Starting phenix.real_space_refine on Wed Nov 15 01:00:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/11_2023/3j6e_5895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/11_2023/3j6e_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_5895/11_2023/3j6e_5895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/11_2023/3j6e_5895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/11_2023/3j6e_5895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/11_2023/3j6e_5895_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.468 sd= 1.871 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 18 5.21 5 S 414 5.16 5 C 38223 2.51 5 N 10395 2.21 5 O 11880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 251": "OD1" <-> "OD2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 251": "OD1" <-> "OD2" Residue "H PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 330": "OE1" <-> "OE2" Residue "H TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 417": "OE1" <-> "OE2" Residue "H PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 71": "OE1" <-> "OE2" Residue "J PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 251": "OD1" <-> "OD2" Residue "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 330": "OE1" <-> "OE2" Residue "J TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 417": "OE1" <-> "OE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 437": "OD1" <-> "OD2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 207": "OE1" <-> "OE2" Residue "K TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 71": "OE1" <-> "OE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 251": "OD1" <-> "OD2" Residue "L PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 330": "OE1" <-> "OE2" Residue "L TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 417": "OE1" <-> "OE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 437": "OD1" <-> "OD2" Residue "M TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 251": "OD1" <-> "OD2" Residue "N PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 330": "OE1" <-> "OE2" Residue "N TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 417": "OE1" <-> "OE2" Residue "N PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 437": "OD1" <-> "OD2" Residue "O TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 251": "OD1" <-> "OD2" Residue "P PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 330": "OE1" <-> "OE2" Residue "P TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 417": "OE1" <-> "OE2" Residue "P PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 437": "OD1" <-> "OD2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 207": "OE1" <-> "OE2" Residue "Q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 251": "OD1" <-> "OD2" Residue "R PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 330": "OE1" <-> "OE2" Residue "R TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 417": "OE1" <-> "OE2" Residue "R PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 437": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 60984 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "G" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "H" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "I" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "J" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "L" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "M" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "N" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "O" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "P" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "Q" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "R" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 23.66, per 1000 atoms: 0.39 Number of scatterers: 60984 At special positions: 0 Unit cell: (168.78, 88.74, 295.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 414 16.00 P 54 15.00 Mg 18 11.99 O 11880 8.00 N 10395 7.00 C 38223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.10 Conformation dependent library (CDL) restraints added in 8.4 seconds 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 360 helices and 54 sheets defined 48.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.04 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: 23.87 Time building geometry restraints manager: 21.94 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 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: 0.080 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: 3.380 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 131.260 Find NCS groups from input model: 5.290 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.253 62298 Z= 1.365 Angle : 2.598 27.047 84645 Z= 1.704 Chirality : 0.134 0.965 9216 Planarity : 0.008 0.082 11043 Dihedral : 13.246 165.753 22725 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.42 % Favored : 96.23 % Rotamer: Outliers : 0.28 % Allowed : 0.41 % Favored : 99.31 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.09), residues: 7632 helix: -0.52 (0.07), residues: 3510 sheet: 1.04 (0.13), residues: 1197 loop : -0.83 (0.11), residues: 2925 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2736 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2718 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.6510 time to fit residues: 2866.7298 Evaluate side-chains 1374 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1372 time to evaluate : 5.374 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.8885 time to fit residues: 9.6128 ------------------------------------------------------------------------------- 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 102 ASN D 133 GLN D 192 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 31 GLN 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** H 37 HIS H 102 ASN H 133 GLN ** H 282 GLN ** 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** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 301 GLN P 14 ASN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 HIS ** 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: 0.6957 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 62298 Z= 0.242 Angle : 0.702 9.800 84645 Z= 0.372 Chirality : 0.046 0.204 9216 Planarity : 0.006 0.107 11043 Dihedral : 11.494 162.374 8532 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.17 % Allowed : 2.72 % Favored : 97.11 % 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: 0.49 (0.09), residues: 7632 helix: 0.38 (0.08), residues: 3564 sheet: 1.70 (0.15), residues: 1035 loop : -0.07 (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 1920 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1909 time to evaluate : 5.420 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 outliers start: 11 outliers final: 1 residues processed: 1916 average time/residue: 0.6189 time to fit residues: 1965.9416 Evaluate side-chains 1194 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1193 time to evaluate : 5.