Starting phenix.real_space_refine (version: dev) on Sat May 14 08:53:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o09_3726/05_2022/5o09_3726_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o09_3726/05_2022/5o09_3726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o09_3726/05_2022/5o09_3726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o09_3726/05_2022/5o09_3726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o09_3726/05_2022/5o09_3726_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o09_3726/05_2022/5o09_3726_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "1A ARG 67": "NH1" <-> "NH2" Residue "1A ARG 97": "NH1" <-> "NH2" Residue "1A ARG 114": "NH1" <-> "NH2" Residue "1A ARG 123": "NH1" <-> "NH2" Residue "1A ARG 197": "NH1" <-> "NH2" Residue "1A ARG 198": "NH1" <-> "NH2" Residue "1A ARG 245": "NH1" <-> "NH2" Residue "1A ARG 257": "NH1" <-> "NH2" Residue "1A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A ARG 315": "NH1" <-> "NH2" Residue "1A ARG 324": "NH1" <-> "NH2" Residue "1A ARG 341": "NH1" <-> "NH2" Residue "1A ARG 367": "NH1" <-> "NH2" Residue "1A ARG 381": "NH1" <-> "NH2" Residue "1A ARG 385": "NH1" <-> "NH2" Residue "1A ARG 396": "NH1" <-> "NH2" Residue "1A ARG 417": "NH1" <-> "NH2" Residue "1B ARG 2": "NH1" <-> "NH2" Residue "1B ARG 22": "NH1" <-> "NH2" Residue "1B ARG 56": "NH1" <-> "NH2" Residue "1B ARG 63": "NH1" <-> "NH2" Residue "1B ARG 76": "NH1" <-> "NH2" Residue "1B ARG 93": "NH1" <-> "NH2" Residue "1B ARG 104": "NH1" <-> "NH2" Residue "1B ARG 155": "NH1" <-> "NH2" Residue "1B ARG 157": "NH1" <-> "NH2" Residue "1B ARG 192": "NH1" <-> "NH2" Residue "1B ARG 210": "NH1" <-> "NH2" Residue "1B ARG 218": "NH1" <-> "NH2" Residue "1B ARG 241": "NH1" <-> "NH2" Residue "1B ARG 283": "NH1" <-> "NH2" Residue "1B ARG 291": "NH1" <-> "NH2" Residue "1B ARG 318": "NH1" <-> "NH2" Residue "1B ARG 334": "NH1" <-> "NH2" Residue "1B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B ARG 380": "NH1" <-> "NH2" Residue "1B ARG 405": "NH1" <-> "NH2" Residue "1B ARG 412": "NH1" <-> "NH2" Residue "1B ARG 423": "NH1" <-> "NH2" Residue "1C GLU 17": "OE1" <-> "OE2" Residue "1C ASP 26": "OD1" <-> "OD2" Residue "1C ARG 44": "NH1" <-> "NH2" Residue "1C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C ARG 132": "NH1" <-> "NH2" Residue "1C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C GLU 146": "OE1" <-> "OE2" Residue "1C ASP 177": "OD1" <-> "OD2" Residue "1C ARG 178": "NH1" <-> "NH2" Residue "1C ASP 199": "OD1" <-> "OD2" Residue "1C GLU 224": "OE1" <-> "OE2" Residue "1C ASP 228": "OD1" <-> "OD2" Residue "2A ARG 67": "NH1" <-> "NH2" Residue "2A ARG 97": "NH1" <-> "NH2" Residue "2A ARG 114": "NH1" <-> "NH2" Residue "2A ARG 123": "NH1" <-> "NH2" Residue "2A ARG 197": "NH1" <-> "NH2" Residue "2A ARG 198": "NH1" <-> "NH2" Residue "2A ARG 245": "NH1" <-> "NH2" Residue "2A ARG 257": "NH1" <-> "NH2" Residue "2A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A ARG 315": "NH1" <-> "NH2" Residue "2A ARG 324": "NH1" <-> "NH2" Residue "2A ARG 341": "NH1" <-> "NH2" Residue "2A ARG 367": "NH1" <-> "NH2" Residue "2A ARG 381": "NH1" <-> "NH2" Residue "2A ARG 385": "NH1" <-> "NH2" Residue "2A ARG 396": "NH1" <-> "NH2" Residue "2A ARG 417": "NH1" <-> "NH2" Residue "2B ARG 2": "NH1" <-> "NH2" Residue "2B ARG 22": "NH1" <-> "NH2" Residue "2B ARG 56": "NH1" <-> "NH2" Residue "2B ARG 63": "NH1" <-> "NH2" Residue "2B ARG 76": "NH1" <-> "NH2" Residue "2B ARG 93": "NH1" <-> "NH2" Residue "2B ARG 104": "NH1" <-> "NH2" Residue "2B ARG 155": "NH1" <-> "NH2" Residue "2B ARG 157": "NH1" <-> "NH2" Residue "2B ARG 192": "NH1" <-> "NH2" Residue "2B ARG 210": "NH1" <-> "NH2" Residue "2B ARG 218": "NH1" <-> "NH2" Residue "2B ARG 241": "NH1" <-> "NH2" Residue "2B ARG 283": "NH1" <-> "NH2" Residue "2B ARG 291": "NH1" <-> "NH2" Residue "2B ARG 318": "NH1" <-> "NH2" Residue "2B ARG 334": "NH1" <-> "NH2" Residue "2B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B ARG 380": "NH1" <-> "NH2" Residue "2B ARG 405": "NH1" <-> "NH2" Residue "2B ARG 412": "NH1" <-> "NH2" Residue "2B ARG 423": "NH1" <-> "NH2" Residue "2C GLU 17": "OE1" <-> "OE2" Residue "2C ASP 26": "OD1" <-> "OD2" Residue "2C ARG 44": "NH1" <-> "NH2" Residue "2C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C ARG 132": "NH1" <-> "NH2" Residue "2C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C GLU 146": "OE1" <-> "OE2" Residue "2C ASP 177": "OD1" <-> "OD2" Residue "2C ARG 178": "NH1" <-> "NH2" Residue "2C ASP 199": "OD1" <-> "OD2" Residue "2C GLU 224": "OE1" <-> "OE2" Residue "2C ASP 228": "OD1" <-> "OD2" Residue "3A ARG 67": "NH1" <-> "NH2" Residue "3A ARG 97": "NH1" <-> "NH2" Residue "3A ARG 114": "NH1" <-> "NH2" Residue "3A ARG 123": "NH1" <-> "NH2" Residue "3A ARG 197": "NH1" <-> "NH2" Residue "3A ARG 198": "NH1" <-> "NH2" Residue "3A ARG 245": "NH1" <-> "NH2" Residue "3A ARG 257": "NH1" <-> "NH2" Residue "3A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A ARG 315": "NH1" <-> "NH2" Residue "3A ARG 324": "NH1" <-> "NH2" Residue "3A ARG 341": "NH1" <-> "NH2" Residue "3A ARG 367": "NH1" <-> "NH2" Residue "3A ARG 381": "NH1" <-> "NH2" Residue "3A ARG 385": "NH1" <-> "NH2" Residue "3A ARG 396": "NH1" <-> "NH2" Residue "3A ARG 417": "NH1" <-> "NH2" Residue "3B ARG 2": "NH1" <-> "NH2" Residue "3B ARG 22": "NH1" <-> "NH2" Residue "3B ARG 56": "NH1" <-> "NH2" Residue "3B ARG 63": "NH1" <-> "NH2" Residue "3B ARG 76": "NH1" <-> "NH2" Residue "3B ARG 93": "NH1" <-> "NH2" Residue "3B ARG 104": "NH1" <-> "NH2" Residue "3B ARG 155": "NH1" <-> "NH2" Residue "3B ARG 157": "NH1" <-> "NH2" Residue "3B ARG 192": "NH1" <-> "NH2" Residue "3B ARG 210": "NH1" <-> "NH2" Residue "3B ARG 218": "NH1" <-> "NH2" Residue "3B ARG 241": "NH1" <-> "NH2" Residue "3B ARG 283": "NH1" <-> "NH2" Residue "3B ARG 291": "NH1" <-> "NH2" Residue "3B ARG 318": "NH1" <-> "NH2" Residue "3B ARG 334": "NH1" <-> "NH2" Residue "3B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B ARG 380": "NH1" <-> "NH2" Residue "3B ARG 405": "NH1" <-> "NH2" Residue "3B ARG 412": "NH1" <-> "NH2" Residue "3B ARG 423": "NH1" <-> "NH2" Residue "3C GLU 17": "OE1" <-> "OE2" Residue "3C ASP 26": "OD1" <-> "OD2" Residue "3C ARG 44": "NH1" <-> "NH2" Residue "3C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C ARG 132": "NH1" <-> "NH2" Residue "3C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C GLU 146": "OE1" <-> "OE2" Residue "3C ASP 177": "OD1" <-> "OD2" Residue "3C ARG 178": "NH1" <-> "NH2" Residue "3C ASP 199": "OD1" <-> "OD2" Residue "3C GLU 224": "OE1" <-> "OE2" Residue "3C ASP 228": "OD1" <-> "OD2" Residue "4A ARG 67": "NH1" <-> "NH2" Residue "4A ARG 97": "NH1" <-> "NH2" Residue "4A ARG 114": "NH1" <-> "NH2" Residue "4A ARG 123": "NH1" <-> "NH2" Residue "4A ARG 197": "NH1" <-> "NH2" Residue "4A ARG 198": "NH1" <-> "NH2" Residue "4A ARG 245": "NH1" <-> "NH2" Residue "4A ARG 257": "NH1" <-> "NH2" Residue "4A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A ARG 315": "NH1" <-> "NH2" Residue "4A ARG 324": "NH1" <-> "NH2" Residue "4A ARG 341": "NH1" <-> "NH2" Residue "4A ARG 367": "NH1" <-> "NH2" Residue "4A ARG 381": "NH1" <-> "NH2" Residue "4A ARG 385": "NH1" <-> "NH2" Residue "4A ARG 396": "NH1" <-> "NH2" Residue "4A ARG 417": "NH1" <-> "NH2" Residue "4B ARG 2": "NH1" <-> "NH2" Residue "4B ARG 22": "NH1" <-> "NH2" Residue "4B ARG 56": "NH1" <-> "NH2" Residue "4B ARG 63": "NH1" <-> "NH2" Residue "4B ARG 76": "NH1" <-> "NH2" Residue "4B ARG 93": "NH1" <-> "NH2" Residue "4B ARG 104": "NH1" <-> "NH2" Residue "4B ARG 155": "NH1" <-> "NH2" Residue "4B ARG 157": "NH1" <-> "NH2" Residue "4B ARG 192": "NH1" <-> "NH2" Residue "4B ARG 210": "NH1" <-> "NH2" Residue "4B ARG 218": "NH1" <-> "NH2" Residue "4B ARG 241": "NH1" <-> "NH2" Residue "4B ARG 283": "NH1" <-> "NH2" Residue "4B ARG 291": "NH1" <-> "NH2" Residue "4B ARG 318": "NH1" <-> "NH2" Residue "4B ARG 334": "NH1" <-> "NH2" Residue "4B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B ARG 380": "NH1" <-> "NH2" Residue "4B ARG 405": "NH1" <-> "NH2" Residue "4B ARG 412": "NH1" <-> "NH2" Residue "4B ARG 423": "NH1" <-> "NH2" Residue "4C GLU 17": "OE1" <-> "OE2" Residue "4C ASP 26": "OD1" <-> "OD2" Residue "4C ARG 44": "NH1" <-> "NH2" Residue "4C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C ARG 132": "NH1" <-> "NH2" Residue "4C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C GLU 146": "OE1" <-> "OE2" Residue "4C ASP 177": "OD1" <-> "OD2" Residue "4C ARG 178": "NH1" <-> "NH2" Residue "4C ASP 199": "OD1" <-> "OD2" Residue "4C GLU 224": "OE1" <-> "OE2" Residue "4C ASP 228": "OD1" <-> "OD2" Residue "5A ARG 67": "NH1" <-> "NH2" Residue "5A ARG 97": "NH1" <-> "NH2" Residue "5A ARG 114": "NH1" <-> "NH2" Residue "5A ARG 123": "NH1" <-> "NH2" Residue "5A ARG 197": "NH1" <-> "NH2" Residue "5A ARG 198": "NH1" <-> "NH2" Residue "5A ARG 245": "NH1" <-> "NH2" Residue "5A ARG 257": "NH1" <-> "NH2" Residue "5A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A ARG 315": "NH1" <-> "NH2" Residue "5A ARG 324": "NH1" <-> "NH2" Residue "5A ARG 341": "NH1" <-> "NH2" Residue "5A ARG 367": "NH1" <-> "NH2" Residue "5A ARG 381": "NH1" <-> "NH2" Residue "5A ARG 385": "NH1" <-> "NH2" Residue "5A ARG 396": "NH1" <-> "NH2" Residue "5A ARG 417": "NH1" <-> "NH2" Residue "5B ARG 2": "NH1" <-> "NH2" Residue "5B ARG 22": "NH1" <-> "NH2" Residue "5B ARG 56": "NH1" <-> "NH2" Residue "5B ARG 63": "NH1" <-> "NH2" Residue "5B ARG 76": "NH1" <-> "NH2" Residue "5B ARG 93": "NH1" <-> "NH2" Residue "5B ARG 104": "NH1" <-> "NH2" Residue "5B ARG 155": "NH1" <-> "NH2" Residue "5B ARG 157": "NH1" <-> "NH2" Residue "5B ARG 192": "NH1" <-> "NH2" Residue "5B ARG 210": "NH1" <-> "NH2" Residue "5B ARG 218": "NH1" <-> "NH2" Residue "5B ARG 241": "NH1" <-> "NH2" Residue "5B ARG 283": "NH1" <-> "NH2" Residue "5B ARG 291": "NH1" <-> "NH2" Residue "5B ARG 318": "NH1" <-> "NH2" Residue "5B ARG 334": "NH1" <-> "NH2" Residue "5B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ARG 380": "NH1" <-> "NH2" Residue "5B ARG 405": "NH1" <-> "NH2" Residue "5B ARG 412": "NH1" <-> "NH2" Residue "5B ARG 423": "NH1" <-> "NH2" Residue "5C GLU 17": "OE1" <-> "OE2" Residue "5C ASP 26": "OD1" <-> "OD2" Residue "5C ARG 44": "NH1" <-> "NH2" Residue "5C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C ARG 132": "NH1" <-> "NH2" Residue "5C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C GLU 146": "OE1" <-> "OE2" Residue "5C ASP 177": "OD1" <-> "OD2" Residue "5C ARG 178": "NH1" <-> "NH2" Residue "5C ASP 199": "OD1" <-> "OD2" Residue "5C GLU 224": "OE1" <-> "OE2" Residue "5C ASP 228": "OD1" <-> "OD2" Residue "6A ARG 67": "NH1" <-> "NH2" Residue "6A ARG 97": "NH1" <-> "NH2" Residue "6A ARG 114": "NH1" <-> "NH2" Residue "6A ARG 123": "NH1" <-> "NH2" Residue "6A ARG 197": "NH1" <-> "NH2" Residue "6A ARG 198": "NH1" <-> "NH2" Residue "6A ARG 245": "NH1" <-> "NH2" Residue "6A ARG 257": "NH1" <-> "NH2" Residue "6A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6A ARG 315": "NH1" <-> "NH2" Residue "6A ARG 324": "NH1" <-> "NH2" Residue "6A ARG 341": "NH1" <-> "NH2" Residue "6A ARG 367": "NH1" <-> "NH2" Residue "6A ARG 381": "NH1" <-> "NH2" Residue "6A ARG 385": "NH1" <-> "NH2" Residue "6A ARG 396": "NH1" <-> "NH2" Residue "6A ARG 417": "NH1" <-> "NH2" Residue "6B ARG 2": "NH1" <-> "NH2" Residue "6B ARG 22": "NH1" <-> "NH2" Residue "6B ARG 56": "NH1" <-> "NH2" Residue "6B ARG 63": "NH1" <-> "NH2" Residue "6B ARG 76": "NH1" <-> "NH2" Residue "6B ARG 93": "NH1" <-> "NH2" Residue "6B ARG 104": "NH1" <-> "NH2" Residue "6B ARG 155": "NH1" <-> "NH2" Residue "6B ARG 157": "NH1" <-> "NH2" Residue "6B ARG 192": "NH1" <-> "NH2" Residue "6B ARG 210": "NH1" <-> "NH2" Residue "6B ARG 218": "NH1" <-> "NH2" Residue "6B ARG 241": "NH1" <-> "NH2" Residue "6B ARG 283": "NH1" <-> "NH2" Residue "6B ARG 291": "NH1" <-> "NH2" Residue "6B ARG 318": "NH1" <-> "NH2" Residue "6B ARG 334": "NH1" <-> "NH2" Residue "6B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6B ARG 380": "NH1" <-> "NH2" Residue "6B ARG 405": "NH1" <-> "NH2" Residue "6B ARG 412": "NH1" <-> "NH2" Residue "6B ARG 423": "NH1" <-> "NH2" Residue "6C GLU 17": "OE1" <-> "OE2" Residue "6C ASP 26": "OD1" <-> "OD2" Residue "6C ARG 44": "NH1" <-> "NH2" Residue "6C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6C ARG 132": "NH1" <-> "NH2" Residue "6C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6C GLU 146": "OE1" <-> "OE2" Residue "6C ASP 177": "OD1" <-> "OD2" Residue "6C ARG 178": "NH1" <-> "NH2" Residue "6C ASP 199": "OD1" <-> "OD2" Residue "6C GLU 224": "OE1" <-> "OE2" Residue "6C ASP 228": "OD1" <-> "OD2" Residue "7A ARG 67": "NH1" <-> "NH2" Residue "7A ARG 97": "NH1" <-> "NH2" Residue "7A ARG 114": "NH1" <-> "NH2" Residue "7A ARG 123": "NH1" <-> "NH2" Residue "7A ARG 197": "NH1" <-> "NH2" Residue "7A ARG 198": "NH1" <-> "NH2" Residue "7A ARG 245": "NH1" <-> "NH2" Residue "7A ARG 257": "NH1" <-> "NH2" Residue "7A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7A ARG 315": "NH1" <-> "NH2" Residue "7A ARG 324": "NH1" <-> "NH2" Residue "7A ARG 341": "NH1" <-> "NH2" Residue "7A ARG 367": "NH1" <-> "NH2" Residue "7A ARG 381": "NH1" <-> "NH2" Residue "7A ARG 385": "NH1" <-> "NH2" Residue "7A ARG 396": "NH1" <-> "NH2" Residue "7A ARG 417": "NH1" <-> "NH2" Residue "7B ARG 2": "NH1" <-> "NH2" Residue "7B ARG 22": "NH1" <-> "NH2" Residue "7B ARG 56": "NH1" <-> "NH2" Residue "7B ARG 63": "NH1" <-> "NH2" Residue "7B ARG 76": "NH1" <-> "NH2" Residue "7B ARG 93": "NH1" <-> "NH2" Residue "7B ARG 104": "NH1" <-> "NH2" Residue "7B ARG 155": "NH1" <-> "NH2" Residue "7B ARG 157": "NH1" <-> "NH2" Residue "7B ARG 192": "NH1" <-> "NH2" Residue "7B ARG 210": "NH1" <-> "NH2" Residue "7B ARG 218": "NH1" <-> "NH2" Residue "7B ARG 241": "NH1" <-> "NH2" Residue "7B ARG 283": "NH1" <-> "NH2" Residue "7B ARG 291": "NH1" <-> "NH2" Residue "7B ARG 318": "NH1" <-> "NH2" Residue "7B ARG 334": "NH1" <-> "NH2" Residue "7B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7B ARG 380": "NH1" <-> "NH2" Residue "7B ARG 405": "NH1" <-> "NH2" Residue "7B ARG 412": "NH1" <-> "NH2" Residue "7B ARG 423": "NH1" <-> "NH2" Residue "7C GLU 17": "OE1" <-> "OE2" Residue "7C ASP 26": "OD1" <-> "OD2" Residue "7C ARG 44": "NH1" <-> "NH2" Residue "7C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7C ARG 132": "NH1" <-> "NH2" Residue "7C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7C GLU 146": "OE1" <-> "OE2" Residue "7C ASP 177": "OD1" <-> "OD2" Residue "7C ARG 178": "NH1" <-> "NH2" Residue "7C ASP 199": "OD1" <-> "OD2" Residue "7C GLU 224": "OE1" <-> "OE2" Residue "7C ASP 228": "OD1" <-> "OD2" Residue "8A ARG 67": "NH1" <-> "NH2" Residue "8A ARG 97": "NH1" <-> "NH2" Residue "8A ARG 114": "NH1" <-> "NH2" Residue "8A ARG 123": "NH1" <-> "NH2" Residue "8A ARG 197": "NH1" <-> "NH2" Residue "8A ARG 198": "NH1" <-> "NH2" Residue "8A ARG 245": "NH1" <-> "NH2" Residue "8A ARG 257": "NH1" <-> "NH2" Residue "8A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8A ARG 315": "NH1" <-> "NH2" Residue "8A ARG 324": "NH1" <-> "NH2" Residue "8A ARG 341": "NH1" <-> "NH2" Residue "8A ARG 367": "NH1" <-> "NH2" Residue "8A ARG 381": "NH1" <-> "NH2" Residue "8A ARG 385": "NH1" <-> "NH2" Residue "8A ARG 396": "NH1" <-> "NH2" Residue "8A ARG 417": "NH1" <-> "NH2" Residue "8B ARG 2": "NH1" <-> "NH2" Residue "8B ARG 22": "NH1" <-> "NH2" Residue "8B ARG 