Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:11:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/04_2022/3j6e_5895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/04_2022/3j6e_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_5895/04_2022/3j6e_5895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/04_2022/3j6e_5895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/04_2022/3j6e_5895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/04_2022/3j6e_5895_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.468 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 Convert atoms to be neutral 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 407, 'PCIS': 1} 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: {'PTRANS': 19, 'TRANS': 405, 'PCIS': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: {'GTP': 1, ' MG': 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: 24.44, per 1000 atoms: 0.40 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: 18.78 Conformation dependent library (CDL) restraints added in 6.6 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: 5.12 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: 21.10 Time building geometry restraints manager: 20.56 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: 36286 33.15 - 66.30: 488 66.30 - 99.45: 117 99.45 - 132.60: 18 132.60 - 165.75: 18 Dihedral angle restraints: 36927 sinusoidal: 14760 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 36924 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 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. 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: 0.050 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: 0.050 Extract box with map and model: 5.860 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.530 Process input model: 118.260 Find NCS groups from input model: 3.670 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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 : 13.246 165.753 22725 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.42 % Favored : 96.23 % Rotamer Outliers : 0.28 % 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 *********************** 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 : 6.260 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 outliers start: 18 outliers final: 2 residues processed: 2730 average time/residue: 0.6499 time to fit residues: 2891.0910 Evaluate side-chains 1372 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1370 time to evaluate : 5.226 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.8714 time to fit residues: 9.5300 ------------------------------------------------------------------------------- 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: 0.9990 chunk 317 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 386 optimal weight: 4.9990 chunk 306 optimal weight: 30.0000 chunk 592 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 360 optimal weight: 7.9990 chunk 441 optimal weight: 9.9990 chunk 686 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 14 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 15 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 102 ASN F 133 GLN F 193 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 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 350 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 M 15 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN N 101 ASN N 229 HIS ** N 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 301 GLN P 14 ASN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN P 107 HIS P 331 GLN Q 15 GLN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN R 102 ASN R 192 HIS R 339 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 62298 Z= 0.240 Angle : 0.699 9.670 84645 Z= 0.370 Chirality : 0.046 0.216 9216 Planarity : 0.006 0.110 11043 Dihedral : 11.485 162.965 8532 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.17 % 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: 0.49 (0.09), residues: 7632 helix: 0.38 (0.08), residues: 3564 sheet: 1.69 (0.15), residues: 1035 loop : -0.06 (0.12), residues: 3033 *********************** 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 1925 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1914 time to evaluate : 5.278 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 outliers start: 11 outliers final: 2 residues processed: 1921 average time/residue: 0.5778 time to fit residues: 1849.4508 Evaluate side-chains 1209 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1207 time to evaluate : 5.292 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4745 time to fit residues: 8.7219 ------------------------------------------------------------------------------- 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: 1.9990 chunk 213 optimal weight: 9.9990 chunk 571 optimal weight: 20.0000 chunk 467 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 687 optimal weight: 50.0000 chunk 742 optimal weight: 8.9990 chunk 612 optimal weight: 20.0000 chunk 682 optimal weight: 4.9990 chunk 234 optimal weight: 50.0000 chunk 551 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 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 193 GLN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN F 15 GLN F 133 GLN F 192 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS H 337 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN ** 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 193 GLN J 331 GLN ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS L 193 GLN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS M 228 ASN ** N 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN O 15 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 228 ASN P 15 GLN P 28 HIS P 107 HIS ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN R 96 GLN R 309 HIS R 331 GLN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 62298 Z= 0.215 Angle : 0.633 8.769 84645 Z= 0.332 Chirality : 0.044 0.170 9216 Planarity : 0.006 0.098 11043 Dihedral : 10.671 166.929 8532 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.15 % 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: 0.65 (0.10), residues: 7632 helix: 0.40 (0.08), residues: 3483 sheet: 1.44 (0.14), residues: 1197 loop : 0.24 (0.12), residues: 2952 *********************** 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 1604 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1594 time to evaluate : 5.246 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 outliers start: 10 outliers final: 1 residues processed: 1603 average time/residue: 0.5843 time to fit residues: 1574.4670 Evaluate side-chains 1087 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1086 time to evaluate : 5.295 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5010 time to fit residues: 7.9424 ------------------------------------------------------------------------------- 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: 7.9990 chunk 517 optimal weight: 40.0000 chunk 356 optimal weight: 0.9980 chunk 76 optimal weight: 40.0000 chunk 328 optimal weight: 20.0000 chunk 461 optimal weight: 0.0470 chunk 690 optimal weight: 4.9990 chunk 730 optimal weight: 20.0000 chunk 360 optimal weight: 7.9990 chunk 654 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 overall best weight: 4.2084 ------------------------------------------------------------------------------- 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 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 ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 206 ASN F 281 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN H 6 HIS H 37 HIS ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 