mt) cc_final: 0.8716 (mt) REVERT: I 378 LEU cc_start: 0.8841 (mt) cc_final: 0.8450 (mp) REVERT: I 380 ASN cc_start: 0.6892 (t0) cc_final: 0.6684 (t0) REVERT: I 386 GLU cc_start: 0.7969 (mp0) cc_final: 0.7560 (mm-30) REVERT: I 409 VAL cc_start: 0.8167 (m) cc_final: 0.7658 (p) REVERT: J 235 MET cc_start: 0.8065 (mtp) cc_final: 0.7595 (mtm) REVERT: J 277 SER cc_start: 0.6245 (t) cc_final: 0.4550 (t) REVERT: K 116 ASP cc_start: 0.7317 (p0) cc_final: 0.6957 (p0) REVERT: K 117 LEU cc_start: 0.8380 (tp) cc_final: 0.7797 (tp) REVERT: K 121 ARG cc_start: 0.7198 (mmt180) cc_final: 0.6944 (mmt-90) REVERT: K 334 THR cc_start: 0.8196 (p) cc_final: 0.7983 (p) REVERT: K 335 ILE cc_start: 0.7511 (mm) cc_final: 0.7121 (mm) REVERT: L 21 TRP cc_start: 0.7865 (m100) cc_final: 0.7594 (m100) REVERT: L 301 MET cc_start: 0.7555 (tpt) cc_final: 0.7014 (tpt) REVERT: L 372 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8456 (mmmt) REVERT: M 21 TRP cc_start: 0.8181 (m100) cc_final: 0.7640 (m100) REVERT: M 25 CYS cc_start: 0.8037 (t) cc_final: 0.7654 (t) REVERT: M 75 ILE cc_start: 0.8442 (mm) cc_final: 0.8072 (tp) REVERT: M 80 THR cc_start: 0.7492 (p) cc_final: 0.7176 (t) REVERT: M 113 GLU cc_start: 0.8443 (mp0) cc_final: 0.8200 (mp0) REVERT: M 213 CYS cc_start: 0.6531 (t) cc_final: 0.6321 (t) REVERT: M 313 MET cc_start: 0.5726 (mmm) cc_final: 0.5453 (mmm) REVERT: M 334 THR cc_start: 0.7216 (m) cc_final: 0.6950 (m) REVERT: M 391 LEU cc_start: 0.8041 (mm) cc_final: 0.7781 (mp) REVERT: M 398 MET cc_start: 0.6154 (mtm) cc_final: 0.5481 (mmt) REVERT: N 14 ASN cc_start: 0.7946 (m-40) cc_final: 0.7147 (m110) REVERT: N 21 TRP cc_start: 0.8419 (m100) cc_final: 0.8092 (m100) REVERT: N 47 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6884 (mt-10) REVERT: N 115 VAL cc_start: 0.8845 (t) cc_final: 0.8599 (t) REVERT: N 119 LEU cc_start: 0.7821 (tp) cc_final: 0.7465 (tp) REVERT: N 122 VAL cc_start: 0.8715 (t) cc_final: 0.8448 (t) REVERT: N 129 CYS cc_start: 0.8577 (m) cc_final: 0.8294 (m) REVERT: N 268 PHE cc_start: 0.6588 (m-80) cc_final: 0.5902 (m-10) REVERT: N 288 VAL cc_start: 0.8090 (t) cc_final: 0.7867 (t) REVERT: N 413 MET cc_start: 0.7653 (mmp) cc_final: 0.7437 (mmp) REVERT: O 36 MET cc_start: 0.5533 (tmm) cc_final: 0.4853 (tmm) REVERT: O 132 LEU cc_start: 0.8713 (tp) cc_final: 0.8406 (tp) REVERT: O 154 MET cc_start: 0.7358 (tmm) cc_final: 0.7012 (tmm) REVERT: O 413 MET cc_start: 0.8141 (mmm) cc_final: 0.7352 (mmm) REVERT: P 5 VAL cc_start: 0.8094 (t) cc_final: 0.7882 (t) REVERT: P 53 TYR cc_start: 0.6856 (m-10) cc_final: 0.6311 (m-10) REVERT: P 120 ASP cc_start: 0.6912 (t70) cc_final: 0.6653 (t70) REVERT: P 166 MET cc_start: 0.6434 (tpt) cc_final: 0.5511 (tpp) REVERT: P 259 MET cc_start: 0.7660 (mmp) cc_final: 0.7431 (mmm) REVERT: P 266 HIS cc_start: 0.7443 (p-80) cc_final: 0.7238 (p90) REVERT: P 323 MET cc_start: 0.7702 (mpp) cc_final: 0.7471 (mpp) REVERT: P 327 GLU cc_start: 0.7239 (pt0) cc_final: 0.6948 (pt0) REVERT: Q 217 LEU cc_start: 0.8268 (mm) cc_final: 0.7887 (mm) REVERT: Q 318 LEU cc_start: 0.6933 (mt) cc_final: 0.6713 (mt) REVERT: Q 377 MET cc_start: 0.8171 (tmm) cc_final: 0.7951 (tmm) REVERT: Q 388 TRP cc_start: 0.6140 (m-10) cc_final: 0.5255 (m-90) REVERT: R 14 ASN cc_start: 0.7477 (m110) cc_final: 0.7153 (m110) REVERT: R 119 LEU cc_start: 0.8226 (mt) cc_final: 0.7852 (mt) REVERT: R 231 VAL cc_start: 0.9050 (t) cc_final: 0.8823 (t) REVERT: R 266 HIS cc_start: 0.7553 (p90) cc_final: 0.7279 (p90) REVERT: R 295 MET cc_start: 0.8409 (ttt) cc_final: 0.8036 (tmm) REVERT: R 297 ASP cc_start: 0.7504 (t0) cc_final: 0.6849 (t0) REVERT: R 301 MET cc_start: 0.6496 (ptp) cc_final: 0.5748 (mtm) outliers start: 11 outliers final: 4 residues processed: 1360 average time/residue: 0.5847 time to fit residues: 1337.2729 Evaluate side-chains 1018 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1013 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 0.0020 chunk 82 optimal weight: 0.9980 chunk 416 optimal weight: 7.9990 chunk 534 optimal weight: 20.0000 chunk 413 optimal weight: 0.0470 chunk 615 optimal weight: 8.9990 chunk 408 optimal weight: 9.9990 chunk 728 optimal weight: 50.0000 chunk 456 optimal weight: 6.9990 chunk 444 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 overall best weight: 3.