56": "NH1" <-> "NH2" Residue "8B ARG 63": "NH1" <-> "NH2" Residue "8B ARG 76": "NH1" <-> "NH2" Residue "8B ARG 93": "NH1" <-> "NH2" Residue "8B ARG 104": "NH1" <-> "NH2" Residue "8B ARG 155": "NH1" <-> "NH2" Residue "8B ARG 157": "NH1" <-> "NH2" Residue "8B ARG 192": "NH1" <-> "NH2" Residue "8B ARG 210": "NH1" <-> "NH2" Residue "8B ARG 218": "NH1" <-> "NH2" Residue "8B ARG 241": "NH1" <-> "NH2" Residue "8B ARG 283": "NH1" <-> "NH2" Residue "8B ARG 291": "NH1" <-> "NH2" Residue "8B ARG 318": "NH1" <-> "NH2" Residue "8B ARG 334": "NH1" <-> "NH2" Residue "8B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8B ARG 380": "NH1" <-> "NH2" Residue "8B ARG 405": "NH1" <-> "NH2" Residue "8B ARG 412": "NH1" <-> "NH2" Residue "8B ARG 423": "NH1" <-> "NH2" Residue "8C GLU 17": "OE1" <-> "OE2" Residue "8C ASP 26": "OD1" <-> "OD2" Residue "8C ARG 44": "NH1" <-> "NH2" Residue "8C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8C ARG 132": "NH1" <-> "NH2" Residue "8C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8C GLU 146": "OE1" <-> "OE2" Residue "8C ASP 177": "OD1" <-> "OD2" Residue "8C ARG 178": "NH1" <-> "NH2" Residue "8C ASP 199": "OD1" <-> "OD2" Residue "8C GLU 224": "OE1" <-> "OE2" Residue "8C ASP 228": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 67424 Number of models: 1 Model: "" Number of chains: 40 Chain: "1A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "1B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "1C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "2A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "2B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "2C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "3A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "3B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "3C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "4A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "4B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "4C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "5B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "5C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "6A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "6B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "6C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "7A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "7B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "7C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "8A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 410, 'PCIS': 1} Chain: "8B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3167 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 13, 'CIS': 1, 'TRANS': 393, 'PCIS': 2} Chain breaks: 2 Chain: "8C" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1898 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 234} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "1A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "1B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "2A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "2B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "3A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "3B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "4A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "4B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "5A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "5B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "6A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "6B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "7A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "7B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "8A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "8B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.64, per 1000 atoms: 0.40 Number of scatterers: 67424 At special positions: 0 Unit cell: (188.94, 187.6, 221.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 296 16.00 P 32 15.00 O 12816 8.00 N 11744 7.00 C 42536 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: 20.21 Conformation dependent library (CDL) restraints added in 7.2 seconds 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 352 helices and 72 sheets defined 47.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain '1A' and resid 12 through 29 removed outlier: 3.533A pdb=" N SER1A 21 " --> pdb=" O GLN1A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS1A 24 " --> pdb=" O ALA1A 20 " (cutoff:3.500A) Processing helix chain '1A' and resid 49 through 51 No H-bonds generated for 'chain '1A' and resid 49 through 51' Processing helix chain '1A' and resid 75 through 83 Processing helix chain '1A' and resid 105 through 108 No H-bonds generated for 'chain '1A' and resid 105 through 108' Processing helix chain '1A' and resid 112 through 130 Proline residue: 1A 118 - end of helix removed outlier: 3.518A pdb=" N SER1A 122 " --> pdb=" O PRO1A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR1A 126 " --> pdb=" O SER1A 122 " (cutoff:3.500A) Processing helix chain '1A' and resid 151 through 158 removed outlier: 3.649A pdb=" N GLU1A 157 " --> pdb=" O ALA1A 153 " (cutoff:3.500A) Processing helix chain '1A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL1A 190 " --> pdb=" O PRO1A 186 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN1A 194 " --> pdb=" O VAL1A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR1A 195 " --> pdb=" O PHE1A 191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG1A 197 " --> pdb=" O LEU1A 193 " (cutoff:3.500A) Processing helix chain '1A' and resid 208 through 216 removed outlier: 3.713A pdb=" N ALA1A 215 " --> pdb=" O LEU1A 211 " (cutoff:3.500A) Processing helix chain '1A' and resid 226 through 237 removed outlier: 3.807A pdb=" N LEU1A 231 " --> pdb=" O ASP1A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR1A 234 " --> pdb=" O ASN1A 230 " (cutoff:3.500A) Processing helix chain '1A' and resid 242 through 245 No H-bonds generated for 'chain '1A' and resid 242 through 245' Processing helix chain '1A' and resid 256 through 260 Processing helix chain '1A' and resid 292 through 299 removed outlier: 3.765A pdb=" N ILE1A 296 " --> pdb=" O ILE1A 292 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS1A 297 " --> pdb=" O GLU1A 293 " (cutoff:3.500A) Processing helix chain '1A' and resid 302 through 304 No H-bonds generated for 'chain '1A' and resid 302 through 304' Processing helix chain '1A' and resid 311 through 313 No H-bonds generated for 'chain '1A' and resid 311 through 313' Processing helix chain '1A' and resid 336 through 343 removed outlier: 3.622A pdb=" N GLU1A 342 " --> pdb=" O ALA1A 338 " (cutoff:3.500A) Processing helix chain '1A' and resid 378 through 395 removed outlier: 3.888A pdb=" N VAL1A 382 " --> pdb=" O ILE1A 379 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP1A 384 " --> pdb=" O ARG1A 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE1A 386 " --> pdb=" O LEU1A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN1A 389 " --> pdb=" O ILE1A 386 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE1A 390 " --> pdb=" O CYS1A 387 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS1A 392 " --> pdb=" O ASN1A 389 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN1A 395 " --> pdb=" O LYS1A 392 " (cutoff:3.500A) Processing helix chain '1A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR1A 427 " --> pdb=" O LEU1A 423 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU1A 432 " --> pdb=" O GLN1A 428 " (cutoff:3.500A) Processing helix chain '1B' and resid 10 through 27 removed outlier: 3.643A pdb=" N ARG1B 22 " --> pdb=" O ASP1B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU1B 25 " --> pdb=" O TRP1B 21 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG1B 26 " --> pdb=" O ARG1B 22 " (cutoff:3.500A) Processing helix chain '1B' and resid 73 through 80 removed outlier: 3.671A pdb=" N GLY1B 80 " --> pdb=" O ARG1B 76 " (cutoff:3.500A) Processing helix chain '1B' and resid 102 through 106 Processing helix chain '1B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER1B 123 " --> pdb=" O ASN1B 119 " (cutoff:3.500A) Processing helix chain '1B' and resid 148 through 159 removed outlier: 3.601A pdb=" N GLU1B 154 " --> pdb=" O SER1B 150 " (cutoff:3.500A) Processing helix chain '1B' and resid 182 through 196 removed outlier: 3.910A pdb=" N ILE1B 187 " --> pdb=" O PRO1B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG1B 192 " --> pdb=" O LEU1B 188 " (cutoff:3.500A) Processing helix chain '1B' and resid 205 through 215 removed outlier: 3.650A pdb=" N ALA1B 212 " --> pdb=" O LEU1B 208 " (cutoff:3.500A) Processing helix chain '1B' and resid 226 through 236 Processing helix chain '1B' and resid 250 through 252 No H-bonds generated for 'chain '1B' and resid 250 through 252' Processing helix chain '1B' and resid 289 through 293 Processing helix chain '1B' and resid 325 through 327 No H-bonds generated for 'chain '1B' and resid 325 through 327' Processing helix chain '1B' and resid 330 through 336 removed outlier: 3.514A pdb=" N LYS1B 335 " --> pdb=" O ALA1B 331 " (cutoff:3.500A) Processing helix chain '1B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU1B 379 " --> pdb=" O ALA1B 376 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN1B 384 " --> pdb=" O LEU1B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP1B 386 " --> pdb=" O ALA1B 383 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE1B 387 " --> pdb=" O GLN1B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET1B 388 " --> pdb=" O PHE1B 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE1B 389 " --> pdb=" O ASP1B 386 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP1B 390 " --> pdb=" O ILE1B 387 " (cutoff:3.500A) Processing helix chain '1B' and resid 395 through 401 removed outlier: 4.403A pdb=" N ASN1B 400 " --> pdb=" O TRP1B 397 " (cutoff:3.500A) Processing helix chain '1B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA1B 411 " --> pdb=" O MET1B 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN1B 414 " --> pdb=" O LYS1B 410 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE1B 415 " --> pdb=" O ALA1B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG1B 423 " --> pdb=" O ALA1B 419 " (cutoff:3.500A) Processing helix chain '1C' and resid 4 through 25 Processing helix chain '1C' and resid 30 through 46 removed outlier: 3.531A pdb=" N VAL1C 39 " --> pdb=" O GLU1C 35 " (cutoff:3.500A) Processing helix chain '1C' and resid 50 through 66 Processing helix chain '1C' and resid 72 through 89 Processing helix chain '1C' and resid 92 through 108 Processing helix chain '1C' and resid 111 through 113 No H-bonds generated for 'chain '1C' and resid 111 through 113' Processing helix chain '1C' and resid 115 through 130 Processing helix chain '1C' and resid 134 through 151 Processing helix chain '1C' and resid 157 through 172 Processing helix chain '1C' and resid 176 through 192 removed outlier: 3.823A pdb=" N ASN1C 192 " --> pdb=" O ALA1C 188 " (cutoff:3.500A) Processing helix chain '1C' and resid 200 through 216 Processing helix chain '1C' and resid 220 through 236 Processing helix chain '2A' and resid 12 through 29 removed outlier: 3.532A pdb=" N SER2A 21 " --> pdb=" O GLN2A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS2A 24 " --> pdb=" O ALA2A 20 " (cutoff:3.500A) Processing helix chain '2A' and resid 49 through 51 No H-bonds generated for 'chain '2A' and resid 49 through 51' Processing helix chain '2A' and resid 75 through 83 Processing helix chain '2A' and resid 105 through 108 No H-bonds generated for 'chain '2A' and resid 105 through 108' Processing helix chain '2A' and resid 112 through 130 Proline residue: 2A 118 - end of helix removed outlier: 3.518A pdb=" N SER2A 122 " --> pdb=" O PRO2A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR2A 126 " --> pdb=" O SER2A 122 " (cutoff:3.500A) Processing helix chain '2A' and resid 151 through 158 removed outlier: 3.650A pdb=" N GLU2A 157 " --> pdb=" O ALA2A 153 " (cutoff:3.500A) Processing helix chain '2A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL2A 190 " --> pdb=" O PRO2A 186 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN2A 194 " --> pdb=" O VAL2A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR2A 195 " --> pdb=" O PHE2A 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG2A 197 " --> pdb=" O LEU2A 193 " (cutoff:3.500A) Processing helix chain '2A' and resid 208 through 216 removed outlier: 3.713A pdb=" N ALA2A 215 " --> pdb=" O LEU2A 211 " (cutoff:3.500A) Processing helix chain '2A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU2A 231 " --> pdb=" O ASP2A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR2A 234 " --> pdb=" O ASN2A 230 " (cutoff:3.500A) Processing helix chain '2A' and resid 242 through 245 No H-bonds generated for 'chain '2A' and resid 242 through 245' Processing helix chain '2A' and resid 256 through 260 Processing helix chain '2A' and resid 292 through 299 removed outlier: 3.766A pdb=" N ILE2A 296 " --> pdb=" O ILE2A 292 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS2A 297 " --> pdb=" O GLU2A 293 " (cutoff:3.500A) Processing helix chain '2A' and resid 302 through 304 No H-bonds generated for 'chain '2A' and resid 302 through 304' Processing helix chain '2A' and resid 311 through 313 No H-bonds generated for 'chain '2A' and resid 311 through 313' Processing helix chain '2A' and resid 336 through 343 removed outlier: 3.622A pdb=" N GLU2A 342 " --> pdb=" O ALA2A 338 " (cutoff:3.500A) Processing helix chain '2A' and resid 378 through 395 removed outlier: 3.889A pdb=" N VAL2A 382 " --> pdb=" O ILE2A 379 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP2A 384 " --> pdb=" O ARG2A 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE2A 386 " --> pdb=" O LEU2A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN2A 389 " --> pdb=" O ILE2A 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE2A 390 " --> pdb=" O CYS2A 387 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS2A 392 " --> pdb=" O ASN2A 389 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN2A 395 " --> pdb=" O LYS2A 392 " (cutoff:3.500A) Processing helix chain '2A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR2A 427 " --> pdb=" O LEU2A 423 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU2A 432 " --> pdb=" O GLN2A 428 " (cutoff:3.500A) Processing helix chain '2B' and resid 10 through 27 removed outlier: 3.643A pdb=" N ARG2B 22 " --> pdb=" O ASP2B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU2B 25 " --> pdb=" O TRP2B 21 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG2B 26 " --> pdb=" O ARG2B 22 " (cutoff:3.500A) Processing helix chain '2B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY2B 80 " --> pdb=" O ARG2B 76 " (cutoff:3.500A) Processing helix chain '2B' and resid 102 through 106 Processing helix chain '2B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER2B 123 " --> pdb=" O ASN2B 119 " (cutoff:3.500A) Processing helix chain '2B' and resid 148 through 159 removed outlier: 3.601A pdb=" N GLU2B 154 " --> pdb=" O SER2B 150 " (cutoff:3.500A) Processing helix chain '2B' and resid 182 through 196 removed outlier: 3.909A pdb=" N ILE2B 187 " --> pdb=" O PRO2B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG2B 192 " --> pdb=" O LEU2B 188 " (cutoff:3.500A) Processing