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5024 time to fit residues: 7.9489 ------------------------------------------------------------------------------- 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: 0.5980 chunk 213 optimal weight: 3.9990 chunk 571 optimal weight: 20.0000 chunk 467 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 chunk 687 optimal weight: 40.0000 chunk 742 optimal weight: 30.0000 chunk 612 optimal weight: 30.0000 chunk 682 optimal weight: 4.9990 chunk 234 optimal weight: 50.0000 chunk 551 optimal weight: 20.0000 overall best weight: 7.7190 ------------------------------------------------------------------------------- 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 B 339 ASN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 GLN J 6 HIS ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN J 294 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS M 228 ASN ** 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 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 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62298 Z= 0.230 Angle : 0.641 9.697 84645 Z= 0.338 Chirality : 0.044 0.173 9216 Planarity : 0.005 0.061 11043 Dihedral : 10.786 167.344 8532 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.20 % Allowed : 3.10 % Favored : 96.70 % 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: 0.69 (0.10), residues: 7632 helix: 0.43 (0.08), residues: 3501 sheet: 1.38 (0.14), residues: 1251 loop : 0.27 (0.13), residues: 2880 *********************** 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 1558 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1545 time to evaluate : 5.402 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 outliers start: 13 outliers final: 5 residues processed: 1557 average time/residue: 0.6019 time to fit residues: 1571.3379 Evaluate side-chains 1081 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1076 time to evaluate : 5.417 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5162 time to fit residues: 11.6487 ------------------------------------------------------------------------------- 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: 20.0000 chunk 517 optimal weight: 20.0000 chunk 356 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 461 optimal weight: 2.9990 chunk 690 optimal weight: 40.0000 chunk 730 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 654 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** 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 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 206 ASN F 281 GLN ** F 331 GLN ** 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 GLN L 337 ASN M 91 GLN ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** 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** N 281 GLN N 294 GLN ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 136 GLN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 GLN R 309 HIS R 337 ASN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 62298 Z= 0.209 Angle : 0.615 9.006 84645 Z= 0.320 Chirality : 0.044 0.325 9216 Planarity : 0.005 0.061 11043 Dihedral : 10.441 160.770 8532 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.18 % Allowed : 2.32 % Favored : 97.49 % 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: 0.67 (0.10), residues: 7632 helix: 0.42 (0.08), residues: 3528 sheet: 1.37 (0.14), residues: 1251 loop : 0.27 (0.13), residues: 2853 *********************** 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 1500 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1488 time to evaluate : 5.833 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 outliers start: 12 outliers final: 5 residues processed: 1498 average time/residue: 0.6169 time to fit residues: 1556.6618 Evaluate side-chains 1019 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1014 time to evaluate : 5.514 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5273 time to fit residues: 11.7841 ------------------------------------------------------------------------------- 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: 6.9990 chunk 414 optimal weight: 50.0000 chunk 10 optimal weight: 0.2980 chunk 544 optimal weight: 50.0000 chunk 301 optimal weight: 20.0000 chunk 623 optimal weight: 0.0000 chunk 505 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 373 optimal weight: 10.0000 chunk 655 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 overall best weight: 4.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 331 GLN C 11 GLN C 186 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 206 ASN F 281 GLN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN G 88 HIS ** G 101 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS J 249 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN 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** O 372 GLN ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 136 GLN ** 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 301 GLN R 37 HIS ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 ASN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 62298 Z= 0.181 Angle : 0.591 12.423 84645 Z= 0.304 Chirality : 0.043 0.181 9216 Planarity : 0.005 0.092 11043 Dihedral : 10.134 153.747 8532 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % 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: 0.70 (0.10), residues: 7632 helix: 0.48 (0.08), residues: 3537 