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 256 GLN D 282 GLN D 309 HIS ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN F 350 ASN F 380 ASN ** G 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN N 339 ASN ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 372 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 ASN P 107 HIS ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 293 ASN R 37 HIS ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.8068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 62298 Z= 0.176 Angle : 0.602 10.598 84645 Z= 0.313 Chirality : 0.044 0.254 9216 Planarity : 0.005 0.055 11043 Dihedral : 11.295 177.910 8784 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 1.13 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.10), residues: 7632 helix: 0.42 (0.09), residues: 3519 sheet: 0.93 (0.14), residues: 1251 loop : -0.06 (0.12), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP F 21 HIS 0.007 0.001 HIS F 6 PHE 0.026 0.001 PHE P 268 TYR 0.028 0.001 TYR P 161 ARG 0.007 0.001 ARG O 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1355 time to evaluate : 6.383 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: A 24 TYR cc_start: 0.7622 (m-80) cc_final: 0.7376 (m-80) REVERT: A 132 LEU cc_start: 0.7734 (tp) cc_final: 0.6750 (mp) REVERT: A 214 ARG cc_start: 0.6604 (ptm-80) cc_final: 0.5872 (ptm-80) REVERT: A 221 ARG cc_start: 0.6634 (mmt180) cc_final: 0.5887 (mmt180) REVERT: A 378 LEU cc_start: 0.8071 (mp) cc_final: 0.7798 (mp) REVERT: A 433 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 5 VAL cc_start: 0.8940 (t) cc_final: 0.8466 (t) REVERT: B 14 ASN cc_start: 0.8766 (m-40) cc_final: 0.8552 (m-40) REVERT: B 41 ASP cc_start: 0.7055 (p0) cc_final: 0.6843 (m-30) REVERT: B 44 LEU cc_start: 0.8508 (mt) cc_final: 0.8113 (mt) REVERT: B 124 LYS cc_start: 0.8817 (pptt) cc_final: 0.7743 (ttpp) REVERT: B 136 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 210 TYR cc_start: 0.7089 (m-80) cc_final: 0.6730 (m-80) REVERT: B 235 MET cc_start: 0.8163 (mtt) cc_final: 0.7841 (ttt) REVERT: B 259 MET cc_start: 0.8106 (mmp) cc_final: 0.7292 (mmm) REVERT: B 268 PHE cc_start: 0.8270 (m-80) cc_final: 0.7905 (m-80) REVERT: B 377 PHE cc_start: 0.5581 (t80) cc_final: 0.5270 (t80) REVERT: C 66 VAL cc_start: 0.7366 (t) cc_final: 0.7121 (t) REVERT: C 217 LEU cc_start: 0.8176 (tp) cc_final: 0.7784 (tp) REVERT: C 395 PHE cc_start: 0.8456 (t80) cc_final: 0.8161 (t80) REVERT: D 14 ASN cc_start: 0.8155 (m-40) cc_final: 0.7414 (m-40) REVERT: D 210 TYR cc_start: 0.6557 (m-80) cc_final: 0.6330 (m-80) REVERT: D 259 MET cc_start: 0.7077 (mmm) cc_final: 0.6711 (mmm) REVERT: D 302 MET cc_start: 0.6531 (mtm) cc_final: 0.5998 (mtm) REVERT: D 323 MET cc_start: 0.7142 (mmm) cc_final: 0.6885 (mmm) REVERT: E 337 THR cc_start: 0.6678 (p) cc_final: 0.6303 (p) REVERT: E 377 MET cc_start: 0.8015 (tmm) cc_final: 0.7182 (tmm) REVERT: E 378 LEU cc_start: 0.8172 (mt) cc_final: 0.7567 (mp) REVERT: F 14 ASN cc_start: 0.8579 (m-40) cc_final: 0.8086 (m-40) REVERT: F 120 ASP cc_start: 0.6246 (t70) cc_final: 0.5750 (t70) REVERT: F 227 LEU cc_start: 0.9035 (mt) cc_final: 0.8470 (mt) REVERT: F 235 MET cc_start: 0.7717 (mtt) cc_final: 0.7516 (ttm) REVERT: F 327 GLU cc_start: 0.6938 (pt0) cc_final: 0.6557 (pt0) REVERT: F 328 VAL cc_start: 0.8749 (t) cc_final: 0.8482 (t) REVERT: F 373 MET cc_start: 0.8833 (pmm) cc_final: 0.8302 (pmm) REVERT: F 395 PHE cc_start: 0.7756 (t80) cc_final: 0.7534 (t80) REVERT: G 244 PHE cc_start: 0.5070 (t80) cc_final: 0.4723 (t80) REVERT: G 378 LEU cc_start: 0.8059 (mt) cc_final: 0.7328 (mp) REVERT: H 124 LYS cc_start: 0.8656 (pptt) cc_final: 0.7866 (ptmt) REVERT: H 149 MET cc_start: 0.5369 (ppp) cc_final: 0.5068 (ppp) REVERT: H 259 MET cc_start: 0.7500 (mmm) cc_final: 0.7214 (mmm) REVERT: H 292 THR cc_start: 0.8501 (p) cc_final: 0.7589 (p) REVERT: H 295 MET cc_start: 0.8404 (ppp) cc_final: 0.7980 (ppp) REVERT: H 332 MET cc_start: 0.6774 (mmm) cc_final: 0.6489 (mmm) REVERT: H 425 MET cc_start: 0.6891 (mmt) cc_final: 0.6635 (mmt) REVERT: I 132 LEU cc_start: 0.7533 (tp) cc_final: 0.7315 (tp) REVERT: I 335 ILE cc_start: 0.7885 (mm) cc_final: 0.7671 (mm) REVERT: I 377 MET cc_start: 0.7916 (tmm) cc_final: 0.7560 (tmm) REVERT: I 378 LEU cc_start: 0.8951 (mt) cc_final: 0.8659 (mp) REVERT: I 380 ASN cc_start: 0.6604 (t0) cc_final: 0.6264 (t0) REVERT: I 409 VAL cc_start: 0.8140 (m) cc_final: 0.7725 (p) REVERT: J 218 LYS cc_start: 0.4358 (mttt) cc_final: 0.3880 (mtmt) REVERT: J 235 MET cc_start: 0.7717 (mtp) cc_final: 0.7131 (mtm) REVERT: J 259 MET cc_start: 0.7712 (tpt) cc_final: 0.6907 (tpp) REVERT: J 277 SER cc_start: 0.6559 (t) cc_final: 0.5761 (t) REVERT: K 14 VAL cc_start: 0.8883 (m) cc_final: 0.8632 (p) REVERT: K 117 LEU cc_start: 0.8408 (tp) cc_final: 0.8171 (tp) REVERT: K 209 ILE cc_start: 0.8872 (mp) cc_final: 0.8222 (mp) REVERT: K 295 CYS cc_start: 0.8936 (m) cc_final: 0.8646 (m) REVERT: K 335 ILE cc_start: 0.7563 (mm) cc_final: 0.6959 (mm) REVERT: K 377 MET cc_start: 0.7559 (ttt) cc_final: 0.6652 (tmm) REVERT: K 378 LEU cc_start: 0.8263 (mp) cc_final: 0.7787 (mp) REVERT: L 19 LYS cc_start: 0.8805 (mmpt) cc_final: 0.8569 (mmmm) REVERT: L 21 TRP cc_start: 0.7724 (m100) cc_final: 0.7518 (m100) REVERT: L 264 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6646 (mmt90) REVERT: M 21 TRP cc_start: 0.7900 (m100) cc_final: 0.7518 (m100) REVERT: M 75 ILE cc_start: 0.8317 (mm) cc_final: 0.7884 (tt) REVERT: M 80 THR cc_start: 0.7323 (p) cc_final: 0.7038 (t) REVERT: M 113 GLU cc_start: 0.8362 (mp0) cc_final: 0.8152 (mp0) REVERT: M 295 CYS cc_start: 0.8456 (m) cc_final: 0.8036 (m) REVERT: M 368 LEU cc_start: 0.7999 (mp) cc_final: 0.7673 (mt) REVERT: M 398 MET cc_start: 0.6048 (mtm) cc_final: 0.5440 (mmt) REVERT: N 14 ASN cc_start: 0.7859 (m-40) cc_final: 0.6872 (m110) REVERT: N 47 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7122 (mt-10) REVERT: N 115 VAL cc_start: 0.8856 (t) cc_final: 0.8625 (t) REVERT: N 119 LEU cc_start: 0.7742 (tp) cc_final: 0.7442 (tp) REVERT: N 124 LYS cc_start: 0.9140 (pptt) cc_final: 0.8611 (pptt) REVERT: N 129 CYS cc_start: 0.8514 (m) cc_final: 0.8240 (m) REVERT: N 268 PHE cc_start: 0.6305 (m-80) cc_final: 0.5410 (m-80) REVERT: N 334 ASN cc_start: 0.6885 (t0) cc_final: 0.6286 (t0) REVERT: N 413 MET cc_start: 0.7678 (mmp) cc_final: 0.7434 (mmp) REVERT: O 36 MET cc_start: 0.4937 (tmm) cc_final: 0.4695 (tmm) REVERT: O 132 LEU cc_start: 0.8756 (tp) cc_final: 0.8490 (tp) REVERT: O 169 PHE cc_start: 0.5863 (m-10) cc_final: 0.5466 (m-10) REVERT: O 229 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7862 (mtt90) REVERT: O 413 MET cc_start: 0.8031 (mmm) cc_final: 0.7244 (mmm) REVERT: P 75 MET cc_start: 0.8508 (mmp) cc_final: 0.8229 (mmp) REVERT: P 115 VAL cc_start: 0.8618 (t) cc_final: 0.8352 (t) REVERT: P 166 MET cc_start: 0.6765 (tpt) cc_final: 0.6150 (tpp) REVERT: P 295 MET cc_start: 0.7692 (ppp) cc_final: 0.7271 (ppp) REVERT: P 323 MET cc_start: 0.7572 (mpp) cc_final: 0.7367 (mpp) REVERT: P 332 MET cc_start: 0.5530 (mmt) cc_final: 0.4987 (mmt) REVERT: P 398 MET cc_start: 0.5834 (mmp) cc_final: 0.5463 (mmp) REVERT: Q 191 THR cc_start: 0.7498 (p) cc_final: 0.7291 (p) REVERT: Q 318 LEU cc_start: 0.6919 (mt) cc_final: 0.6676 (mt) REVERT: Q 388 TRP cc_start: 0.5785 (m-10) cc_final: 0.5037 (m-10) REVERT: R 14 ASN cc_start: 0.7509 (m110) cc_final: 0.7217 (m-40) REVERT: R 47 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7258 (mt-10) REVERT: R 119 LEU cc_start: 0.8028 (mt) cc_final: 0.7717 (mt) REVERT: R 231 VAL cc_start: 0.8953 (t) cc_final: 0.8752 (t) REVERT: R 301 MET cc_start: 0.6460 (ptp) cc_final: 0.5586 (mtm) outliers start: 4 outliers final: 1 residues processed: 1358 average time/residue: 0.5703 time to fit residues: 1307.7553 Evaluate side-chains 1013 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1012 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 50.0000 chunk 290 optimal weight: 5.9990 chunk 435 optimal weight: 6.9990 chunk 219 optimal weight: 0.0370 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 40.0000 chunk 463 optimal weight: 30.0000 chunk 496 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 572 optimal weight: 50.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 281 GLN C 176 GLN C 283 HIS C 309 HIS ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN F 380 ASN G 300 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS L 331 GLN ** L 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.8305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62298 Z= 0.181 Angle : 0.604 10.203 84645 Z= 0.312 Chirality : 0.045 0.286 9216 Planarity : 0.005 0.062 11043 Dihedral : 11.126 179.288 8784 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 7632 helix: 0.55 (0.09), residues: 3429 sheet: 0.93 (0.14), residues: 1251 loop : -0.11 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP K 21 HIS 0.009 0.001 HIS B 28 PHE 0.031 0.001 PHE L 296 TYR 0.026 0.001 TYR P 161 ARG 0.010 0.001 ARG L 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1319 time to evaluate : 5.474 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: A 66 VAL cc_start: 0.7426 (t) cc_final: 0.7136 (t) REVERT: A 132 LEU cc_start: 0.7835 (tp) cc_final: 0.6780 (mp) REVERT: A 221 ARG cc_start: 0.6783 (mmt180) cc_final: 0.5913 (mmt180) REVERT: A 243 ARG cc_start: 0.6362 (tmt170) cc_final: 0.6096 (ttt-90) REVERT: A 244 PHE cc_start: 0.4072 (m-80) cc_final: 0.3104 (m-80) REVERT: A 397 LEU cc_start: 0.7447 (mm) cc_final: 0.7155 (mm) REVERT: A 433 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 5 VAL cc_start: 0.8774 (t) cc_final: 0.8568 (t) REVERT: B 14 ASN cc_start: 0.8702 (m-40) cc_final: 0.8312 (m-40) REVERT: B 41 ASP cc_start: 0.7178 (p0) cc_final: 0.6886 (m-30) REVERT: B 44 LEU cc_start: 0.8496 (mt) cc_final: 0.8160 (mt) REVERT: B 53 TYR cc_start: 0.5212 (m-80) cc_final: 0.4958 (m-80) REVERT: B 124 LYS cc_start: 0.8685 (pptt) cc_final: 0.7728 (ttpp) REVERT: B 136 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 210 TYR cc_start: 0.7177 (m-80) cc_final: 0.6495 (m-80) REVERT: B 235 MET cc_start: 0.8141 (mtt) cc_final: 0.7826 (ttt) REVERT: B 268 PHE cc_start: 0.8507 (m-10) cc_final: 0.8163 (m-80) REVERT: B 327 GLU cc_start: 0.6168 (pt0) cc_final: 0.5807 (pt0) REVERT: C 