helix chain '2B' and resid 205 through 215 removed outlier: 3.650A pdb=" N ALA2B 212 " --> pdb=" O LEU2B 208 " (cutoff:3.500A) Processing helix chain '2B' and resid 226 through 236 Processing helix chain '2B' and resid 250 through 252 No H-bonds generated for 'chain '2B' and resid 250 through 252' Processing helix chain '2B' and resid 289 through 293 Processing helix chain '2B' and resid 325 through 327 No H-bonds generated for 'chain '2B' and resid 325 through 327' Processing helix chain '2B' and resid 330 through 336 removed outlier: 3.515A pdb=" N LYS2B 335 " --> pdb=" O ALA2B 331 " (cutoff:3.500A) Processing helix chain '2B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU2B 379 " --> pdb=" O ALA2B 376 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN2B 384 " --> pdb=" O LEU2B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP2B 386 " --> pdb=" O ALA2B 383 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE2B 387 " --> pdb=" O GLN2B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET2B 388 " --> pdb=" O PHE2B 385 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE2B 389 " --> pdb=" O ASP2B 386 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP2B 390 " --> pdb=" O ILE2B 387 " (cutoff:3.500A) Processing helix chain '2B' and resid 395 through 401 removed outlier: 4.402A pdb=" N ASN2B 400 " --> pdb=" O TRP2B 397 " (cutoff:3.500A) Processing helix chain '2B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA2B 411 " --> pdb=" O MET2B 407 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN2B 414 " --> pdb=" O LYS2B 410 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2B 415 " --> pdb=" O ALA2B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG2B 423 " --> pdb=" O ALA2B 419 " (cutoff:3.500A) Processing helix chain '2C' and resid 4 through 25 Processing helix chain '2C' and resid 30 through 46 removed outlier: 3.530A pdb=" N VAL2C 39 " --> pdb=" O GLU2C 35 " (cutoff:3.500A) Processing helix chain '2C' and resid 50 through 66 Processing helix chain '2C' and resid 72 through 89 Processing helix chain '2C' and resid 92 through 108 Processing helix chain '2C' and resid 111 through 113 No H-bonds generated for 'chain '2C' and resid 111 through 113' Processing helix chain '2C' and resid 115 through 130 Processing helix chain '2C' and resid 134 through 151 Processing helix chain '2C' and resid 157 through 172 Processing helix chain '2C' and resid 176 through 192 removed outlier: 3.822A pdb=" N ASN2C 192 " --> pdb=" O ALA2C 188 " (cutoff:3.500A) Processing helix chain '2C' and resid 200 through 216 Processing helix chain '2C' and resid 220 through 236 Processing helix chain '3A' and resid 12 through 29 removed outlier: 3.533A pdb=" N SER3A 21 " --> pdb=" O GLN3A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS3A 24 " --> pdb=" O ALA3A 20 " (cutoff:3.500A) Processing helix chain '3A' and resid 49 through 51 No H-bonds generated for 'chain '3A' and resid 49 through 51' Processing helix chain '3A' and resid 75 through 83 Processing helix chain '3A' and resid 105 through 108 No H-bonds generated for 'chain '3A' and resid 105 through 108' Processing helix chain '3A' and resid 112 through 130 Proline residue: 3A 118 - end of helix removed outlier: 3.518A pdb=" N SER3A 122 " --> pdb=" O PRO3A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR3A 126 " --> pdb=" O SER3A 122 " (cutoff:3.500A) Processing helix chain '3A' and resid 151 through 158 removed outlier: 3.650A pdb=" N GLU3A 157 " --> pdb=" O ALA3A 153 " (cutoff:3.500A) Processing helix chain '3A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL3A 190 " --> pdb=" O PRO3A 186 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN3A 194 " --> pdb=" O VAL3A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR3A 195 " --> pdb=" O PHE3A 191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG3A 197 " --> pdb=" O LEU3A 193 " (cutoff:3.500A) Processing helix chain '3A' and resid 208 through 216 removed outlier: 3.713A pdb=" N ALA3A 215 " --> pdb=" O LEU3A 211 " (cutoff:3.500A) Processing helix chain '3A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU3A 231 " --> pdb=" O ASP3A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR3A 234 " --> pdb=" O ASN3A 230 " (cutoff:3.500A) Processing helix chain '3A' and resid 242 through 245 No H-bonds generated for 'chain '3A' and resid 242 through 245' Processing helix chain '3A' and resid 256 through 260 Processing helix chain '3A' and resid 292 through 299 removed outlier: 3.766A pdb=" N ILE3A 296 " --> pdb=" O ILE3A 292 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS3A 297 " --> pdb=" O GLU3A 293 " (cutoff:3.500A) Processing helix chain '3A' and resid 302 through 304 No H-bonds generated for 'chain '3A' and resid 302 through 304' Processing helix chain '3A' and resid 311 through 313 No H-bonds generated for 'chain '3A' and resid 311 through 313' Processing helix chain '3A' and resid 336 through 343 removed outlier: 3.622A pdb=" N GLU3A 342 " --> pdb=" O ALA3A 338 " (cutoff:3.500A) Processing helix chain '3A' and resid 378 through 395 removed outlier: 3.888A pdb=" N VAL3A 382 " --> pdb=" O ILE3A 379 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP3A 384 " --> pdb=" O ARG3A 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE3A 386 " --> pdb=" O LEU3A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN3A 389 " --> pdb=" O ILE3A 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE3A 390 " --> pdb=" O CYS3A 387 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS3A 392 " --> pdb=" O ASN3A 389 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN3A 395 " --> pdb=" O LYS3A 392 " (cutoff:3.500A) Processing helix chain '3A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR3A 427 " --> pdb=" O LEU3A 423 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU3A 432 " --> pdb=" O GLN3A 428 " (cutoff:3.500A) Processing helix chain '3B' and resid 10 through 27 removed outlier: 3.644A pdb=" N ARG3B 22 " --> pdb=" O ASP3B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU3B 25 " --> pdb=" O TRP3B 21 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG3B 26 " --> pdb=" O ARG3B 22 " (cutoff:3.500A) Processing helix chain '3B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY3B 80 " --> pdb=" O ARG3B 76 " (cutoff:3.500A) Processing helix chain '3B' and resid 102 through 106 Processing helix chain '3B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER3B 123 " --> pdb=" O ASN3B 119 " (cutoff:3.500A) Processing helix chain '3B' and resid 148 through 159 removed outlier: 3.601A pdb=" N GLU3B 154 " --> pdb=" O SER3B 150 " (cutoff:3.500A) Processing helix chain '3B' and resid 182 through 196 removed outlier: 3.909A pdb=" N ILE3B 187 " --> pdb=" O PRO3B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG3B 192 " --> pdb=" O LEU3B 188 " (cutoff:3.500A) Processing helix chain '3B' and resid 205 through 215 removed outlier: 3.650A pdb=" N ALA3B 212 " --> pdb=" O LEU3B 208 " (cutoff:3.500A) Processing helix chain '3B' and resid 226 through 236 Processing helix chain '3B' and resid 250 through 252 No H-bonds generated for 'chain '3B' and resid 250 through 252' Processing helix chain '3B' and resid 289 through 293 Processing helix chain '3B' and resid 325 through 327 No H-bonds generated for 'chain '3B' and resid 325 through 327' Processing helix chain '3B' and resid 330 through 336 removed outlier: 3.515A pdb=" N LYS3B 335 " --> pdb=" O ALA3B 331 " (cutoff:3.500A) Processing helix chain '3B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU3B 379 " --> pdb=" O ALA3B 376 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN3B 384 " --> pdb=" O LEU3B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP3B 386 " --> pdb=" O ALA3B 383 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE3B 387 " --> pdb=" O GLN3B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET3B 388 " --> pdb=" O PHE3B 385 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE3B 389 " --> pdb=" O ASP3B 386 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP3B 390 " --> pdb=" O ILE3B 387 " (cutoff:3.500A) Processing helix chain '3B' and resid 395 through 401 removed outlier: 4.403A pdb=" N ASN3B 400 " --> pdb=" O TRP3B 397 " (cutoff:3.500A) Processing helix chain '3B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA3B 411 " --> pdb=" O MET3B 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN3B 414 " --> pdb=" O LYS3B 410 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3B 415 " --> pdb=" O ALA3B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG3B 423 " --> pdb=" O ALA3B 419 " (cutoff:3.500A) Processing helix chain '3C' and resid 4 through 25 Processing helix chain '3C' and resid 30 through 46 removed outlier: 3.531A pdb=" N VAL3C 39 " --> pdb=" O GLU3C 35 " (cutoff:3.500A) Processing helix chain '3C' and resid 50 through 66 Processing helix chain '3C' and resid 72 through 89 Processing helix chain '3C' and resid 92 through 108 Processing helix chain '3C' and resid 111 through 113 No H-bonds generated for 'chain '3C' and resid 111 through 113' Processing helix chain '3C' and resid 115 through 130 Processing helix chain '3C' and resid 134 through 151 Processing helix chain '3C' and resid 157 through 172 Processing helix chain '3C' and resid 176 through 192 removed outlier: 3.822A pdb=" N ASN3C 192 " --> pdb=" O ALA3C 188 " (cutoff:3.500A) Processing helix chain '3C' and resid 200 through 216 Processing helix chain '3C' and resid 220 through 236 Processing helix chain '4A' and resid 12 through 29 removed outlier: 3.533A pdb=" N SER4A 21 " --> pdb=" O GLN4A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS4A 24 " --> pdb=" O ALA4A 20 " (cutoff:3.500A) Processing helix chain '4A' and resid 49 through 51 No H-bonds generated for 'chain '4A' and resid 49 through 51' Processing helix chain '4A' and resid 75 through 83 Processing helix chain '4A' and resid 105 through 108 No H-bonds generated for 'chain '4A' and resid 105 through 108' Processing helix chain '4A' and resid 112 through 130 Proline residue: 4A 118 - end of helix removed outlier: 3.518A pdb=" N SER4A 122 " --> pdb=" O PRO4A 118 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR4A 126 " --> pdb=" O SER4A 122 " (cutoff:3.500A) Processing helix chain '4A' and resid 151 through 158 removed outlier: 3.649A pdb=" N GLU4A 157 " --> pdb=" O ALA4A 153 " (cutoff:3.500A) Processing helix chain '4A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL4A 190 " --> pdb=" O PRO4A 186 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN4A 194 " --> pdb=" O VAL4A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR4A 195 " --> pdb=" O PHE4A 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG4A 197 " --> pdb=" O LEU4A 193 " (cutoff:3.500A) Processing helix chain '4A' and resid 208 through 216 removed outlier: 3.713A pdb=" N ALA4A 215 " --> pdb=" O LEU4A 211 " (cutoff:3.500A) Processing helix chain '4A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU4A 231 " --> pdb=" O ASP4A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR4A 234 " --> pdb=" O ASN4A 230 " (cutoff:3.500A) Processing helix chain '4A' and resid 242 through 245 No H-bonds generated for 'chain '4A' and resid 242 through 245' Processing helix chain '4A' and resid 256 through 260 Processing helix chain '4A' and resid 292 through 299 removed outlier: 3.765A pdb=" N ILE4A 296 " --> pdb=" O ILE4A 292 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS4A 297 " --> pdb=" O GLU4A 293 " (cutoff:3.500A) Processing helix chain '4A' and resid 302 through 304 No H-bonds generated for 'chain '4A' and resid 302 through 304' Processing helix chain '4A' and resid 311 through 313 No H-bonds generated for 'chain '4A' and resid 311 through 313' Processing helix chain '4A' and resid 336 through 343 removed outlier: 3.623A pdb=" N GLU4A 342 " --> pdb=" O ALA4A 338 " (cutoff:3.500A) Processing helix chain '4A' and resid 378 through 395 removed outlier: 3.889A pdb=" N VAL4A 382 " --> pdb=" O ILE4A 379 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP4A 384 " --> pdb=" O ARG4A 381 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE4A 386 " --> pdb=" O LEU4A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN4A 389 " --> pdb=" O ILE4A 386 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE4A 390 " --> pdb=" O CYS4A 387 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS4A 392 " --> pdb=" O ASN4A 389 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN4A 395 " --> pdb=" O LYS4A 392 " (cutoff:3.500A) Processing helix chain '4A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR4A 427 " --> pdb=" O LEU4A 423 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU4A 432 " --> pdb=" O GLN4A 428 " (cutoff:3.500A) Processing helix chain '4B' and resid 10 through 27 removed outlier: 3.643A pdb=" N ARG4B 22 " --> pdb=" O ASP4B 18 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU4B 25 " --> pdb=" O TRP4B 21 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG4B 26 " --> pdb=" O ARG4B 22 " (cutoff:3.500A) Processing helix chain '4B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY4B 80 " --> pdb=" O ARG4B 76 " (cutoff:3.500A) Processing helix chain '4B' and resid 102 through 106 Processing helix chain '4B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER4B 123 " --> pdb=" O ASN4B 119 " (cutoff:3.500A) Processing helix chain '4B' and resid 148 through 159 removed outlier: 3.600A pdb=" N GLU4B 154 " --> pdb=" O SER4B 150 " (cutoff:3.500A) Processing helix chain '4B' and resid 182 through 196 removed outlier: 3.909A pdb=" N ILE4B 187 " --> pdb=" O PRO4B 183 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG4B 192 " --> pdb=" O LEU4B 188 " (cutoff:3.500A) Processing helix chain '4B' and resid 205 through 215 removed outlier: 3.649A pdb=" N ALA4B 212 " --> pdb=" O LEU4B 208 " (cutoff:3.500A) Processing helix chain '4B' and resid 226 through 236 Processing helix chain '4B' and resid 250 through 252 No H-bonds generated for 'chain '4B' and resid 250 through 252' Processing helix chain '4B' and resid 289 through 293 Processing helix chain '4B' and resid 325 through 327 No H-bonds generated for 'chain '4B' and resid 325 through 327' Processing helix chain '4B' and resid 330 through 336 removed outlier: 3.515A pdb=" N LYS4B 335 " --> pdb=" O ALA4B 331 " (cutoff:3.500A) Processing helix chain '4B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU4B 379 " --> pdb=" O ALA4B 376 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN4B 384 " --> pdb=" O LEU4B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP4B 386 " --> pdb=" O ALA4B 383 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE4B 387 " --> pdb=" O GLN4B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET4B 388 " --> pdb=" O PHE4B 385 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE4B 389 " --> pdb=" O ASP4B 386 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP4B 390 " --> pdb=" O ILE4B 387 " (cutoff:3.500A) Processing helix chain '4B' and resid 395 through 401 removed outlier: 4.403A pdb=" N ASN4B 400 " --> pdb=" O TRP4B 397 " (cutoff:3.500A) Processing helix chain '4B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA4B 411 " --> pdb=" O MET4B 407 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN4B 414 " --> pdb=" O LYS4B 410 