GLN M 91 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN ** 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** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 136 GLN ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 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** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 136 GLN R 309 HIS ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 62298 Z= 0.190 Angle : 0.604 10.782 84645 Z= 0.313 Chirality : 0.044 0.308 9216 Planarity : 0.005 0.088 11043 Dihedral : 10.269 159.033 8532 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.81 % Favored : 98.18 % Rotamer Outliers : 0.11 % 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: 0.58 (0.10), residues: 7632 helix: 0.46 (0.08), residues: 3537 sheet: 1.06 (0.14), residues: 1269 loop : 0.18 (0.13), residues: 2826 *********************** 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 1532 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1525 time to evaluate : 5.299 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 outliers start: 7 outliers final: 3 residues processed: 1531 average time/residue: 0.5882 time to fit residues: 1517.8387 Evaluate side-chains 1053 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1050 time to evaluate : 5.274 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5073 time to fit residues: 9.7140 ------------------------------------------------------------------------------- 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: 8.9990 chunk 414 optimal weight: 50.0000 chunk 10 optimal weight: 0.3980 chunk 544 optimal weight: 8.9990 chunk 301 optimal weight: 20.0000 chunk 623 optimal weight: 2.9990 chunk 505 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 373 optimal weight: 10.0000 chunk 655 optimal weight: 5.9990 chunk 184 optimal weight: 0.0970 overall best weight: 3.6984 ------------------------------------------------------------------------------- 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN E 372 GLN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 206 ASN F 281 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 HIS ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** O 35 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** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 136 GLN P 337 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS R 101 ASN ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 ASN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 62298 Z= 0.180 Angle : 0.590 12.411 84645 Z= 0.302 Chirality : 0.043 0.178 9216 Planarity : 0.005 0.097 11043 Dihedral : 9.913 152.914 8532 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.06 % 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: 0.72 (0.10), residues: 7632 helix: 0.55 (0.09), residues: 3483 sheet: 1.03 (0.14), residues: 1314 loop : 0.35 (0.13), residues: 2835 *********************** 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 1465 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1461 time to evaluate : 5.309 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 outliers start: 4 outliers final: 0 residues processed: 1465 average time/residue: 0.5727 time to fit residues: 1424.7040 Evaluate side-chains 1049 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1049 time to evaluate : 5.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.0971 ------------------------------------------------------------------------------- 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: 8.9990 chunk 658 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 chunk 731 optimal weight: 40.0000 chunk 607 optimal weight: 8.9990 chunk 338 optimal weight: 50.0000 chunk 60 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 overall best weight: 7.5988 ------------------------------------------------------------------------------- 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 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS D 133 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 206 ASN F 380 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** I 101 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** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS ** M 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** 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 35 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** ** 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 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 ASN ** 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 301 GLN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 62298 Z= 0.213 Angle : 0.617 11.817 84645 Z= 0.317 Chirality : 0.044 0.340 9216 Planarity : 0.005 0.085 11043 Dihedral : 9.780 148.761 8532 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.08 % 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: 0.63 (0.10), residues: 7632 helix: 0.52 (0.09), residues: 3447 sheet: 1.07 (0.14), residues: 1269 loop : 0.20 (0.12), residues: 2916 *********************** 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 1416 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1411 time to evaluate : 5.296 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 outliers start: 5 outliers final: 0 residues processed: 1414 average time/residue: 0.5891 time to fit residues: 1424.0982 Evaluate side-chains 999 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 999 time to evaluate : 5.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1523 ------------------------------------------------------------------------------- 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: 40.0000 chunk 82 optimal weight: 6.9990 chunk 416 optimal weight: 0.5980 chunk 534 optimal weight: 9.9990 chunk 413 optimal weight: 8.9990 chunk 615 optimal weight: 40.0000 chunk 408 optimal weight: 10.0000 chunk 728 optimal weight: 10.0000 chunk 456 optimal weight: 50.0000 chunk 444 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 overall best weight: 7.3190 ------------------------------------------------------------------------------- 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN C 28 HIS C 256 GLN C 309 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 342 GLN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN H 59 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN ** N 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 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** ** 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 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 HIS ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 ASN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 62298 Z= 0.202 Angle : 0.612 10.482 84645 Z= 0.313 Chirality : 0.044 0.272 9216 Planarity : 0.005 0.083 11043 Dihedral : 9.550 149.802 8532 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.06 % 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: 0.58 (0.10), residues: 7632 helix: 0.54 (0.09), residues: 3492 sheet: 0.95 (0.14), residues: 1287 loop : 0.12 (0.13), residues: 2853 *********************** 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 1356 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1352 time to evaluate : 5.372 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 outliers start: 4 outliers final: 2 residues processed: 1355 average time/residue: 0.5690 time to fit residues: 1311.3366 Evaluate side-chains 975 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 973 time to evaluate : 5.261 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4943 time to fit residues: 8.8066 ------------------------------------------------------------------------------- 