217 LEU cc_start: 0.8216 (tp) cc_final: 0.7776 (tp) REVERT: C 395 PHE cc_start: 0.8402 (t80) cc_final: 0.8018 (t80) REVERT: C 425 MET cc_start: 0.7959 (tpp) cc_final: 0.7554 (tpp) REVERT: D 14 ASN cc_start: 0.8067 (m-40) cc_final: 0.7470 (m-40) REVERT: D 210 TYR cc_start: 0.6390 (m-80) cc_final: 0.6116 (m-80) REVERT: D 235 MET cc_start: 0.7314 (ttt) cc_final: 0.6798 (ttt) REVERT: D 302 MET cc_start: 0.6184 (mtm) cc_final: 0.5953 (mtm) REVERT: D 306 ASP cc_start: 0.5907 (t0) cc_final: 0.5358 (t0) REVERT: D 425 MET cc_start: 0.6286 (tpt) cc_final: 0.5972 (mmm) REVERT: E 377 MET cc_start: 0.7806 (tmm) cc_final: 0.7304 (tmm) REVERT: E 378 LEU cc_start: 0.8053 (mt) cc_final: 0.7398 (mt) REVERT: E 425 MET cc_start: 0.8292 (tpt) cc_final: 0.7785 (tpp) REVERT: F 14 ASN cc_start: 0.8576 (m-40) cc_final: 0.8133 (m-40) REVERT: F 66 ILE cc_start: 0.8601 (mm) cc_final: 0.8360 (mm) REVERT: F 120 ASP cc_start: 0.5639 (t70) cc_final: 0.5372 (t70) REVERT: F 351 VAL cc_start: 0.8600 (t) cc_final: 0.8341 (t) REVERT: F 373 MET cc_start: 0.8667 (pmm) cc_final: 0.8183 (pmm) REVERT: F 395 PHE cc_start: 0.7822 (t80) cc_final: 0.7544 (t80) REVERT: G 317 LEU cc_start: 0.7602 (mt) cc_final: 0.7216 (mt) REVERT: G 378 LEU cc_start: 0.7970 (mt) cc_final: 0.7223 (mp) REVERT: H 124 LYS cc_start: 0.8788 (pptt) cc_final: 0.7793 (ptmt) REVERT: H 149 MET cc_start: 0.5532 (ppp) cc_final: 0.5186 (ppp) REVERT: H 235 MET cc_start: 0.7545 (mmt) cc_final: 0.7118 (mmt) REVERT: H 259 MET cc_start: 0.7488 (mmm) cc_final: 0.7223 (mmm) REVERT: H 292 THR cc_start: 0.8525 (p) cc_final: 0.7889 (p) REVERT: H 295 MET cc_start: 0.8173 (ppp) cc_final: 0.7704 (ppp) REVERT: H 297 ASP cc_start: 0.7839 (t0) cc_final: 0.7565 (t0) REVERT: H 332 MET cc_start: 0.6954 (mmm) cc_final: 0.6595 (mmm) REVERT: I 75 ILE cc_start: 0.6716 (mm) cc_final: 0.6302 (tt) REVERT: I 322 ASP cc_start: 0.6993 (t0) cc_final: 0.6419 (p0) REVERT: I 378 LEU cc_start: 0.8908 (mt) cc_final: 0.8404 (mp) REVERT: I 380 ASN cc_start: 0.6509 (t0) cc_final: 0.6169 (t0) REVERT: I 409 VAL cc_start: 0.8217 (m) cc_final: 0.7788 (p) REVERT: J 218 LYS cc_start: 0.4306 (mttt) cc_final: 0.3860 (mtmt) REVERT: J 235 MET cc_start: 0.8137 (mtp) cc_final: 0.7366 (mtm) REVERT: J 259 MET cc_start: 0.7753 (tpt) cc_final: 0.6413 (tpp) REVERT: J 277 SER cc_start: 0.6709 (t) cc_final: 0.5710 (t) REVERT: J 314 THR cc_start: 0.8525 (p) cc_final: 0.7188 (p) REVERT: K 116 ASP cc_start: 0.7543 (p0) cc_final: 0.7086 (p0) REVERT: K 122 ILE cc_start: 0.7856 (pt) cc_final: 0.7445 (pt) REVERT: K 295 CYS cc_start: 0.8937 (m) cc_final: 0.8523 (m) REVERT: K 313 MET cc_start: 0.8138 (mpp) cc_final: 0.7700 (mpp) REVERT: K 377 MET cc_start: 0.7618 (ttt) cc_final: 0.6754 (tmm) REVERT: K 378 LEU cc_start: 0.8167 (mp) cc_final: 0.7752 (mp) REVERT: L 19 LYS cc_start: 0.8820 (mmpt) cc_final: 0.8585 (mmmm) REVERT: L 116 ASP cc_start: 0.7612 (m-30) cc_final: 0.7309 (m-30) REVERT: L 235 MET cc_start: 0.6023 (mtt) cc_final: 0.5769 (mtt) REVERT: L 301 MET cc_start: 0.7114 (tpt) cc_final: 0.6806 (tpp) REVERT: M 21 TRP cc_start: 0.8224 (m100) cc_final: 0.7606 (m100) REVERT: M 75 ILE cc_start: 0.8399 (mm) cc_final: 0.7874 (tt) REVERT: M 196 GLU cc_start: 0.7288 (tp30) cc_final: 0.6705 (tp30) REVERT: M 213 CYS cc_start: 0.6455 (t) cc_final: 0.6182 (t) REVERT: M 295 CYS cc_start: 0.8526 (m) cc_final: 0.8163 (m) REVERT: M 368 LEU cc_start: 0.8125 (mp) cc_final: 0.7707 (mt) REVERT: M 378 LEU cc_start: 0.8221 (mp) cc_final: 0.7844 (mp) REVERT: M 391 LEU cc_start: 0.7769 (mp) cc_final: 0.7515 (mp) REVERT: M 398 MET cc_start: 0.5771 (mtm) cc_final: 0.5263 (mmt) REVERT: N 47 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7105 (mt-10) REVERT: N 50 ASN cc_start: 0.8491 (p0) cc_final: 0.8192 (p0) REVERT: N 115 VAL cc_start: 0.8891 (t) cc_final: 0.8630 (t) REVERT: N 119 LEU cc_start: 0.7725 (tp) cc_final: 0.7338 (tp) REVERT: N 124 LYS cc_start: 0.9264 (pptt) cc_final: 0.8700 (pptt) REVERT: N 259 MET cc_start: 0.7509 (mmp) cc_final: 0.7270 (mmm) REVERT: N 268 PHE cc_start: 0.6326 (m-80) cc_final: 0.5549 (m-80) REVERT: N 413 MET cc_start: 0.7722 (mmp) cc_final: 0.7516 (mmp) REVERT: O 132 LEU cc_start: 0.8745 (tp) cc_final: 0.8528 (tp) REVERT: O 229 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7740 (mtt90) REVERT: P 5 VAL cc_start: 0.8286 (t) cc_final: 0.8084 (t) REVERT: P 115 VAL cc_start: 0.8602 (t) cc_final: 0.8364 (t) REVERT: P 166 MET cc_start: 0.6784 (tpt) cc_final: 0.6384 (tpp) REVERT: P 268 PHE cc_start: 0.5814 (m-80) cc_final: 0.5611 (m-80) REVERT: P 398 MET cc_start: 0.5884 (mmp) cc_final: 0.5538 (mmp) REVERT: P 415 GLU cc_start: 0.6862 (pm20) cc_final: 0.6635 (pm20) REVERT: P 422 GLU cc_start: 0.5924 (tp30) cc_final: 0.5211 (tp30) REVERT: Q 133 GLN cc_start: 0.5457 (tm-30) cc_final: 0.5146 (tm-30) REVERT: Q 217 LEU cc_start: 0.7631 (mm) cc_final: 0.7246 (mm) REVERT: Q 388 TRP