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4B 415 " --> pdb=" O ALA4B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG4B 423 " --> pdb=" O ALA4B 419 " (cutoff:3.500A) Processing helix chain '4C' and resid 4 through 25 Processing helix chain '4C' and resid 30 through 46 removed outlier: 3.531A pdb=" N VAL4C 39 " --> pdb=" O GLU4C 35 " (cutoff:3.500A) Processing helix chain '4C' and resid 50 through 66 Processing helix chain '4C' and resid 72 through 89 Processing helix chain '4C' and resid 92 through 108 Processing helix chain '4C' and resid 111 through 113 No H-bonds generated for 'chain '4C' and resid 111 through 113' Processing helix chain '4C' and resid 115 through 130 Processing helix chain '4C' and resid 134 through 151 Processing helix chain '4C' and resid 157 through 172 Processing helix chain '4C' and resid 176 through 192 removed outlier: 3.821A pdb=" N ASN4C 192 " --> pdb=" O ALA4C 188 " (cutoff:3.500A) Processing helix chain '4C' and resid 200 through 216 Processing helix chain '4C' and resid 220 through 236 Processing helix chain '5A' and resid 12 through 29 removed outlier: 3.533A pdb=" N SER5A 21 " --> pdb=" O GLN5A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS5A 24 " --> pdb=" O ALA5A 20 " (cutoff:3.500A) Processing helix chain '5A' and resid 49 through 51 No H-bonds generated for 'chain '5A' and resid 49 through 51' Processing helix chain '5A' and resid 75 through 83 Processing helix chain '5A' and resid 105 through 108 No H-bonds generated for 'chain '5A' and resid 105 through 108' Processing helix chain '5A' and resid 112 through 130 Proline residue: 5A 118 - end of helix removed outlier: 3.518A pdb=" N SER5A 122 " --> pdb=" O PRO5A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR5A 126 " --> pdb=" O SER5A 122 " (cutoff:3.500A) Processing helix chain '5A' and resid 151 through 158 removed outlier: 3.648A pdb=" N GLU5A 157 " --> pdb=" O ALA5A 153 " (cutoff:3.500A) Processing helix chain '5A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL5A 190 " --> pdb=" O PRO5A 186 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN5A 194 " --> pdb=" O VAL5A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR5A 195 " --> pdb=" O PHE5A 191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG5A 197 " --> pdb=" O LEU5A 193 " (cutoff:3.500A) Processing helix chain '5A' and resid 208 through 216 removed outlier: 3.714A pdb=" N ALA5A 215 " --> pdb=" O LEU5A 211 " (cutoff:3.500A) Processing helix chain '5A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU5A 231 " --> pdb=" O ASP5A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR5A 234 " --> pdb=" O ASN5A 230 " (cutoff:3.500A) Processing helix chain '5A' and resid 242 through 245 No H-bonds generated for 'chain '5A' and resid 242 through 245' Processing helix chain '5A' and resid 256 through 260 Processing helix chain '5A' and resid 292 through 299 removed outlier: 3.765A pdb=" N ILE5A 296 " --> pdb=" O ILE5A 292 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS5A 297 " --> pdb=" O GLU5A 293 " (cutoff:3.500A) Processing helix chain '5A' and resid 302 through 304 No H-bonds generated for 'chain '5A' and resid 302 through 304' Processing helix chain '5A' and resid 311 through 313 No H-bonds generated for 'chain '5A' and resid 311 through 313' Processing helix chain '5A' and resid 336 through 343 removed outlier: 3.622A pdb=" N GLU5A 342 " --> pdb=" O ALA5A 338 " (cutoff:3.500A) Processing helix chain '5A' and resid 378 through 395 removed outlier: 3.888A pdb=" N VAL5A 382 " --> pdb=" O ILE5A 379 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP5A 384 " --> pdb=" O ARG5A 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE5A 386 " --> pdb=" O LEU5A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN5A 389 " --> pdb=" O ILE5A 386 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE5A 390 " --> pdb=" O CYS5A 387 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS5A 392 " --> pdb=" O ASN5A 389 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN5A 395 " --> pdb=" O LYS5A 392 " (cutoff:3.500A) Processing helix chain '5A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR5A 427 " --> pdb=" O LEU5A 423 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU5A 432 " --> pdb=" O GLN5A 428 " (cutoff:3.500A) Processing helix chain '5B' and resid 10 through 27 removed outlier: 3.642A pdb=" N ARG5B 22 " --> pdb=" O ASP5B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU5B 25 " --> pdb=" O TRP5B 21 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG5B 26 " --> pdb=" O ARG5B 22 " (cutoff:3.500A) Processing helix chain '5B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY5B 80 " --> pdb=" O ARG5B 76 " (cutoff:3.500A) Processing helix chain '5B' and resid 102 through 106 Processing helix chain '5B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER5B 123 " --> pdb=" O ASN5B 119 " (cutoff:3.500A) Processing helix chain '5B' and resid 148 through 159 removed outlier: 3.601A pdb=" N GLU5B 154 " --> pdb=" O SER5B 150 " (cutoff:3.500A) Processing helix chain '5B' and resid 182 through 196 removed outlier: 3.910A pdb=" N ILE5B 187 " --> pdb=" O PRO5B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG5B 192 " --> pdb=" O LEU5B 188 " (cutoff:3.500A) Processing helix chain '5B' and resid 205 through 215 removed outlier: 3.650A pdb=" N ALA5B 212 " --> pdb=" O LEU5B 208 " (cutoff:3.500A) Processing helix chain '5B' and resid 226 through 236 Processing helix chain '5B' and resid 250 through 252 No H-bonds generated for 'chain '5B' and resid 250 through 252' Processing helix chain '5B' and resid 289 through 293 Processing helix chain '5B' and resid 325 through 327 No H-bonds generated for 'chain '5B' and resid 325 through 327' Processing helix chain '5B' and resid 330 through 336 removed outlier: 3.515A pdb=" N LYS5B 335 " --> pdb=" O ALA5B 331 " (cutoff:3.500A) Processing helix chain '5B' and resid 372 through 390 removed outlier: 3.584A pdb=" N GLU5B 379 " --> pdb=" O ALA5B 376 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN5B 384 " --> pdb=" O LEU5B 381 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP5B 386 " --> pdb=" O ALA5B 383 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE5B 387 " --> pdb=" O GLN5B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET5B 388 " --> pdb=" O PHE5B 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE5B 389 " --> pdb=" O ASP5B 386 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP5B 390 " --> pdb=" O ILE5B 387 " (cutoff:3.500A) Processing helix chain '5B' and resid 395 through 401 removed outlier: 4.403A pdb=" N ASN5B 400 " --> pdb=" O TRP5B 397 " (cutoff:3.500A) Processing helix chain '5B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA5B 411 " --> pdb=" O MET5B 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN5B 414 " --> pdb=" O LYS5B 410 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE5B 415 " --> pdb=" O ALA5B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG5B 423 " --> pdb=" O ALA5B 419 " (cutoff:3.500A) Processing helix chain '5C' and resid 4 through 25 Processing helix chain '5C' and resid 30 through 46 removed outlier: 3.531A pdb=" N VAL5C 39 " --> pdb=" O GLU5C 35 " (cutoff:3.500A) Processing helix chain '5C' and resid 50 through 66 Processing helix chain '5C' and resid 72 through 89 Processing helix chain '5C' and resid 92 through 108 Processing helix chain '5C' and resid 111 through 113 No H-bonds generated for 'chain '5C' and resid 111 through 113' Processing helix chain '5C' and resid 115 through 130 Processing helix chain '5C' and resid 134 through 151 Processing helix chain '5C' and resid 157 through 172 Processing helix chain '5C' and resid 176 through 192 removed outlier: 3.823A pdb=" N ASN5C 192 " --> pdb=" O ALA5C 188 " (cutoff:3.500A) Processing helix chain '5C' and resid 200 through 216 Processing helix chain '5C' and resid 220 through 236 Processing helix chain '6A' and resid 12 through 29 removed outlier: 3.532A pdb=" N SER6A 21 " --> pdb=" O GLN6A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS6A 24 " --> pdb=" O ALA6A 20 " (cutoff:3.500A) Processing helix chain '6A' and resid 49 through 51 No H-bonds generated for 'chain '6A' and resid 49 through 51' Processing helix chain '6A' and resid 75 through 83 Processing helix chain '6A' and resid 105 through 108 No H-bonds generated for 'chain '6A' and resid 105 through 108' Processing helix chain '6A' and resid 112 through 130 Proline residue: 6A 118 - end of helix removed outlier: 3.518A pdb=" N SER6A 122 " --> pdb=" O PRO6A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR6A 126 " --> pdb=" O SER6A 122 " (cutoff:3.500A) Processing helix chain '6A' and resid 151 through 158 removed outlier: 3.650A pdb=" N GLU6A 157 " --> pdb=" O ALA6A 153 " (cutoff:3.500A) Processing helix chain '6A' and resid 185 through 198 removed outlier: 3.935A pdb=" N VAL6A 190 " --> pdb=" O PRO6A 186 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN6A 194 " --> pdb=" O VAL6A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR6A 195 " --> pdb=" O PHE6A 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG6A 197 " --> pdb=" O LEU6A 193 " (cutoff:3.500A) Processing helix chain '6A' and resid 208 through 216 removed outlier: 3.714A pdb=" N ALA6A 215 " --> pdb=" O LEU6A 211 " (cutoff:3.500A) Processing helix chain '6A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU6A 231 " --> pdb=" O ASP6A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR6A 234 " --> pdb=" O ASN6A 230 " (cutoff:3.500A) Processing helix chain '6A' and resid 242 through 245 No H-bonds generated for 'chain '6A' and resid 242 through 245' Processing helix chain '6A' and resid 256 through 260 Processing helix chain '6A' and resid 292 through 299 removed outlier: 3.766A pdb=" N ILE6A 296 " --> pdb=" O ILE6A 292 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS6A 297 " --> pdb=" O GLU6A 293 " (cutoff:3.500A) Processing helix chain '6A' and resid 302 through 304 No H-bonds generated for 'chain '6A' and resid 302 through 304' Processing helix chain '6A' and resid 311 through 313 No H-bonds generated for 'chain '6A' and resid 311 through 313' Processing helix chain '6A' and resid 336 through 343 removed outlier: 3.622A pdb=" N GLU6A 342 " --> pdb=" O ALA6A 338 " (cutoff:3.500A) Processing helix chain '6A' and resid 378 through 395 removed outlier: 3.888A pdb=" N VAL6A 382 " --> pdb=" O ILE6A 379 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP6A 384 " --> pdb=" O ARG6A 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE6A 386 " --> pdb=" O LEU6A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN6A 389 " --> pdb=" O ILE6A 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE6A 390 " --> pdb=" O CYS6A 387 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS6A 392 " --> pdb=" O ASN6A 389 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN6A 395 " --> pdb=" O LYS6A 392 " (cutoff:3.500A) Processing helix chain '6A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR6A 427 " --> pdb=" O LEU6A 423 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU6A 432 " --> pdb=" O GLN6A 428 " (cutoff:3.500A) Processing helix chain '6B' and resid 10 through 27 removed outlier: 3.643A pdb=" N ARG6B 22 " --> pdb=" O ASP6B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU6B 25 " --> pdb=" O TRP6B 21 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG6B 26 " --> pdb=" O ARG6B 22 " (cutoff:3.500A) Processing helix chain '6B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY6B 80 " --> pdb=" O ARG6B 76 " (cutoff:3.500A) Processing helix chain '6B' and resid 102 through 106 Processing helix chain '6B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER6B 123 " --> pdb=" O ASN6B 119 " (cutoff:3.500A) Processing helix chain '6B' and resid 148 through 159 removed outlier: 3.601A pdb=" N GLU6B 154 " --> pdb=" O SER6B 150 " (cutoff:3.500A) Processing helix chain '6B' and resid 182 through 196 removed outlier: 3.909A pdb=" N ILE6B 187 " --> pdb=" O PRO6B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG6B 192 " --> pdb=" O LEU6B 188 " (cutoff:3.500A) Processing helix chain '6B' and resid 205 through 215 removed outlier: 3.650A pdb=" N ALA6B 212 " --> pdb=" O LEU6B 208 " (cutoff:3.500A) Processing helix chain '6B' and resid 226 through 236 Processing helix chain '6B' and resid 250 through 252 No H-bonds generated for 'chain '6B' and resid 250 through 252' Processing helix chain '6B' and resid 289 through 293 Processing helix chain '6B' and resid 325 through 327 No H-bonds generated for 'chain '6B' and resid 325 through 327' Processing helix chain '6B' and resid 330 through 336 removed outlier: 3.515A pdb=" N LYS6B 335 " --> pdb=" O ALA6B 331 " (cutoff:3.500A) Processing helix chain '6B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU6B 379 " --> pdb=" O ALA6B 376 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLN6B 384 " --> pdb=" O LEU6B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP6B 386 " --> pdb=" O ALA6B 383 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE6B 387 " --> pdb=" O GLN6B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET6B 388 " --> pdb=" O PHE6B 385 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE6B 389 " --> pdb=" O ASP6B 386 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP6B 390 " --> pdb=" O ILE6B 387 " (cutoff:3.500A) Processing helix chain '6B' and resid 395 through 401 removed outlier: 4.403A pdb=" N ASN6B 400 " --> pdb=" O TRP6B 397 " (cutoff:3.500A) Processing helix chain '6B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA6B 411 " --> pdb=" O MET6B 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN6B 414 " --> pdb=" O LYS6B 410 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE6B 415 " --> pdb=" O ALA6B 411 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG6B 423 " --> pdb=" O ALA6B 419 " (cutoff:3.500A) Processing helix chain '6C' and resid 4 through 25 Processing helix chain '6C' and resid 30 through 46 removed outlier: 3.530A pdb=" N VAL6C 39 " --> pdb=" O GLU6C 35 " (cutoff:3.500A) Processing helix chain '6C' and resid 50 through 66 Processing helix chain '6C' and resid 72 through 89 Processing helix chain '6C' and resid 92 through 108 Processing helix chain '6C' and resid 111 through 113 No H-bonds generated for 'chain '6C' and resid 111 through 113' Processing helix chain '6C' and resid 115 through 130 Processing helix chain '6C' and resid 134 through 151 Processing helix chain '6C' and resid 157 through 172 Processing helix chain '6C' and resid 176 through 192 removed outlier: 3.822A pdb=" N ASN6C 192 " --> pdb=" O ALA6C 188 " (cutoff:3.500A) Processing helix chain '6C' and resid 200 through 216 Processing helix chain '6C' and resid 220 through 236 Processing helix chain '7A' and resid 12 through 29 removed outlier: 3.533A pdb=" N SER7A 21 " --> pdb=" O GLN7A 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS7A 24 " --> pdb=" O ALA7A 20 " (cutoff:3.500A) Processing helix chain '7A' and resid 49 through 51 No H-bonds generated for 'chain '7A' and resid 49 through 51' Processing helix chain '7A' and resid 75 through 83 Processing helix chain '7A' and resid 105 through 108 No H-bonds generated for 'chain '7A' and resid 105 through 108' Processing helix chain '7A' and resid 112 through 130 Proline residue: 7A 118 - end