sheet: 1.31 (0.14), residues: 1251 loop : 0.26 (0.13), residues: 2844 *********************** 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 1461 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1455 time to evaluate : 5.759 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 outliers start: 6 outliers final: 4 residues processed: 1461 average time/residue: 0.6077 time to fit residues: 1496.5357 Evaluate side-chains 1028 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1024 time to evaluate : 5.418 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5156 time to fit residues: 10.7962 ------------------------------------------------------------------------------- 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: 0.0870 chunk 658 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 chunk 731 optimal weight: 0.0770 chunk 607 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 384 optimal weight: 40.0000 overall best weight: 3.4322 ------------------------------------------------------------------------------- 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 ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 192 HIS F 206 ASN F 380 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 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 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 342 GLN 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 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 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 339 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 372 GLN ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 62298 Z= 0.170 Angle : 0.589 10.319 84645 Z= 0.301 Chirality : 0.044 0.275 9216 Planarity : 0.005 0.095 11043 Dihedral : 9.863 150.915 8532 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.12 % Allowed : 1.31 % Favored : 98.56 % 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: 3528 sheet: 1.21 (0.14), residues: 1251 loop : 0.14 (0.13), residues: 2853 *********************** 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 1436 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1428 time to evaluate : 5.719 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 outliers start: 8 outliers final: 4 residues processed: 1435 average time/residue: 0.6398 time to fit residues: 1564.9077 Evaluate side-chains 1025 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1021 time to evaluate : 5.549 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5697 time to fit residues: 11.6639 ------------------------------------------------------------------------------- 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: 10.0000 chunk 534 optimal weight: 30.0000 chunk 413 optimal weight: 40.0000 chunk 615 optimal weight: 40.0000 chunk 408 optimal weight: 50.0000 chunk 728 optimal weight: 7.9990 chunk 456 optimal weight: 50.0000 chunk 444 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 A 342 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 197 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 339 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN E 266 HIS E 342 GLN F 133 GLN F 192 HIS F 206 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN M 300 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 258 ASN ** 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 136 GLN ** P 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 ASN ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.7695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 62298 Z= 0.207 Angle : 0.624 14.720 84645 Z= 0.319 Chirality : 0.044 0.214 9216 Planarity : 0.005 0.075 11043 Dihedral : 9.784 153.364 8532 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.06 % Allowed : 1.39 % Favored : 98.55 % 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: 0.55 (0.10), residues: 7632 helix: 0.56 (0.09), residues: 3447 sheet: 1.19 (0.15), residues: 1062 loop : 0.01 (0.12), residues: 3123 *********************** 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 1348 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1344 time to evaluate : 5.366 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 outliers start: 4 outliers final: 0 residues processed: 1347 average time/residue: 0.5855 time to fit residues: 1336.6680 Evaluate side-chains 973 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 973 time to evaluate : 5.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0026 ------------------------------------------------------------------------------- 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: 6.9990 chunk 435 optimal weight: 50.0000 chunk 219 optimal weight: 50.0000 chunk 143 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 496 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 572 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 339 ASN B 406 HIS C 256 GLN C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 380 ASN G 88 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** 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 8 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 61 HIS ** 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 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 HIS ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 HIS ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 GLN R 350 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.8001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 62298 Z= 0.211 Angle : 0.636 14.634 84645 Z= 0.326 Chirality : 0.044 0.257 9216 Planarity : 0.005 0.071 11043 Dihedral : 9.651 157.081 8532 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.03 % Allowed : 0.87 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 7632 helix: 0.61 (0.09), residues: 3420 sheet: 1.08 (0.14), residues: 1170 loop : -0.05 (0.12), residues: 3042 *********************** 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 1317 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1315 time to evaluate : 5.488 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: 1316 average time/residue: 0.6088 time to fit residues: 1357.2208 Evaluate side-chains 961 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 961 time to evaluate : 5.