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: 10.0000 chunk 435 optimal weight: 50.0000 chunk 219 optimal weight: 40.0000 chunk 143 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 chunk 463 optimal weight: 7.9990 chunk 496 optimal weight: 40.0000 chunk 360 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 572 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- 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 342 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN E 309 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 380 ASN G 88 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 342 GLN ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** L 334 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 226 ASN ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 339 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN P 59 ASN ** 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 258 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.8014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 62298 Z= 0.224 Angle : 0.639 12.659 84645 Z= 0.328 Chirality : 0.045 0.277 9216 Planarity : 0.005 0.088 11043 Dihedral : 9.415 153.634 8532 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.06 % 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: 0.46 (0.09), residues: 3492 sheet: 0.57 (0.14), residues: 1323 loop : 0.11 (0.13), residues: 2817 *********************** 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 1308 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1304 time to evaluate : 5.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 1306 average time/residue: 0.5638 time to fit residues: 1255.9950 Evaluate side-chains 957 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 957 time to evaluate : 5.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9850 ------------------------------------------------------------------------------- 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: 40.0000 chunk 698 optimal weight: 9.9990 chunk 636 optimal weight: 9.9990 chunk 679 optimal weight: 20.0000 chunk 697 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 295 optimal weight: 40.0000 chunk 533 optimal weight: 0.1980 chunk 208 optimal weight: 20.0000 chunk 613 optimal weight: 30.0000 chunk 642 optimal weight: 9.9990 overall best weight: 7.2388 ------------------------------------------------------------------------------- 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 14 ASN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN G 88 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 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 ** 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 226 ASN M 301 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 258 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN P 339 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7041 moved from start: 0.8258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 62298 Z= 0.211 Angle : 0.633 12.870 84645 Z= 0.323 Chirality : 0.045 0.241 9216 Planarity : 0.005 0.131 11043 Dihedral : 9.231 155.637 8532 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.03 % 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: 0.40 (0.10), residues: 7632 helix: 0.51 (0.09), residues: 3474 sheet: 0.50 (0.14), residues: 1341 loop : 0.07 (0.13), residues: 2817 *********************** 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 1291 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1289 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1290 average time/residue: 0.5674 time to fit residues: 1251.4662 Evaluate side-chains 964 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 964 time to evaluate : 5.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1411 ------------------------------------------------------------------------------- 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: 6.9990 chunk 445 optimal weight: 0.7980 chunk 718 optimal weight: 1.9990 chunk 438 optimal weight: 0.0970 chunk 340 optimal weight: 20.0000 chunk 499 optimal weight: 8.9990 chunk 753 optimal weight: 8.9990 chunk 693 optimal weight: 0.8980 chunk 599 optimal weight: 0.0270 chunk 62 optimal weight: 9.9990 chunk 463 optimal weight: 6.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 309 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 337 ASN F 380 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 102 ASN H 282 GLN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 ASN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 HIS ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN M 228 ASN ** N 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 258 ASN ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 HIS ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 HIS ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 HIS ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.8487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.184 62298 Z= 0.191 Angle : 0.644 16.419 84645 Z= 0.326 Chirality : 0.045 0.250 9216 Planarity : 0.005 0.137 11043 Dihedral : 8.767 146.927 8532 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.38 % Favored : 97.60 % Rotamer Outliers : 0.03 % 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: 0.47 (0.09), residues: 3483 sheet: 0.58 (0.14), residues: 1305 loop : 0.05 (0.13), residues: 2844 ********************** 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 1365 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1363 time to evaluate : 6.242 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 outliers start: 2 outliers final: 0 residues processed: 1363 average time/residue: 0.5701 time to fit residues: 1322.7228 Evaluate side-chains 980 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 5.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0292 ------------------------------------------------------------------------------- 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: 7.9990 chunk 476 optimal weight: 50.0000 chunk 638 optimal weight: 0.0470 chunk 183 optimal weight: 20.0000 chunk 553 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 600 optimal weight: 20.0000 chunk 251 optimal weight: 50.0000 chunk 616 optimal weight: 40.0000 chunk 76 optimal weight: 3.9990 overall best weight: 6.0086 ------------------------------------------------------------------------------- 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 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 309 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 ASN F 380 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 ASN L 309 HIS ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN M 228 ASN M 293 ASN ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.090065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.075495 restraints weight = 182355.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.078574 restraints weight = 110391.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.080783 restraints weight = 72354.197| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.8693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.145 62298 Z= 0.206 Angle : 0.650 13.234 84645 Z= 0.331 Chirality : 0.045 0.228 9216 Planarity : 0.005 0.104 11043 Dihedral : 8.581 147.047 8532 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.02 % 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: 0.38 (0.10), residues: 7632 helix: 0.47 (0.09), residues: 3411 sheet: 0.57 (0.14), residues: 1305 loop : 0.05 (0.12), residues: 2916 =============================================================================== Job complete usr+sys time: 19571.64 seconds wall clock time: 342 minutes 21.52 seconds (20541.52 seconds total)