of helix removed outlier: 3.518A pdb=" N SER7A 122 " --> pdb=" O PRO7A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR7A 126 " --> pdb=" O SER7A 122 " (cutoff:3.500A) Processing helix chain '7A' and resid 151 through 158 removed outlier: 3.650A pdb=" N GLU7A 157 " --> pdb=" O ALA7A 153 " (cutoff:3.500A) Processing helix chain '7A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL7A 190 " --> pdb=" O PRO7A 186 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN7A 194 " --> pdb=" O VAL7A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR7A 195 " --> pdb=" O PHE7A 191 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG7A 197 " --> pdb=" O LEU7A 193 " (cutoff:3.500A) Processing helix chain '7A' and resid 208 through 216 removed outlier: 3.713A pdb=" N ALA7A 215 " --> pdb=" O LEU7A 211 " (cutoff:3.500A) Processing helix chain '7A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU7A 231 " --> pdb=" O ASP7A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR7A 234 " --> pdb=" O ASN7A 230 " (cutoff:3.500A) Processing helix chain '7A' and resid 242 through 245 No H-bonds generated for 'chain '7A' and resid 242 through 245' Processing helix chain '7A' and resid 256 through 260 Processing helix chain '7A' and resid 292 through 299 removed outlier: 3.766A pdb=" N ILE7A 296 " --> pdb=" O ILE7A 292 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS7A 297 " --> pdb=" O GLU7A 293 " (cutoff:3.500A) Processing helix chain '7A' and resid 302 through 304 No H-bonds generated for 'chain '7A' and resid 302 through 304' Processing helix chain '7A' and resid 311 through 313 No H-bonds generated for 'chain '7A' and resid 311 through 313' Processing helix chain '7A' and resid 336 through 343 removed outlier: 3.622A pdb=" N GLU7A 342 " --> pdb=" O ALA7A 338 " (cutoff:3.500A) Processing helix chain '7A' and resid 378 through 395 removed outlier: 3.888A pdb=" N VAL7A 382 " --> pdb=" O ILE7A 379 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP7A 384 " --> pdb=" O ARG7A 381 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE7A 386 " --> pdb=" O LEU7A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN7A 389 " --> pdb=" O ILE7A 386 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE7A 390 " --> pdb=" O CYS7A 387 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS7A 392 " --> pdb=" O ASN7A 389 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN7A 395 " --> pdb=" O LYS7A 392 " (cutoff:3.500A) Processing helix chain '7A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR7A 427 " --> pdb=" O LEU7A 423 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU7A 432 " --> pdb=" O GLN7A 428 " (cutoff:3.500A) Processing helix chain '7B' and resid 10 through 27 removed outlier: 3.644A pdb=" N ARG7B 22 " --> pdb=" O ASP7B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU7B 25 " --> pdb=" O TRP7B 21 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG7B 26 " --> pdb=" O ARG7B 22 " (cutoff:3.500A) Processing helix chain '7B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY7B 80 " --> pdb=" O ARG7B 76 " (cutoff:3.500A) Processing helix chain '7B' and resid 102 through 106 Processing helix chain '7B' and resid 114 through 125 removed outlier: 3.575A pdb=" N SER7B 123 " --> pdb=" O ASN7B 119 " (cutoff:3.500A) Processing helix chain '7B' and resid 148 through 159 removed outlier: 3.601A pdb=" N GLU7B 154 " --> pdb=" O SER7B 150 " (cutoff:3.500A) Processing helix chain '7B' and resid 182 through 196 removed outlier: 3.909A pdb=" N ILE7B 187 " --> pdb=" O PRO7B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG7B 192 " --> pdb=" O LEU7B 188 " (cutoff:3.500A) Processing helix chain '7B' and resid 205 through 215 removed outlier: 3.650A pdb=" N ALA7B 212 " --> pdb=" O LEU7B 208 " (cutoff:3.500A) Processing helix chain '7B' and resid 226 through 236 Processing helix chain '7B' and resid 250 through 252 No H-bonds generated for 'chain '7B' and resid 250 through 252' Processing helix chain '7B' and resid 289 through 293 Processing helix chain '7B' and resid 325 through 327 No H-bonds generated for 'chain '7B' and resid 325 through 327' Processing helix chain '7B' and resid 330 through 336 removed outlier: 3.516A pdb=" N LYS7B 335 " --> pdb=" O ALA7B 331 " (cutoff:3.500A) Processing helix chain '7B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU7B 379 " --> pdb=" O ALA7B 376 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN7B 384 " --> pdb=" O LEU7B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP7B 386 " --> pdb=" O ALA7B 383 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE7B 387 " --> pdb=" O GLN7B 384 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET7B 388 " --> pdb=" O PHE7B 385 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE7B 389 " --> pdb=" O ASP7B 386 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP7B 390 " --> pdb=" O ILE7B 387 " (cutoff:3.500A) Processing helix chain '7B' and resid 395 through 401 removed outlier: 4.404A pdb=" N ASN7B 400 " --> pdb=" O TRP7B 397 " (cutoff:3.500A) Processing helix chain '7B' and resid 405 through 423 removed outlier: 3.633A pdb=" N ALA7B 411 " --> pdb=" O MET7B 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN7B 414 " --> pdb=" O LYS7B 410 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE7B 415 " --> pdb=" O ALA7B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG7B 423 " --> pdb=" O ALA7B 419 " (cutoff:3.500A) Processing helix chain '7C' and resid 4 through 25 Processing helix chain '7C' and resid 30 through 46 removed outlier: 3.531A pdb=" N VAL7C 39 " --> pdb=" O GLU7C 35 " (cutoff:3.500A) Processing helix chain '7C' and resid 50 through 66 Processing helix chain '7C' and resid 72 through 89 Processing helix chain '7C' and resid 92 through 108 Processing helix chain '7C' and resid 111 through 113 No H-bonds generated for 'chain '7C' and resid 111 through 113' Processing helix chain '7C' and resid 115 through 130 Processing helix chain '7C' and resid 134 through 151 Processing helix chain '7C' and resid 157 through 172 Processing helix chain '7C' and resid 176 through 192 removed outlier: 3.822A pdb=" N ASN7C 192 " --> pdb=" O ALA7C 188 " (cutoff:3.500A) Processing helix chain '7C' and resid 200 through 216 Processing helix chain '7C' and resid 220 through 236 Processing helix chain '8A' and resid 12 through 29 removed outlier: 3.533A pdb=" N SER8A 21 " --> pdb=" O GLN8A 17 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS8A 24 " --> pdb=" O ALA8A 20 " (cutoff:3.500A) Processing helix chain '8A' and resid 49 through 51 No H-bonds generated for 'chain '8A' and resid 49 through 51' Processing helix chain '8A' and resid 75 through 83 Processing helix chain '8A' and resid 105 through 108 No H-bonds generated for 'chain '8A' and resid 105 through 108' Processing helix chain '8A' and resid 112 through 130 Proline residue: 8A 118 - end of helix removed outlier: 3.518A pdb=" N SER8A 122 " --> pdb=" O PRO8A 118 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR8A 126 " --> pdb=" O SER8A 122 " (cutoff:3.500A) Processing helix chain '8A' and resid 151 through 158 removed outlier: 3.649A pdb=" N GLU8A 157 " --> pdb=" O ALA8A 153 " (cutoff:3.500A) Processing helix chain '8A' and resid 185 through 198 removed outlier: 3.934A pdb=" N VAL8A 190 " --> pdb=" O PRO8A 186 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN8A 194 " --> pdb=" O VAL8A 190 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR8A 195 " --> pdb=" O PHE8A 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG8A 197 " --> pdb=" O LEU8A 193 " (cutoff:3.500A) Processing helix chain '8A' and resid 208 through 216 removed outlier: 3.713A pdb=" N ALA8A 215 " --> pdb=" O LEU8A 211 " (cutoff:3.500A) Processing helix chain '8A' and resid 226 through 237 removed outlier: 3.806A pdb=" N LEU8A 231 " --> pdb=" O ASP8A 227 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR8A 234 " --> pdb=" O ASN8A 230 " (cutoff:3.500A) Processing helix chain '8A' and resid 242 through 245 No H-bonds generated for 'chain '8A' and resid 242 through 245' Processing helix chain '8A' and resid 256 through 260 Processing helix chain '8A' and resid 292 through 299 removed outlier: 3.764A pdb=" N ILE8A 296 " --> pdb=" O ILE8A 292 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS8A 297 " --> pdb=" O GLU8A 293 " (cutoff:3.500A) Processing helix chain '8A' and resid 302 through 304 No H-bonds generated for 'chain '8A' and resid 302 through 304' Processing helix chain '8A' and resid 311 through 313 No H-bonds generated for 'chain '8A' and resid 311 through 313' Processing helix chain '8A' and resid 336 through 343 removed outlier: 3.623A pdb=" N GLU8A 342 " --> pdb=" O ALA8A 338 " (cutoff:3.500A) Processing helix chain '8A' and resid 378 through 395 removed outlier: 3.888A pdb=" N VAL8A 382 " --> pdb=" O ILE8A 379 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP8A 384 " --> pdb=" O ARG8A 381 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE8A 386 " --> pdb=" O LEU8A 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN8A 389 " --> pdb=" O ILE8A 386 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE8A 390 " --> pdb=" O CYS8A 387 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS8A 392 " --> pdb=" O ASN8A 389 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN8A 395 " --> pdb=" O LYS8A 392 " (cutoff:3.500A) Processing helix chain '8A' and resid 410 through 432 removed outlier: 3.573A pdb=" N TYR8A 427 " --> pdb=" O LEU8A 423 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU8A 432 " --> pdb=" O GLN8A 428 " (cutoff:3.500A) Processing helix chain '8B' and resid 10 through 27 removed outlier: 3.643A pdb=" N ARG8B 22 " --> pdb=" O ASP8B 18 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU8B 25 " --> pdb=" O TRP8B 21 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG8B 26 " --> pdb=" O ARG8B 22 " (cutoff:3.500A) Processing helix chain '8B' and resid 73 through 80 removed outlier: 3.670A pdb=" N GLY8B 80 " --> pdb=" O ARG8B 76 " (cutoff:3.500A) Processing helix chain '8B' and resid 102 through 106 Processing helix chain '8B' and resid 114 through 125 removed outlier: 3.574A pdb=" N SER8B 123 " --> pdb=" O ASN8B 119 " (cutoff:3.500A) Processing helix chain '8B' and resid 148 through 159 removed outlier: 3.600A pdb=" N GLU8B 154 " --> pdb=" O SER8B 150 " (cutoff:3.500A) Processing helix chain '8B' and resid 182 through 196 removed outlier: 3.910A pdb=" N ILE8B 187 " --> pdb=" O PRO8B 183 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG8B 192 " --> pdb=" O LEU8B 188 " (cutoff:3.500A) Processing helix chain '8B' and resid 205 through 215 removed outlier: 3.649A pdb=" N ALA8B 212 " --> pdb=" O LEU8B 208 " (cutoff:3.500A) Processing helix chain '8B' and resid 226 through 236 Processing helix chain '8B' and resid 250 through 252 No H-bonds generated for 'chain '8B' and resid 250 through 252' Processing helix chain '8B' and resid 289 through 293 Processing helix chain '8B' and resid 325 through 327 No H-bonds generated for 'chain '8B' and resid 325 through 327' Processing helix chain '8B' and resid 330 through 336 removed outlier: 3.515A pdb=" N LYS8B 335 " --> pdb=" O ALA8B 331 " (cutoff:3.500A) Processing helix chain '8B' and resid 372 through 390 removed outlier: 3.585A pdb=" N GLU8B 379 " --> pdb=" O ALA8B 376 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN8B 384 " --> pdb=" O LEU8B 381 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP8B 386 " --> pdb=" O ALA8B 383 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE8B 387 " --> pdb=" O GLN8B 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET8B 388 " --> pdb=" O PHE8B 385 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE8B 389 " --> pdb=" O ASP8B 386 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP8B 390 " --> pdb=" O ILE8B 387 " (cutoff:3.500A) Processing helix chain '8B' and resid 395 through 401 removed outlier: 4.403A pdb=" N ASN8B 400 " --> pdb=" O TRP8B 397 " (cutoff:3.500A) Processing helix chain '8B' and resid 405 through 423 removed outlier: 3.634A pdb=" N ALA8B 411 " --> pdb=" O MET8B 407 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN8B 414 " --> pdb=" O LYS8B 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE8B 415 " --> pdb=" O ALA8B 411 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG8B 423 " --> pdb=" O ALA8B 419 " (cutoff:3.500A) Processing helix chain '8C' and resid 4 through 25 Processing helix chain '8C' and resid 30 through 46 removed outlier: 3.531A pdb=" N VAL8C 39 " --> pdb=" O GLU8C 35 " (cutoff:3.500A) Processing helix chain '8C' and resid 50 through 66 Processing helix chain '8C' and resid 72 through 89 Processing helix chain '8C' and resid 92 through 108 Processing helix chain '8C' and resid 111 through 113 No H-bonds generated for 'chain '8C' and resid 111 through 113' Processing helix chain '8C' and resid 115 through 130 Processing helix chain '8C' and resid 134 through 151 Processing helix chain '8C' and resid 157 through 172 Processing helix chain '8C' and resid 176 through 192 removed outlier: 3.822A pdb=" N ASN8C 192 " --> pdb=" O ALA8C 188 " (cutoff:3.500A) Processing helix chain '8C' and resid 200 through 216 Processing helix chain '8C' and resid 220 through 236 Processing sheet with id= A, first strand: chain '1A' and resid 53 through 55 Processing sheet with id= B, first strand: chain '1A' and resid 70 through 72 removed outlier: 3.668A pdb=" N ASP1A 72 " --> pdb=" O ILE1A 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1A' and resid 140 through 142 removed outlier: 6.307A pdb=" N CYS1A 171 " --> pdb=" O HIS1A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain '1A' and resid 275 through 277 Processing sheet with id= E, first strand: chain '1B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG1B 164 " --> pdb=" O PHE1B 134 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET1B 136 " --> pdb=" O ARG1B 164 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE1B 166 " --> pdb=" O MET1B 136 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY1B 199 " --> pdb=" O THR1B 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER1B 169 " --> pdb=" O GLY1B 199 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL1B 201 " --> pdb=" O SER1B 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL1B 171 " --> pdb=" O VAL1B 201 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU1B 203 " --> pdb=" O VAL1B 171 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1B' and resid 52 through 54 Processing sheet with id= G, first strand: chain '1B' and resid 66 through 69 removed outlier: 3.537A pdb=" N VAL1B 92 " --> pdb=" O LEU1B 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS1B 94 " --> pdb=" O ASP1B 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1B' and resid 266 through 271 removed outlier: 6.332A pdb=" N GLY1B 352 " --> pdb=" O PHE1B 317 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY1B 319 " --> pdb=" O GLY1B 352 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA1B 354 " --> pdb=" O GLY1B 319 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1B' and resid 310 through 313 removed outlier: 6.786A pdb=" N ASN1B 370 " --> pdb=" O LEU1B 311 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2A' and resid 53 through 55 Processing sheet with id= K, first strand: chain '2A' and