cc_start: 0.6011 (m-10) cc_final: 0.5717 (m-10) REVERT: R 14 ASN cc_start: 0.7744 (m110) cc_final: 0.7263 (m-40) REVERT: R 47 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7185 (mt-10) REVERT: R 259 MET cc_start: 0.7716 (mmm) cc_final: 0.7098 (mmm) REVERT: R 301 MET cc_start: 0.6419 (ptp) cc_final: 0.5431 (mtm) outliers start: 3 outliers final: 0 residues processed: 1321 average time/residue: 0.5765 time to fit residues: 1283.8535 Evaluate side-chains 1002 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1002 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 0.4980 chunk 698 optimal weight: 8.9990 chunk 636 optimal weight: 40.0000 chunk 679 optimal weight: 0.6980 chunk 697 optimal weight: 0.8980 chunk 408 optimal weight: 20.0000 chunk 295 optimal weight: 40.0000 chunk 533 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 613 optimal weight: 0.6980 chunk 642 optimal weight: 8.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 11 GLN ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN F 350 ASN F 380 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS L 334 ASN ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 91 GLN ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 309 HIS ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 ASN ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 HIS ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.8522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 62298 Z= 0.163 Angle : 0.606 11.067 84645 Z= 0.311 Chirality : 0.045 0.222 9216 Planarity : 0.005 0.058 11043 Dihedral : 10.914 178.685 8784 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.03 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7632 helix: 0.51 (0.09), residues: 3510 sheet: 0.94 (0.14), residues: 1242 loop : -0.15 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP O 21 HIS 0.007 0.001 HIS R 6 PHE 0.033 0.001 PHE E 149 TYR 0.028 0.001 TYR P 432 ARG 0.009 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1346 time to evaluate : 5.852 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: A 21 TRP cc_start: 0.7790 (m100) cc_final: 0.7473 (m100) REVERT: A 75 ILE cc_start: 0.8721 (mt) cc_final: 0.7785 (tt) REVERT: A 132 LEU cc_start: 0.7686 (tp) cc_final: 0.7307 (mp) REVERT: A 210 TYR cc_start: 0.8406 (m-80) cc_final: 0.8164 (m-80) REVERT: A 221 ARG cc_start: 0.7265 (mmt180) cc_final: 0.6454 (mmt180) REVERT: A 243 ARG cc_start: 0.6152 (tmt170) cc_final: 0.5717 (ttt-90) REVERT: A 244 PHE cc_start: 0.4218 (m-80) cc_final: 0.3503 (m-80) REVERT: A 351 PHE cc_start: 0.6147 (m-80) cc_final: 0.5902 (m-80) REVERT: A 397 LEU cc_start: 0.7575 (mm) cc_final: 0.6984 (tp) REVERT: B 14 ASN cc_start: 0.8384 (m-40) cc_final: 0.8107 (m-40) REVERT: B 16 ILE cc_start: 0.7880 (mt) cc_final: 0.7669 (mt) REVERT: B 41 ASP cc_start: 0.7067 (p0) cc_final: 0.6863 (m-30) REVERT: B 44 LEU cc_start: 0.8323 (mt) cc_final: 0.8031 (mt) REVERT: B 53 TYR cc_start: 0.5071 (m-80) cc_final: 0.4854 (m-80) REVERT: B 116 ASP cc_start: 0.8447 (p0) cc_final: 0.8196 (p0) REVERT: B 124 LYS cc_start: 0.8593 (pptt) cc_final: 0.7654 (ttpp) REVERT: B 235 MET cc_start: 0.8133 (mtt) cc_final: 0.7822 (ttm) REVERT: B 268 PHE cc_start: 0.8901 (m-10) cc_final: 0.8457 (m-10) REVERT: B 291 LEU cc_start: 0.8944 (mm) cc_final: 0.8660 (tp) REVERT: B 327 GLU cc_start: 0.6325 (pt0) cc_final: 0.5866 (pt0) REVERT: C 66 VAL cc_start: 0.7379 (t) cc_final: 0.7067 (t) REVERT: C 176 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6809 (mm-40) REVERT: C 302 MET cc_start: 0.8880 (tpp) cc_final: 0.8646 (tpt) REVERT: C 395 PHE cc_start: 0.8306 (t80) cc_final: 0.7761 (t80) REVERT: C 425 MET cc_start: 0.8105 (tpp) cc_final: 0.7641 (tpp) REVERT: D 14 ASN cc_start: 0.7969 (m-40) cc_final: 0.7546 (m-40) REVERT: D 16 ILE cc_start: 0.8420 (mt) cc_final: 0.8216 (mt) REVERT: D 44 LEU cc_start: 0.8522 (mt) cc_final: 0.8165 (mt) REVERT: D 55 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5937 (tm-30) REVERT: D 210 TYR cc_start: 0.6115 (m-80) cc_final: 0.5886 (m-80) REVERT: E 377 MET cc_start: 0.7717 (tmm) cc_final: 0.7044 (tmm) REVERT: E 378 LEU cc_start: 0.7899 (mt) cc_final: 0.7302 (mp) REVERT: E 397 LEU cc_start: 0.7120 (mm) cc_final: 0.6632 (mm) REVERT: E 425 MET cc_start: 0.8184 (tpt) cc_final: 0.7797 (tpp) REVERT: F 14 ASN cc_start: 0.8513 (m-40) cc_final: 0.8168 (m-40) REVERT: F 120 ASP cc_start: 0.6053 (t70) cc_final: 0.5438 (t70) REVERT: F 235 MET cc_start: 0.7295 (mtt) cc_final: 0.6719 (ttm) REVERT: F 291 LEU cc_start: 0.9105 (mm) cc_final: 0.8900 (tp) REVERT: F 327 GLU cc_start: 0.7343 (pt0) cc_final: 0.7136 (pt0) REVERT: F 328 VAL cc_start: 0.8814 (t) cc_final: 0.8398 (p) REVERT: F 373 MET cc_start: 0.8839 (pmm) cc_final: 0.8282 (pmm) REVERT: F 395 PHE cc_start: 0.7674 (t80) cc_final: 0.7353 (t80) REVERT: G 295 CYS cc_start: 0.8458 (m) cc_final: 0.8157 (m) REVERT: G 317 LEU cc_start: 0.7541 (mt) cc_final: 0.7011 (mt) REVERT: G 378 LEU cc_start: 0.7853 (mt) cc_final: 0.7231 (mp) REVERT: H 124 LYS cc_start: 0.8705 (pptt) cc_final: 0.7702 (ptmt) REVERT: H 149 MET cc_start: 0.5277 (ppp) cc_final: 0.4998 (ppp) REVERT: H 235 MET cc_start: 0.7487 (mmt) cc_final: 0.7071 (mmt) REVERT: H 292 THR cc_start: 0.8506 (p) cc_final: 0.7925 (p) REVERT: H 295 MET cc_start: 0.8291 (ppp) cc_final: 0.7912 (ppp) REVERT: H 333 LEU cc_start: 0.8239 (tp) cc_final: 0.7713 (tt) REVERT: I 75 ILE cc_start: 0.6749 (mm) cc_final: 0.6321 (tt) REVERT: I 322 ASP cc_start: 0.7036 (t0) cc_final: 0.6732 (p0) REVERT: I 378 LEU cc_start: 0.8781 (mt) cc_final: 0.8172 (mp) REVERT: I 409 VAL cc_start: 0.8231 (m) cc_final: 0.7783 (p) REVERT: J 31 ASP cc_start: 0.7290 (p0) cc_final: 0.7085 (p0) REVERT: J 125 GLU cc_start: 0.5594 (tp30) cc_final: 0.5207 (tp30) REVERT: J 218 LYS cc_start: 0.4218 (mttt) cc_final: 0.3776 (UNCLASSIFIED) REVERT: J 235 MET cc_start: 0.8123 (mtp) cc_final: 0.7541 (mtm) REVERT: J 259 MET cc_start: 0.7381 (tpt) cc_final: 0.6433 (tpp) REVERT: J 314 THR cc_start: 0.8606 (p) cc_final: 0.7281 (p) REVERT: K 116 ASP cc_start: 0.7421 (p0) cc_final: 0.6910 (p0) REVERT: K 122 ILE cc_start: 0.7821 (pt) cc_final: 0.7068 (pt) REVERT: K 295 CYS cc_start: 0.8963 (m) cc_final: 0.8552 (m) REVERT: K 377 MET cc_start: 0.7497 (ttt) cc_final: 0.7017 (tmm) REVERT: K 378 LEU cc_start: 0.8089 (mp) cc_final: 0.7673 (mp) REVERT: K 380 ASN cc_start: 0.6979 (t0) cc_final: 0.5630 (t0) REVERT: L 19 LYS cc_start: 0.8865 (mmpt) cc_final: 0.8379 (mmmm) REVERT: L 116 ASP cc_start: 0.7371 (m-30) cc_final: 0.7062 (m-30) REVERT: L 125 GLU cc_start: 0.5926 (tp30) cc_final: 0.5691 (tp30) REVERT: L 231 VAL cc_start: 0.8521 (t) cc_final: 0.8289 (t) REVERT: L 432 TYR cc_start: 0.5763 (m-80) cc_final: 0.5428 (m-80) REVERT: M 21 TRP cc_start: 0.8017 (m100) cc_final: 0.7737 (m100) REVERT: M 75 ILE cc_start: 0.8198 (mm) cc_final: 0.7749 (tt) REVERT: M 196 GLU cc_start: 0.7314 (tp30) cc_final: 0.6861 (tp30) REVERT: M 295 CYS cc_start: 0.8633 (m) cc_final: 0.8027 (m) REVERT: M 305 CYS cc_start: 0.7490 (m) cc_final: 0.7137 (m) REVERT: M 391 LEU cc_start: 0.7712 (mp) cc_final: 0.7465 (mp) REVERT: M 398 MET cc_start: 0.5785 (mtm) cc_final: 0.5236 (mmt) REVERT: N 115 VAL cc_start: 0.8841 (t) cc_final: 0.8621 (t) REVERT: N 119 LEU cc_start: 0.7650 (tp) cc_final: 0.7278 (tp) REVERT: N 124 LYS cc_start: 0.9289 (pptt) cc_final: 0.8692 (pptt) REVERT: N 129 CYS cc_start: 0.8363 (m) cc_final: 0.8163 (m) REVERT: N 259 MET cc_start: 0.7408 (mmp) cc_final: 0.6906 (mmm) REVERT: N 265 LEU cc_start: 0.7469 (mp) cc_final: 0.7178 (tt) REVERT: N 268 PHE cc_start: 0.6257 (m-80) cc_final: 0.5464 (m-80) REVERT: N 269 MET cc_start: 0.6291 (mtm) cc_final: 0.5795 (mtm) REVERT: N 398 MET cc_start: 0.5714 (mmm) cc_final: 0.5383 (mmp) REVERT: N 413 MET cc_start: 0.7685 (mmp) cc_final: 0.7479 (mmp) REVERT: N 416 MET cc_start: 0.6694 (ptm) cc_final: 0.5769 (tpt) REVERT: N 428 LEU cc_start: 0.7562 (tt) cc_final: 0.7108 (mt) REVERT: O 191 THR cc_start: 0.7621 (p) cc_final: 0.7328 (p) REVERT: O 213 CYS cc_start: 0.6450 (t) cc_final: 0.6212 (t) REVERT: P 5 VAL cc_start: 0.8239 (t) cc_final: 0.8037 (t) REVERT: P 115 VAL cc_start: 0.8563 (t) cc_final: 0.8313 (t) REVERT: P 166 MET cc_start: 0.6950 (tpt) cc_final: 0.6497 (tpp) REVERT: P 259 MET cc_start: 0.7053 (mmp) cc_final: 0.6818 (mmm) REVERT: P 398 MET cc_start: 0.5651 (mmp) cc_final: 0.5180 (mmp) REVERT: P 422 GLU cc_start: 0.5740 (tp30) cc_final: 0.5157 (tp30) REVERT: Q 16 ILE cc_start: 0.8450 (mt) cc_final: 0.7991 (tp) REVERT: Q 133 GLN cc_start: 0.5421 (tm-30) cc_final: 0.4846 (tm-30) REVERT: Q 154 MET cc_start: 0.7005 (tmm) cc_final: 0.6611 (tmm) REVERT: Q 425 MET cc_start: 0.7319 (mmp) cc_final: 0.6175 (mmm) REVERT: R 5 VAL cc_start: 0.7029 (t) cc_final: 0.6799 (t) REVERT: R 14 ASN cc_start: 0.8199 (m110) cc_final: 0.7866 (m-40) REVERT: R 47 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7250 (mt-10) REVERT: R 119 LEU cc_start: 0.7844 (mt) cc_final: 0.7593 (mt) REVERT: R 301 MET cc_start: 0.6246 (ptp) cc_final: 0.5203 (mtm) REVERT: R 332 MET cc_start: 0.6440 (ttt) cc_final: 0.5397 (tmm) outliers start: 2 outliers final: 0 residues processed: 1347 average time/residue: 0.5853 time to fit residues: 1330.2989 Evaluate side-chains 1016 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1016 time to evaluate : 5.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 50.0000 chunk 445 optimal weight: 8.9990 chunk 718 optimal weight: 50.0000 chunk 438 optimal weight: 30.0000 chunk 340 optimal weight: 40.0000 chunk 499 optimal weight: 30.0000 chunk 753 optimal weight: 5.9990 chunk 693 optimal weight: 10.0000 chunk 599 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 chunk 463 optimal weight: 6.