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1725 ------------------------------------------------------------------------------- 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: 8.9990 chunk 698 optimal weight: 5.9990 chunk 636 optimal weight: 8.9990 chunk 679 optimal weight: 9.9990 chunk 697 optimal weight: 0.0370 chunk 408 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 chunk 533 optimal weight: 40.0000 chunk 208 optimal weight: 5.9990 chunk 613 optimal weight: 0.0670 chunk 642 optimal weight: 6.9990 overall best weight: 3.6202 ------------------------------------------------------------------------------- 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** A 301 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 309 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN ** M 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN ** N 258 ASN ** 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 197 HIS ** O 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 HIS ** 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 101 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** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.8266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 62298 Z= 0.178 Angle : 0.630 14.761 84645 Z= 0.320 Chirality : 0.045 0.251 9216 Planarity : 0.005 0.071 11043 Dihedral : 9.275 154.765 8532 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.02 % Allowed : 0.29 % Favored : 99.69 % 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: 0.55 (0.09), residues: 3492 sheet: 0.76 (0.15), residues: 1125 loop : -0.10 (0.12), residues: 3015 *********************** 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 1328 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1327 time to evaluate : 5.405 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 outliers start: 1 outliers final: 0 residues processed: 1327 average time/residue: 0.5894 time to fit residues: 1326.3835 Evaluate side-chains 972 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 972 time to evaluate : 5.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1662 ------------------------------------------------------------------------------- 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: 0.9990 chunk 445 optimal weight: 0.0970 chunk 718 optimal weight: 0.8980 chunk 438 optimal weight: 20.0000 chunk 340 optimal weight: 9.9990 chunk 499 optimal weight: 7.9990 chunk 753 optimal weight: 30.0000 chunk 693 optimal weight: 6.9990 chunk 599 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 463 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 133 GLN B 309 HIS C 176 GLN C 266 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN F 101 ASN F 133 GLN F 380 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 ASN ** K 133 GLN ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN ** 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 91 GLN ** 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 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN P 339 ASN ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 380 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 HIS ** R 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 62298 Z= 0.175 Angle : 0.637 11.393 84645 Z= 0.324 Chirality : 0.045 0.280 9216 Planarity : 0.005 0.168 11043 Dihedral : 8.998 155.978 8532 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.02 % Allowed : 0.26 % Favored : 99.72 % 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: 0.34 (0.10), residues: 7632 helix: 0.52 (0.09), residues: 3447 sheet: 0.74 (0.15), residues: 1125 loop : -0.16 (0.12), residues: 3060 ********************** 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 1322 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1321 time to evaluate : 5.483 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 outliers start: 1 outliers final: 0 residues processed: 1321 average time/residue: 0.6024 time to fit residues: 1357.2688 Evaluate side-chains 984 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 984 time to evaluate : 5.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2596 ------------------------------------------------------------------------------- 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: 0.0020 chunk 476 optimal weight: 50.0000 chunk 638 optimal weight: 0.4980 chunk 183 optimal weight: 50.0000 chunk 553 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 166 optimal weight: 5.9990 chunk 600 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 616 optimal weight: 20.0000 chunk 76 optimal weight: 0.5980 overall best weight: 3.4194 ------------------------------------------------------------------------------- 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 133 GLN B 337 ASN C 176 GLN C 342 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 GLN H 309 HIS ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 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 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 ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 ASN ** 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** Q 293 ASN ** Q 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3949 r_free = 0.3949 target = 0.092026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.076938 restraints weight = 180373.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.080137 restraints weight = 108911.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082451 restraints weight = 71373.865| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 62298 Z= 0.174 Angle : 0.632 17.220 84645 Z= 0.319 Chirality : 0.044 0.226 9216 Planarity : 0.005 0.124 11043 Dihedral : 8.841 157.870 8532 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.02 % Allowed : 0.17 % Favored : 99.82 % 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: 0.35 (0.10), residues: 7632 helix: 0.53 (0.09), residues: 3447 sheet: 0.71 (0.15), residues: 1125 loop : -0.14 (0.12), residues: 3060 =============================================================================== Job complete usr+sys time: 20630.75 seconds wall clock time: 361 minutes 13.44 seconds (21673.44 seconds total)