resid 70 through 72 removed outlier: 3.667A pdb=" N ASP2A 72 " --> pdb=" O ILE2A 95 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '2A' and resid 140 through 142 removed outlier: 6.308A pdb=" N CYS2A 171 " --> pdb=" O HIS2A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain '2A' and resid 275 through 277 Processing sheet with id= N, first strand: chain '2B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG2B 164 " --> pdb=" O PHE2B 134 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET2B 136 " --> pdb=" O ARG2B 164 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE2B 166 " --> pdb=" O MET2B 136 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY2B 199 " --> pdb=" O THR2B 167 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER2B 169 " --> pdb=" O GLY2B 199 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL2B 201 " --> pdb=" O SER2B 169 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL2B 171 " --> pdb=" O VAL2B 201 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU2B 203 " --> pdb=" O VAL2B 171 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '2B' and resid 52 through 54 Processing sheet with id= P, first strand: chain '2B' and resid 66 through 69 removed outlier: 3.537A pdb=" N VAL2B 92 " --> pdb=" O LEU2B 66 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS2B 94 " --> pdb=" O ASP2B 68 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '2B' and resid 266 through 271 removed outlier: 6.332A pdb=" N GLY2B 352 " --> pdb=" O PHE2B 317 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY2B 319 " --> pdb=" O GLY2B 352 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA2B 354 " --> pdb=" O GLY2B 319 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '2B' and resid 310 through 313 removed outlier: 6.786A pdb=" N ASN2B 370 " --> pdb=" O LEU2B 311 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '3A' and resid 53 through 55 Processing sheet with id= T, first strand: chain '3A' and resid 70 through 72 removed outlier: 3.667A pdb=" N ASP3A 72 " --> pdb=" O ILE3A 95 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '3A' and resid 140 through 142 removed outlier: 6.308A pdb=" N CYS3A 171 " --> pdb=" O HIS3A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '3A' and resid 275 through 277 Processing sheet with id= W, first strand: chain '3B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG3B 164 " --> pdb=" O PHE3B 134 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET3B 136 " --> pdb=" O ARG3B 164 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE3B 166 " --> pdb=" O MET3B 136 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY3B 199 " --> pdb=" O THR3B 167 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER3B 169 " --> pdb=" O GLY3B 199 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL3B 201 " --> pdb=" O SER3B 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL3B 171 " --> pdb=" O VAL3B 201 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU3B 203 " --> pdb=" O VAL3B 171 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '3B' and resid 52 through 54 Processing sheet with id= Y, first strand: chain '3B' and resid 66 through 69 removed outlier: 3.537A pdb=" N VAL3B 92 " --> pdb=" O LEU3B 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS3B 94 " --> pdb=" O ASP3B 68 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '3B' and resid 266 through 271 removed outlier: 6.331A pdb=" N GLY3B 352 " --> pdb=" O PHE3B 317 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY3B 319 " --> pdb=" O GLY3B 352 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA3B 354 " --> pdb=" O GLY3B 319 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '3B' and resid 310 through 313 removed outlier: 6.787A pdb=" N ASN3B 370 " --> pdb=" O LEU3B 311 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '4A' and resid 53 through 55 Processing sheet with id= AC, first strand: chain '4A' and resid 70 through 72 removed outlier: 3.667A pdb=" N ASP4A 72 " --> pdb=" O ILE4A 95 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '4A' and resid 140 through 142 removed outlier: 6.307A pdb=" N CYS4A 171 " --> pdb=" O HIS4A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain '4A' and resid 275 through 277 Processing sheet with id= AF, first strand: chain '4B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG4B 164 " --> pdb=" O PHE4B 134 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET4B 136 " --> pdb=" O ARG4B 164 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE4B 166 " --> pdb=" O MET4B 136 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY4B 199 " --> pdb=" O THR4B 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER4B 169 " --> pdb=" O GLY4B 199 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL4B 201 " --> pdb=" O SER4B 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL4B 171 " --> pdb=" O VAL4B 201 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU4B 203 " --> pdb=" O VAL4B 171 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '4B' and resid 52 through 54 Processing sheet with id= AH, first strand: chain '4B' and resid 66 through 69 removed outlier: 3.536A pdb=" N VAL4B 92 " --> pdb=" O LEU4B 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS4B 94 " --> pdb=" O ASP4B 68 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '4B' and resid 266 through 271 removed outlier: 6.332A pdb=" N GLY4B 352 " --> pdb=" O PHE4B 317 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY4B 319 " --> pdb=" O GLY4B 352 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA4B 354 " --> pdb=" O GLY4B 319 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '4B' and resid 310 through 313 removed outlier: 6.786A pdb=" N ASN4B 370 " --> pdb=" O LEU4B 311 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '5A' and resid 53 through 55 Processing sheet with id= AL, first strand: chain '5A' and resid 70 through 72 removed outlier: 3.668A pdb=" N ASP5A 72 " --> pdb=" O ILE5A 95 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '5A' and resid 140 through 142 removed outlier: 6.307A pdb=" N CYS5A 171 " --> pdb=" O HIS5A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain '5A' and resid 275 through 277 Processing sheet with id= AO, first strand: chain '5B' and resid 5 through 8 removed outlier: 7.279A pdb=" N ARG5B 164 " --> pdb=" O PHE5B 134 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET5B 136 " --> pdb=" O ARG5B 164 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE5B 166 " --> pdb=" O MET5B 136 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY5B 199 " --> pdb=" O THR5B 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER5B 169 " --> pdb=" O GLY5B 199 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL5B 201 " --> pdb=" O SER5B 169 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL5B 171 " --> pdb=" O VAL5B 201 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU5B 203 " --> pdb=" O VAL5B 171 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '5B' and resid 52 through 54 Processing sheet with id= AQ, first strand: chain '5B' and resid 66 through 69 removed outlier: 3.538A pdb=" N VAL5B 92 " --> pdb=" O LEU5B 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS5B 94 " --> pdb=" O ASP5B 68 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '5B' and resid 266 through 271 removed outlier: 3.948A pdb=" N LEU5B 368 " --> pdb=" O SER5B 314 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA5B 354 " --> pdb=" O PHE5B 317 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '5B' and resid 310 through 313 removed outlier: 6.786A pdb=" N ASN5B 370 " --> pdb=" O LEU5B 311 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '6A' and resid 53 through 55 Processing sheet with id= AU, first strand: chain '6A' and resid 70 through 72 removed outlier: 3.666A pdb=" N ASP6A 72 " --> pdb=" O ILE6A 95 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '6A' and resid 140 through 142 removed outlier: 6.308A pdb=" N CYS6A 171 " --> pdb=" O HIS6A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain '6A' and resid 275 through 277 Processing sheet with id= AX, first strand: chain '6B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG6B 164 " --> pdb=" O PHE6B 134 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET6B 136 " --> pdb=" O ARG6B 164 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE6B 166 " --> pdb=" O MET6B 136 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY6B 199 " --> pdb=" O THR6B 167 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER6B 169 " --> pdb=" O GLY6B 199 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL6B 201 " --> pdb=" O SER6B 169 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL6B 171 " --> pdb=" O VAL6B 201 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU6B 203 " --> pdb=" O VAL6B 171 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '6B' and resid 52 through 54 Processing sheet with id= AZ, first strand: chain '6B' and resid 66 through 69 removed outlier: 3.537A pdb=" N VAL6B 92 " --> pdb=" O LEU6B 66 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS6B 94 " --> pdb=" O ASP6B 68 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '6B' and resid 266 through 271 removed outlier: 6.331A pdb=" N GLY6B 352 " --> pdb=" O PHE6B 317 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY6B 319 " --> pdb=" O GLY6B 352 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA6B 354 " --> pdb=" O GLY6B 319 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '6B' and resid 310 through 313 removed outlier: 6.787A pdb=" N ASN6B 370 " --> pdb=" O LEU6B 311 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '7A' and resid 53 through 55 Processing sheet with id= BD, first strand: chain '7A' and resid 70 through 72 removed outlier: 3.667A pdb=" N ASP7A 72 " --> pdb=" O ILE7A 95 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '7A' and resid 140 through 142 removed outlier: 6.308A pdb=" N CYS7A 171 " --> pdb=" O HIS7A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain '7A' and resid 275 through 277 Processing sheet with id= BG, first strand: chain '7B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG7B 164 " --> pdb=" O PHE7B 134 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET7B 136 " --> pdb=" O ARG7B 164 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE7B 166 " --> pdb=" O MET7B 136 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY7B 199 " --> pdb=" O THR7B 167 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER7B 169 " --> pdb=" O GLY7B 199 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL7B 201 " --> pdb=" O SER7B 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL7B 171 " --> pdb=" O VAL7B 201 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU7B 203 " --> pdb=" O VAL7B 171 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '7B' and resid 52 through 54 Processing sheet with id= BI, first strand: chain '7B' and resid 66 through 69 removed outlier: 3.536A pdb=" N VAL7B 92 " --> pdb=" O LEU7B 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS7B 94 " --> pdb=" O ASP7B 68 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '7B' and resid 266 through 271 removed outlier: 6.331A pdb=" N GLY7B 352 " --> pdb=" O PHE7B 317 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY7B 319 " --> pdb=" O GLY7B 352 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA7B 354 " --> pdb=" O GLY7B 319 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain '7B' and resid 310 through 313 removed outlier: 6.786A pdb=" N ASN7B 370 " --> pdb=" O LEU7B 311 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain '8A' and resid 53 through 55 Processing sheet with id= BM, first strand: chain '8A' and resid 70 through 72 removed outlier: 3.667A pdb=" N ASP8A 72 " --> pdb=" O ILE8A 95 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain '8A' and resid 140 through 142 removed outlier: 6.307A pdb=" N CYS8A 171 " --> pdb=" O HIS8A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain '8A' and resid 275 through 277 Processing sheet with id= BP, first strand: chain '8B' and resid 5 through 8 removed outlier: 7.280A pdb=" N ARG8B 164 " --> pdb=" O PHE8B 134 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET8B 136 " --> pdb=" O ARG8B 164 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE8B 166 " --> pdb=" O MET8B 136 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY8B 199 " --> pdb=" O THR8B 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER8B 169 " --> pdb=" O GLY8B 199 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL8B 201 " --> pdb=" O SER8B 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL8B 171 " --> pdb=" O VAL8B 201 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU8B 203 " --> pdb=" O VAL8B 171 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain '8B' and resid 52 through 54 Processing sheet with id= BR, first strand: chain '8B' and resid 66 through 69 removed outlier: 3.536A pdb=" N VAL8B 92 " --> pdb=" O LEU8B 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS8B 94 " --> pdb=" O ASP8B 68 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain '8B' and resid 266 through 271 removed outlier: 6.332A pdb=" N GLY8B 352 " --> pdb=" O PHE8B 317 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY8B 319 " --> pdb=" O GLY8B 352 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA8B 354 " --> pdb=" O GLY8B 319 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain '8B' and resid 310 through 313 removed outlier: 6.786A pdb=" N ASN8B 370 " --> pdb=" O LEU8B 311 " (cutoff:3.500A) 2670 hydrogen bonds defined for protein. 7461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.08 Time building geometry restraints manager: 22.