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 331 GLN ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN O 372 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 281 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62298 Z= 0.209 Angle : 0.632 13.878 84645 Z= 0.328 Chirality : 0.045 0.310 9216 Planarity : 0.005 0.062 11043 Dihedral : 10.976 179.959 8784 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.02 % Allowed : 0.23 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.46 (0.10), residues: 7632 helix: 0.60 (0.09), residues: 3375 sheet: 0.66 (0.14), residues: 1287 loop : -0.01 (0.12), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP O 407 HIS 0.007 0.001 HIS O 309 PHE 0.028 0.002 PHE B 377 TYR 0.034 0.002 TYR C 224 ARG 0.010 0.001 ARG O 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1257 time to evaluate : 6.115 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: A 24 TYR cc_start: 0.6921 (m-80) cc_final: 0.6507 (m-80) REVERT: A 132 LEU cc_start: 0.7894 (tp) cc_final: 0.7007 (mp) REVERT: A 221 ARG cc_start: 0.7486 (mmt180) cc_final: 0.6655 (mmt180) REVERT: A 397 LEU cc_start: 0.7664 (mm) cc_final: 0.7185 (pp) REVERT: A 433 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7019 (tm-30) REVERT: B 5 VAL cc_start: 0.8919 (t) cc_final: 0.8702 (t) REVERT: B 41 ASP cc_start: 0.7055 (p0) cc_final: 0.6701 (m-30) REVERT: B 53 TYR cc_start: 0.5550 (m-80) cc_final: 0.5189 (m-80) REVERT: B 116 ASP cc_start: 0.8496 (p0) cc_final: 0.8233 (p0) REVERT: B 235 MET cc_start: 0.8265 (mtt) cc_final: 0.7977 (ttt) REVERT: B 259 MET cc_start: 0.7920 (mmp) cc_final: 0.7151 (mmm) REVERT: B 265 LEU cc_start: 0.8069 (mt) cc_final: 0.7831 (mp) REVERT: B 268 PHE cc_start: 0.8306 (m-10) cc_final: 0.7791 (m-80) REVERT: B 276 THR cc_start: 0.6902 (p) cc_final: 0.6539 (p) REVERT: B 291 LEU cc_start: 0.8898 (mm) cc_final: 0.8678 (mm) REVERT: B 302 MET cc_start: 0.7074 (mtp) cc_final: 0.6193 (mtp) REVERT: B 325 MET cc_start: 0.7427 (pmm) cc_final: 0.7179 (pmm) REVERT: B 327 GLU cc_start: 0.6355 (pt0) cc_final: 0.5793 (pt0) REVERT: C 176 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7741 (mm-40) REVERT: C 302 MET cc_start: 0.8850 (tpp) cc_final: 0.8644 (tpt) REVERT: C 318 LEU cc_start: 0.8218 (mm) cc_final: 0.7940 (mm) REVERT: C 395 PHE cc_start: 0.8390 (t80) cc_final: 0.7970 (t80) REVERT: C 425 MET cc_start: 0.8096 (tpp) cc_final: 0.7595 (tpp) REVERT: D 14 ASN cc_start: 0.8241 (m-40) cc_final: 0.7652 (m-40) REVERT: D 55 GLU cc_start: 0.6346 (tm-30) cc_final: 0.6094 (tm-30) REVERT: D 210 TYR cc_start: 0.6152 (m-80) cc_final: 0.5901 (m-80) REVERT: D 275 LEU cc_start: 0.8301 (tp) cc_final: 0.8100 (tt) REVERT: D 398 MET cc_start: 0.6009 (mpp) cc_final: 0.5146 (mpp) REVERT: E 221 ARG cc_start: 0.6801 (mmt180) cc_final: 0.6101 (mmm160) REVERT: E 280 LYS cc_start: 0.3580 (tptt) cc_final: 0.2890 (tptt) REVERT: E 377 MET cc_start: 0.7740 (tmm) cc_final: 0.7201 (tmm) REVERT: E 378 LEU cc_start: 0.8043 (mt) cc_final: 0.7455 (mt) REVERT: E 433 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7171 (tm-30) REVERT: F 14 ASN cc_start: 0.8610 (m-40) cc_final: 0.8103 (m-40) REVERT: F 79 ARG cc_start: 0.8375 (ptp-170) cc_final: 0.8137 (ptp-170) REVERT: F 120 ASP cc_start: 0.5423 (t70) cc_final: 0.5075 (t70) REVERT: F 235 MET cc_start: 0.7142 (mtt) cc_final: 0.6847 (ttt) REVERT: F 275 LEU cc_start: 0.7388 (pt) cc_final: 0.7049 (tp) REVERT: F 327 GLU cc_start: 0.7358 (pt0) cc_final: 0.6847 (pt0) REVERT: F 328 VAL cc_start: 0.8733 (t) cc_final: 0.8373 (t) REVERT: F 373 MET cc_start: 0.8683 (pmm) cc_final: 0.8216 (pmm) REVERT: F 395 PHE cc_start: 0.7696 (t80) cc_final: 0.7336 (t80) REVERT: G 295 CYS cc_start: 0.8444 (m) cc_final: 0.8241 (m) REVERT: G 302 MET cc_start: 0.8111 (ppp) cc_final: 0.7886 (ppp) REVERT: G 313 MET cc_start: 0.7290 (mmm) cc_final: 0.7073 (mmt) REVERT: G 317 LEU cc_start: 0.7483 (mt) cc_final: 0.6860 (mt) REVERT: G 378 LEU cc_start: 0.7920 (mt) cc_final: 0.7384 (mp) REVERT: H 124 LYS cc_start: 0.8765 (pptt) cc_final: 0.7708 (ptmt) REVERT: H 149 MET cc_start: 0.5595 (ppp) cc_final: 0.5264 (ppp) REVERT: H 234 THR cc_start: 0.8689 (p) cc_final: 0.8415 (p) REVERT: H 235 MET cc_start: 0.7344 (mmt) cc_final: 0.6436 (mmt) REVERT: H 292 THR cc_start: 0.8596 (p) cc_final: 0.7815 (p) REVERT: H 295 MET cc_start: 0.8359 (ppp) cc_final: 0.7891 (ppp) REVERT: H 333 LEU cc_start: 0.8364 (tp) cc_final: 0.7662 (tt) REVERT: I 322 ASP cc_start: 0.6916 (t0) cc_final: 0.6570 (p0) REVERT: I 380 ASN cc_start: 0.6641 (t0) cc_final: 0.6272 (t0) REVERT: I 409 VAL cc_start: 0.8186 (m) cc_final: 0.7774 (p) REVERT: J 235 MET cc_start: 0.8240 (mtp) cc_final: 0.7451 (mtm) REVERT: J 259 MET cc_start: 0.7562 (tpt) cc_final: 0.6441 (tpp) REVERT: J 314 THR cc_start: 0.8614 (p) cc_final: 0.7382 (p) REVERT: J 332 MET cc_start: 0.5908 (tpp) cc_final: 0.5630 (tpp) REVERT: K 335 ILE cc_start: 0.7886 (mm) cc_final: 0.7620 (mm) REVERT: L 19 LYS cc_start: 0.8762 (mmpt) cc_final: 0.8392 (mmmm) REVERT: L 21 TRP cc_start: 0.7803 (m100) cc_final: 0.7504 (m100) REVERT: L 116 ASP cc_start: 0.7345 (m-30) cc_final: 0.7073 (m-30) REVERT: L 125 GLU cc_start: 0.5545 (tp30) cc_final: 0.5181 (tp30) REVERT: L 301 MET cc_start: 0.7125 (tpt) cc_final: 0.6915 (tpp) REVERT: L 384 ILE cc_start: 0.8307 (pt) cc_final: 0.7928 (pt) REVERT: M 21 TRP cc_start: 0.8142 (m100) cc_final: 0.7796 (m100) REVERT: M 75 ILE cc_start: 0.8004 (mm) cc_final: 0.7574 (tt) REVERT: M 196 GLU cc_start: 0.7376 (tp30) cc_final: 0.6891 (tp30) REVERT: M 221 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8173 (mpt-90) REVERT: M 295 CYS cc_start: 0.8524 (m) cc_final: 0.8196 (m) REVERT: M 391 LEU cc_start: 0.7793 (mp) cc_final: 0.7498 (mp) REVERT: M 398 MET cc_start: 0.5843 (mtm) cc_final: 0.5220 (mmt) REVERT: M 407 TRP cc_start: 0.8786 (m100) cc_final: 0.7820 (m100) REVERT: N 50 ASN cc_start: 0.8484 (p0) cc_final: 0.8198 (p0) REVERT: N 115 VAL cc_start: 0.8874 (t) cc_final: 0.8644 (t) REVERT: N 119 LEU cc_start: 0.7726 (tp) cc_final: 0.7372 (tp) REVERT: N 129 CYS cc_start: 0.8505 (m) cc_final: 0.8299 (m) REVERT: N 259 MET cc_start: 0.7586 (mmp) cc_final: 0.7129 (mmm) REVERT: N 268 PHE cc_start: 0.6576 (m-80) cc_final: 0.5652 (m-80) REVERT: N 269 MET cc_start: 0.6686 (mtm) cc_final: 0.6035 (mtm) REVERT: N 398 MET cc_start: 0.5964 (mmm) cc_final: 0.5700 (mmp) REVERT: N 413 MET cc_start: 0.7771 (mmp) cc_final: 0.7560 (mmp) REVERT: N 416 MET cc_start: 0.6711 (ptm) cc_final: 0.5870 (tpt) REVERT: N 432 TYR cc_start: 0.5869 (m-80) cc_final: 0.5166 (m-80) REVERT: O 191 THR cc_start: 0.7710 (p) cc_final: 0.7431 (p) REVERT: O 196 GLU cc_start: 0.7202 (tp30) cc_final: 0.6835 (tp30) REVERT: O 203 MET cc_start: 0.6301 (ttt) cc_final: 0.5446 (ttm) REVERT: O 413 MET cc_start: 0.7519 (mmm) cc_final: 0.6826 (mmt) REVERT: P 20 PHE cc_start: 0.7305 (t80) cc_final: 0.6857 (t80) REVERT: P 166 MET cc_start: 0.6774 (tpt) cc_final: 0.6171 (tpp) REVERT: P 422 GLU cc_start: 0.5818 (tp30) cc_final: 0.5143 (tp30) REVERT: Q 133 GLN cc_start: 0.5716 (tm-30) cc_final: 0.5077 (tm-30) REVERT: Q 154 MET cc_start: 0.7171 (tmm) cc_final: 0.6801 (tmm) REVERT: Q 191 THR cc_start: 0.7648 (p) cc_final: 0.7383 (p) REVERT: Q 217 LEU cc_start: 0.7690 (mm) cc_final: 0.7349 (mm) REVERT: Q 407 TRP cc_start: 0.8057 (m100) cc_final: 0.7658 (m100) REVERT: R 5 VAL cc_start: 0.7056 (t) cc_final: 0.6766 (t) REVERT: R 14 ASN cc_start: 0.8186 (m110) cc_final: 0.7874 (m-40) REVERT: R 47 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7412 (mt-10) REVERT: R 119 LEU cc_start: 0.7979 (mt) cc_final: 0.7748 (mt) REVERT: R 255 LEU cc_start: 0.8358 (tt) cc_final: 0.8106 (mp) REVERT: R 259 MET cc_start: 0.7746 (mmm) cc_final: 0.7392 (mmm) REVERT: R 301 MET cc_start: 0.6454 (ptp) cc_final: 0.5342 (mtm) REVERT: R 353 THR cc_start: 0.6501 (t) cc_final: 0.5776 (t) outliers start: 1 outliers final: 0 residues processed: 1257 average time/residue: 0.6223 time to fit residues: 1340.1013 Evaluate side-chains 975 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 975 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 5.9990 chunk 476 optimal weight: 2.9990 chunk 638 optimal weight: 30.0000 chunk 183 optimal weight: 0.0170 chunk 553 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 166 optimal weight: 7.9990 chunk 600 optimal weight: 30.0000 chunk 251 optimal weight: 6.9990 chunk 616 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 85 GLN ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 309 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS J 331 GLN ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN L 309 HIS ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 HIS ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.088197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.073997 restraints weight = 183929.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.077081 restraints weight = 109651.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.079253 restraints weight = 71057.548| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.8856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62298 Z= 0.171 Angle : 0.612 14.941 84645 Z= 0.315 Chirality : 0.045 0.291 9216 Planarity : 0.005 0.058 11043 Dihedral : 10.871 178.098 8784 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 7632 helix: 0.61 (0.09), residues: 3411 sheet: 0.77 (0.14), residues: 1260 loop : -0.06 (0.12), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP O 407 HIS 0.007 0.001 HIS N 28 PHE 0.031 0.001 PHE J 296 TYR 0.027 0.001 TYR C 224 ARG 0.010 0.001 ARG C 243 =============================================================================== Job complete usr+sys time: 19839.42 seconds wall clock time: 347 minutes 30.94 seconds (20850.94 seconds total)