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 11798 1.31 - 1.44: 18612 1.44 - 1.57: 37703 1.57 - 1.71: 95 1.71 - 1.84: 512 Bond restraints: 68720 Sorted by residual: bond pdb=" CA ALA6B 268 " pdb=" C ALA6B 268 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.20e-02 6.94e+03 2.93e+01 bond pdb=" CA ALA4B 268 " pdb=" C ALA4B 268 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.20e-02 6.94e+03 2.93e+01 bond pdb=" CA ALA2B 268 " pdb=" C ALA2B 268 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.20e-02 6.94e+03 2.92e+01 bond pdb=" CA ALA1B 268 " pdb=" C ALA1B 268 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.20e-02 6.94e+03 2.92e+01 bond pdb=" CA ALA5B 268 " pdb=" C ALA5B 268 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.20e-02 6.94e+03 2.92e+01 ... (remaining 68715 not shown) Histogram of bond angle deviations from ideal: 93.60 - 102.20: 331 102.20 - 110.80: 20424 110.80 - 119.39: 37792 119.39 - 127.99: 33989 127.99 - 136.59: 584 Bond angle restraints: 93120 Sorted by residual: angle pdb=" N VAL8B 181 " pdb=" CA VAL8B 181 " pdb=" C VAL8B 181 " ideal model delta sigma weight residual 111.91 105.89 6.02 8.90e-01 1.26e+00 4.57e+01 angle pdb=" N VAL1B 181 " pdb=" CA VAL1B 181 " pdb=" C VAL1B 181 " ideal model delta sigma weight residual 111.91 105.91 6.00 8.90e-01 1.26e+00 4.54e+01 angle pdb=" N VAL3B 181 " pdb=" CA VAL3B 181 " pdb=" C VAL3B 181 " ideal model delta sigma weight residual 111.91 105.92 5.99 8.90e-01 1.26e+00 4.54e+01 angle pdb=" N VAL6B 181 " pdb=" CA VAL6B 181 " pdb=" C VAL6B 181 " ideal model delta sigma weight residual 111.91 105.92 5.99 8.90e-01 1.26e+00 4.53e+01 angle pdb=" N VAL7B 181 " pdb=" CA VAL7B 181 " pdb=" C VAL7B 181 " ideal model delta sigma weight residual 111.91 105.92 5.99 8.90e-01 1.26e+00 4.53e+01 ... (remaining 93115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 39437 22.94 - 45.89: 1499 45.89 - 68.83: 264 68.83 - 91.78: 40 91.78 - 114.72: 16 Dihedral angle restraints: 41256 sinusoidal: 16320 harmonic: 24936 Sorted by residual: dihedral pdb=" CA ALA3A 398 " pdb=" C ALA3A 398 " pdb=" N PHE3A 399 " pdb=" CA PHE3A 399 " ideal model delta harmonic sigma weight residual -180.00 -121.32 -58.68 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ALA7A 398 " pdb=" C ALA7A 398 " pdb=" N PHE7A 399 " pdb=" CA PHE7A 399 " ideal model delta harmonic sigma weight residual -180.00 -121.32 -58.68 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ALA4A 398 " pdb=" C ALA4A 398 " pdb=" N PHE4A 399 " pdb=" CA PHE4A 399 " ideal model delta harmonic sigma weight residual -180.00 -121.34 -58.66 0 5.00e+00 4.00e-02 1.38e+02 ... (remaining 41253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 9557 0.170 - 0.339: 811 0.339 - 0.508: 24 0.508 - 0.678: 8 0.678 - 0.847: 8 Chirality restraints: 10408 Sorted by residual: chirality pdb=" CA PHE4A 399 " pdb=" N PHE4A 399 " pdb=" C PHE4A 399 " pdb=" CB PHE4A 399 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA PHE8A 399 " pdb=" N PHE8A 399 " pdb=" C PHE8A 399 " pdb=" CB PHE8A 399 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CA PHE1A 399 " pdb=" N PHE1A 399 " pdb=" C PHE1A 399 " pdb=" CB PHE1A 399 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 10405 not shown) Planarity restraints: 12096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP5B 501 " -0.075 2.00e-02 2.50e+03 2.98e-02 2.67e+01 pdb=" N9 GDP5B 501 " 0.013 2.00e-02 2.50e+03 pdb=" C8 GDP5B 501 " 0.037 2.00e-02 2.50e+03 pdb=" N7 GDP5B 501 " 0.022 2.00e-02 2.50e+03 pdb=" C5 GDP5B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GDP5B 501 " -0.022 2.00e-02 2.50e+03 pdb=" O6 GDP5B 501 " -0.035 2.00e-02 2.50e+03 pdb=" N1 GDP5B 501 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GDP5B 501 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GDP5B 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 GDP5B 501 " 0.031 2.00e-02 2.50e+03 pdb=" C4 GDP5B 501 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP8B 501 " 0.075 2.00e-02 2.50e+03 2.98e-02 2.66e+01 pdb=" N9 GDP8B 501 " -0.013 2.00e-02 2.50e+03 pdb=" C8 GDP8B 501 " -0.038 2.00e-02 2.50e+03 pdb=" N7 GDP8B 501 " -0.021 2.00e-02 2.50e+03 pdb=" C5 GDP8B 501 " -0.002 2.00e-02 2.50e+03 pdb=" C6 GDP8B 501 " 0.022 2.00e-02 2.50e+03 pdb=" O6 GDP8B 501 " 0.035 2.00e-02 2.50e+03 pdb=" N1 GDP8B 501 " 0.004 2.00e-02 2.50e+03 pdb=" C2 GDP8B 501 " -0.008 2.00e-02 2.50e+03 pdb=" N2 GDP8B 501 " -0.007 2.00e-02 2.50e+03 pdb=" N3 GDP8B 501 " -0.031 2.00e-02 2.50e+03 pdb=" C4 GDP8B 501 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP2B 501 " -0.074 2.00e-02 2.50e+03 2.98e-02 2.66e+01 pdb=" N9 GDP2B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C8 GDP2B 501 " 0.037 2.00e-02 2.50e+03 pdb=" N7 GDP2B 501 " 0.022 2.00e-02 2.50e+03 pdb=" C5 GDP2B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GDP2B 501 " -0.022 2.00e-02 2.50e+03 pdb=" O6 GDP2B 501 " -0.035 2.00e-02 2.50e+03 pdb=" N1 GDP2B 501 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GDP2B 501 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GDP2B 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 GDP2B 501 " 0.031 2.00e-02 2.50e+03 pdb=" C4 GDP2B 501 " 0.018 2.00e-02 2.50e+03 ... (remaining 12093 not shown) Histogram of nonbonded interaction distances: 0.18 - 1.12: 53 1.12 - 2.07: 407 2.07 - 3.01: 36653 3.01 - 3.96: 194283 3.96 - 4.90: 367487 Warning: very small nonbonded interaction distances. Nonbonded interactions: 598883 Sorted by model distance: nonbonded pdb=" CB TYR1B 342 " pdb=" CZ ARG5A 396 " model vdw 0.180 3.670 nonbonded pdb=" OG SER1B 346 " pdb=" O GLN5A 178 " model vdw 0.192 2.440 nonbonded pdb=" OD2 ASP2B 327 " pdb=" CE2 PHE6A 212 " model vdw 0.319 3.340 nonbonded pdb=" CG TYR3B 342 " pdb=" CD ARG7A 396 " model vdw 0.391 3.660 nonbonded pdb=" CB TYR2B 342 " pdb=" NE ARG6A 396 " model vdw 0.441 3.520 ... (remaining 598878 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 '1A' selection = chain '2A' selection = chain '3A' selection = chain '4A' selection = chain '5A' selection = chain '6A' selection = chain '7A' selection = chain '8A' } ncs_group { reference = chain '1B' selection = chain '2B' selection = chain '3B' selection = chain '4B' selection = chain '5B' selection = chain '6B' selection = chain '7B' selection = chain '8B' } ncs_group { reference = chain '1C' selection = chain '2C' selection = chain '3C' selection = chain '4C' selection = chain '5C' selection = chain '6C' selection = chain '7C' selection = chain '8C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 296 5.16 5 C 42536 2.51 5 N 11744 2.21 5 O 12816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.040 Extract box with map and model: 9.240 Check model and map are aligned: 0.730 Convert atoms to be neutral: 0.440 Process input model: 123.810 Find NCS groups from input model: 4.140 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 142.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 : 0.014 0.107 68720 Z= 0.940 Angle : 1.477 12.220 93120 Z= 0.867 Chirality : 0.104 0.847 10408 Planarity : 0.009 0.128 12096 Dihedral : 13.273 114.720 25192 Min Nonbonded Distance : 0.180 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.31 % Favored : 92.85 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.07), residues: 8568 helix: -2.75 (0.06), residues: 4560 sheet: -2.88 (0.15), residues: 856 loop : -3.14 (0.09), residues: 3152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2527 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 2431 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 16 residues processed: 2495 average time/residue: 0.6768 time to fit residues: 2772.0719 Evaluate side-chains 1358 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1342 time to evaluate : 5.568 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6350 time to fit residues: 25.9299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 722 optimal weight: 0.9990 chunk 648 optimal weight: 5.9990 chunk 360 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 437 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 670 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 407 optimal weight: 10.0000 chunk 499 optimal weight: 0.2980 chunk 777 optimal weight: 40.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 17 GLN 1A 48 ASN 1A 208 ASN 1A 262 ASN ** 1A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1A 376 ASN 1A 388 HIS 1A 389 ASN 1B 47 ASN 1B 100 ASN 1B 107 ASN ** 1B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1B 196 ASN 1B 217 ASN 1B 256 ASN 1C 84 HIS ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 17 GLN ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 208 ASN 2A 216 HIS ** 2A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 47 ASN ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 132 GLN 2B 217 ASN 2B 256 ASN 2B 391 ASN 2C 122 ASN 2C 165 ASN 2C 180 GLN 3A 5 ASN 3A 17 GLN ** 3A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 428 GLN 3B 15 GLN 3B 47 ASN 3B 100 ASN ** 3B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 205 ASN 3B 217 ASN 3B 256 ASN 3B 392 HIS 3B 414 GLN 3C 45 GLN 4A 17 GLN 4A 216 HIS 4A 262 ASN 4A 361 GLN ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 116 GLN 4B 196 ASN 4B 217 ASN 4B 256 ASN ** 4B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 391 ASN 4B 396 HIS ** 5A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 178 GLN 5A 262 ASN 5A 366 HIS 5A 376 ASN 5B 47 ASN ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 196 ASN 5B 217 ASN 5B 256 ASN 5B 391 ASN ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 208 ASN 6A 262 ASN 6A 389 ASN 6B 47 ASN 6B 107 ASN ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6B 217 ASN 6B 247 ASN 6B 413 ASN 6C 45 GLN 6C 183 HIS ** 7A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7A 389 ASN ** 7B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 47 ASN 7B 53 HIS 7B 107 ASN 7B 196 ASN 7B 205 ASN 7B 217 ASN 7B 256 ASN 7B 329 ASN 7C 130 GLN ** 8A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 48 ASN ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 389 ASN ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 217 ASN 8B 256 ASN 8B 298 ASN 8B 329 ASN 8B 391 ASN 8B 392 HIS Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 68720 Z= 0.288 Angle : 0.784 20.105 93120 Z= 0.392 Chirality : 0.046 0.229 10408 Planarity : 0.007 0.148 12096 Dihedral : 8.344 172.354 9560 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.09 % Favored : 93.88 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.50 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.08), residues: 8568 helix: -0.95 (0.07), residues: 4504 sheet: -2.33 (0.16), residues: 856 loop : -2.68 (0.10), residues: 3208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1938 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1679 time to evaluate : 5.622 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 outliers start: 259 outliers final: 102 residues processed: 1834 average time/residue: 0.6429 time to fit residues: 1979.6668 Evaluate side-chains 1315 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1213 time to evaluate : 5.809 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.4774 time to fit residues: 100.4578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 432 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 646 optimal weight: 3.9990 chunk 529 optimal weight: 30.0000 chunk 214 optimal weight: 10.0000 chunk 778 optimal weight: 8.9990 chunk 841 optimal weight: 7.9990 chunk 693 optimal weight: 2.9990 chunk 772 optimal weight: 0.9990 chunk 265 optimal weight: 0.0370 chunk 624 optimal weight: 1.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 270 HIS 1B 116 GLN ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1B 338 ASN 1B 400 ASN 1C 45 GLN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 376 ASN 2B 14 ASN 2B 100 ASN ** 2B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 205 ASN 2B 396 HIS 2B 400 ASN ** 2C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2C 122 ASN 2C 165 ASN 2C 183 HIS ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 262 ASN 3A 376 ASN 3A 388 HIS ** 3B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 285 ASN ** 3C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 132 GLN ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 205 ASN 4B 329 ASN ** 5A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 30 HIS 5A 270 HIS ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 414 GLN 5C 130 GLN ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6B 205 ASN 6B 256 ASN ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7A 395 GLN ** 7B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 53 HIS 7B 100 ASN 7B 205 ASN 7C 149 GLN 8A 270 HIS ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 388 HIS ** 8B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 107 ASN ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8C 122 ASN 8C 165 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 68720 Z= 0.268 Angle : 0.742 22.101 93120 Z= 0.364 Chirality : 0.045 0.309 10408 Planarity : 0.006 0.156 12096 Dihedral : 7.627 178.387 9560 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.44 % Favored : 94.55 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.50 % Twisted General : 0.24 % 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: -1.91 (0.09), residues: 8568 helix: -0.33 (0.08), residues: 4528 sheet: -2.23 (0.16), residues: 888 loop : -2.27 (0.10), residues: 3152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1446 time to evaluate : 5.951 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 outliers start: 195 outliers final: 87 residues processed: 1561 average time/residue: 0.6430 time to fit residues: 1696.7657 Evaluate side-chains 1231 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1144 time to evaluate : 5.711 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.4926 time to fit residues: 88.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 769 optimal weight: 0.7980 chunk 585 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 522 optimal weight: 10.0000 chunk 781 optimal weight: 0.9980 chunk 827 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 740 optimal weight: 20.0000 chunk 222 optimal weight: 0.9980 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 4 ASN 1B 15 GLN ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 262 ASN ** 2B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 227 ASN 2B 307 GLN 2B 414 GLN ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 208 ASN ** 3A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 388 HIS ** 3B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 100 ASN 3B 116 GLN ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4A 266 GLN ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 15 GLN ** 4B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 205 ASN 4B 370 ASN 4C 36 GLN 4C 149 GLN ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 188 ASN ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 392 HIS 5C 36 GLN ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6B 205 ASN 6B 296 GLN 6B 396 HIS 6C 149 GLN ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7A 270 HIS ** 7A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 11 GLN ** 7B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 53 HIS 7B 205 ASN ** 7B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 366 HIS ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 15 GLN ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 100 ASN 8B 119 ASN 8B 138 HIS ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 68720 Z= 0.344 Angle : 0.767 22.700 93120 Z= 0.379 Chirality : 0.046 0.303 10408 Planarity : 0.006 0.163 12096 Dihedral : 7.549 178.567 9560 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.35 % Favored : 93.63 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.50 % Twisted General : 0.23 % 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: -1.62 (0.09), residues: 8568 helix: -0.06 (0.08), residues: 4472 sheet: -2.27 (0.17), residues: 864 loop : -2.09 (0.11), residues: 3232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1326 time to evaluate : 5.757 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 outliers start: 224 outliers final: 126 residues processed: 1467 average time/residue: 0.6450 time to fit residues: 1609.2931 Evaluate side-chains 1224 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1098 time to evaluate : 7.363 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 0 residues processed: 126 average time/residue: 0.5060 time to fit residues: 129.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 689 optimal weight: 3.9990 chunk 469 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 616 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 706 optimal weight: 4.9990 chunk 571 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 422 optimal weight: 9.9990 chunk 742 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 412 GLN ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1B 285 ASN 1B 307 GLN ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1B 338 ASN 1C 25 HIS 1C 36 GLN ** 2A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2C 130 GLN ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 262 ASN 3A 270 HIS 3A 388 HIS ** 3B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 205 ASN ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 395 GLN ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 263 ASN ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 391 ASN 5B 396 HIS 5C 45 GLN ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 388 HIS 6B 100 ASN ** 6B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6C 149 GLN 7A 4 ASN ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7A 262 ASN ** 7A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 16 ASN ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 262 ASN ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN 8C 45 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.7985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.123 68720 Z= 0.316 Angle : 0.736 23.290 93120 Z= 0.362 Chirality : 0.045 0.247 10408 Planarity : 0.006 0.148 12096 Dihedral : 7.348 168.737 9560 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.23 % 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: -1.41 (0.09), residues: 8568 helix: 0.09 (0.08), residues: 4432 sheet: -2.34 (0.16), residues: 952 loop : -1.84 (0.11), residues: 3184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1264 time to evaluate : 5.677 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 outliers start: 159 outliers final: 78 residues processed: 1366 average time/residue: 0.6406 time to fit residues: 1484.5943 Evaluate side-chains 1174 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1096 time to evaluate : 5.726 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.5079 time to fit residues: 82.1197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 278 optimal weight: 5.9990 chunk 745 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 485 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 828 optimal weight: 6.9990 chunk 687 optimal weight: 2.9990 chunk 383 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 434 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 30 HIS 1B 11 GLN ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1C 36 GLN 2A 4 ASN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 266 GLN ** 2B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 5 ASN ** 3A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 262 ASN 3A 366 HIS 3A 388 HIS 3B 53 HIS ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 263 ASN 3C 36 GLN ** 3C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 205 ASN ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 208 ASN 5A 220 ASN ** 5B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 205 ASN 5B 256 ASN ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 376 ASN 6A 388 HIS ** 6A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6B 285 ASN 7A 4 ASN ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 53 HIS ** 7B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 391 ASN ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 16 ASN 8A 30 HIS ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 262 ASN ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.8267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.181 68720 Z= 0.255 Angle : 0.723 23.254 93120 Z= 0.353 Chirality : 0.043 0.247 10408 Planarity : 0.006 0.190 12096 Dihedral : 7.127 178.095 9560 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.53 % Favored : 94.46 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.22 % 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: -1.19 (0.09), residues: 8568 helix: 0.26 (0.08), residues: 4440 sheet: -2.08 (0.17), residues: 896 loop : -1.82 (0.11), residues: 3232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1225 time to evaluate : 5.674 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 outliers start: 120 outliers final: 54 residues processed: 1297 average time/residue: 0.6271 time to fit residues: 1388.6977 Evaluate side-chains 1124 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1070 time to evaluate : 5.657 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4918 time to fit residues: 57.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 798 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 chunk 471 optimal weight: 1.9990 chunk 604 optimal weight: 3.9990 chunk 468 optimal weight: 0.9980 chunk 697 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 825 optimal weight: 10.0000 chunk 516 optimal weight: 5.9990 chunk 503 optimal weight: 3.9990 chunk 380 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1B 264 HIS ** 1B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 13 GLN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 17 GLN ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 107 ASN ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 132 GLN 4A 220 ASN ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 14 ASN ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 220 ASN ** 5A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5B 11 GLN ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 220 ASN 6A 388 HIS ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7A 366 HIS 7B 100 ASN 7B 138 HIS 7B 306 GLN 7B 307 GLN ** 7B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 178 GLN 8A 220 ASN ** 8A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 388 HIS ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.8645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.320 68720 Z= 0.357 Angle : 0.767 23.651 93120 Z= 0.380 Chirality : 0.045 0.384 10408 Planarity : 0.006 0.149 12096 Dihedral : 7.244 179.196 9560 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.50 % Favored : 93.49 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.21 % 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: -1.19 (0.09), residues: 8568 helix: 0.25 (0.08), residues: 4464 sheet: -2.18 (0.16), residues: 904 loop : -1.76 (0.11), residues: 3200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1152 time to evaluate : 5.760 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 outliers start: 112 outliers final: 57 residues processed: 1221 average time/residue: 0.6431 time to fit residues: 1334.2052 Evaluate side-chains 1118 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1061 time to evaluate : 5.854 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4919 time to fit residues: 61.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 510 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 492 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 524 optimal weight: 0.9990 chunk 562 optimal weight: 5.9990 chunk 407 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 648 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1A 412 GLN ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1B 138 HIS 1B 158 GLN ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 13 GLN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 17 GLN ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 285 ASN 2B 307 GLN ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 5 ASN ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 361 GLN 3A 388 HIS 3B 53 HIS ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 263 ASN 3B 391 ASN ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 14 ASN ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 266 GLN ** 5A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 425 GLN 5B 11 GLN ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 220 ASN ** 6A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 388 HIS ** 6B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 53 HIS 7B 100 ASN ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 388 HIS ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN ** 8C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.711 68720 Z= 0.424 Angle : 0.848 73.900 93120 Z= 0.413 Chirality : 0.045 0.473 10408 Planarity : 0.006 0.141 12096 Dihedral : 7.259 179.777 9560 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.30 % Favored : 93.69 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.21 % 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: -1.16 (0.09), residues: 8568 helix: 0.29 (0.08), residues: 4424 sheet: -2.18 (0.16), residues: 904 loop : -1.75 (0.11), residues: 3240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1085 time to evaluate : 5.796 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 outliers start: 67 outliers final: 39 residues processed: 1117 average time/residue: 0.6319 time to fit residues: 1211.1226 Evaluate side-chains 1075 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1036 time to evaluate : 5.713 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5258 time to fit residues: 45.4530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 750 optimal weight: 0.9990 chunk 790 optimal weight: 0.9990 chunk 721 optimal weight: 0.0670 chunk 768 optimal weight: 6.9990 chunk 462 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 603 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 694 optimal weight: 0.9990 chunk 727 optimal weight: 4.9990 chunk 766 optimal weight: 5.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 13 GLN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 17 GLN ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 14 ASN ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 425 GLN ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 220 ASN ** 6A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 388 HIS ** 6B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7A 388 HIS 7B 100 ASN ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN ** 8C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.8712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.580 68720 Z= 0.364 Angle : 0.824 73.900 93120 Z= 0.396 Chirality : 0.045 0.336 10408 Planarity : 0.006 0.173 12096 Dihedral : 7.244 179.327 9560 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.28 % Favored : 93.71 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.21 % 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: -1.13 (0.09), residues: 8568 helix: 0.30 (0.08), residues: 4432 sheet: -2.18 (0.16), residues: 904 loop : -1.72 (0.11), residues: 3232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1066 time to evaluate : 6.121 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 outliers start: 44 outliers final: 27 residues processed: 1091 average time/residue: 0.6437 time to fit residues: 1204.0077 Evaluate side-chains 1063 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1036 time to evaluate : 5.798 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5112 time to fit residues: 33.9370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 504 optimal weight: 9.9990 chunk 812 optimal weight: 7.9990 chunk 496 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 chunk 565 optimal weight: 0.0470 chunk 852 optimal weight: 0.9980 chunk 784 optimal weight: 7.9990 chunk 679 optimal weight: 0.3980 chunk 70 optimal weight: 0.3980 chunk 524 optimal weight: 2.9990 chunk 416 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 13 GLN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 17 GLN ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 361 GLN ** 2B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 5 ASN 3A 17 GLN ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 266 GLN 3A 361 GLN 3A 388 HIS ** 3B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 263 ASN ** 3C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 14 ASN ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5A 425 GLN ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 220 ASN ** 6A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 388 HIS ** 6B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7B 53 HIS 7B 100 ASN ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A 388 HIS ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN ** 8C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.8720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.010 68720 Z= 0.612 Angle : 0.928 94.845 93120 Z= 0.439 Chirality : 0.045 0.429 10408 Planarity : 0.006 0.174 12096 Dihedral : 7.249 179.244 9560 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.33 % Favored : 93.66 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.21 % 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: -1.13 (0.09), residues: 8568 helix: 0.31 (0.08), residues: 4432 sheet: -2.17 (0.16), residues: 904 loop : -1.72 (0.11), residues: 3232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17136 Ramachandran restraints generated. 8568 Oldfield, 0 Emsley, 8568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1065 time to evaluate : 6.967 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 outliers start: 29 outliers final: 20 residues processed: 1078 average time/residue: 0.6258 time to fit residues: 1157.2480 Evaluate side-chains 1058 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1038 time to evaluate : 5.657 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5090 time to fit residues: 26.6592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 539 optimal weight: 6.9990 chunk 723 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 626 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 680 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 698 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 13 GLN ** 2A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2A 17 GLN ** 2A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4B 14 ASN ** 4B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 220 ASN ** 6A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 388 HIS ** 6B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8B 256 ASN ** 8C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.195655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154430 restraints weight = 101582.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151698 restraints weight = 67436.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151931 restraints weight = 62960.486| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.8722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.010 68720 Z= 0.619 Angle : 0.937 94.845 93120 Z= 0.447 Chirality : 0.045 0.429 10408 Planarity : 0.007 0.180 12096 Dihedral : 7.249 179.244 9560 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.33 % Favored : 93.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.10 % Twisted Proline : 2.19 % Twisted General : 0.21 % 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: -1.13 (0.09), residues: 8568 helix: 0.31 (0.08), residues: 4432 sheet: -2.17 (0.16), residues: 904 loop : -1.72 (0.11), residues: 3232 =============================================================================== Job complete usr+sys time: 20586.37 seconds wall clock time: 359 minutes 38.78 seconds (21578.78 seconds total)