Starting phenix.real_space_refine (version: dev) on Thu Feb 23 03:39:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/02_2023/6v7b_21094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/02_2023/6v7b_21094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/02_2023/6v7b_21094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/02_2023/6v7b_21094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/02_2023/6v7b_21094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/02_2023/6v7b_21094.pdb" } resolution = 3.4 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= 0.012 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 Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 57": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 29": "OD1" <-> "OD2" Residue "I ASP 57": "OD1" <-> "OD2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J ASP 29": "OD1" <-> "OD2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J ASP 57": "OD1" <-> "OD2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "K ASP 57": "OD1" <-> "OD2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L ASP 29": "OD1" <-> "OD2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L ASP 57": "OD1" <-> "OD2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 106": "OD1" <-> "OD2" Residue "L TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N ASP 57": "OD1" <-> "OD2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N GLU 113": "OE1" <-> "OE2" Residue "N TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O GLU 50": "OE1" <-> "OE2" Residue "O ASP 57": "OD1" <-> "OD2" Residue "O TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 106": "OD1" <-> "OD2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P ASP 29": "OD1" <-> "OD2" Residue "P GLU 50": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P GLU 113": "OE1" <-> "OE2" Residue "P TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 29": "OD1" <-> "OD2" Residue "Q GLU 43": "OE1" <-> "OE2" Residue "Q GLU 50": "OE1" <-> "OE2" Residue "Q ASP 57": "OD1" <-> "OD2" Residue "Q TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 106": "OD1" <-> "OD2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 106": "OD1" <-> "OD2" Residue "R GLU 113": "OE1" <-> "OE2" Residue "R TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "S GLU 50": "OE1" <-> "OE2" Residue "S ASP 57": "OD1" <-> "OD2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 103": "OE1" <-> "OE2" Residue "S GLU 113": "OE1" <-> "OE2" Residue "T GLU 12": "OE1" <-> "OE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T ASP 57": "OD1" <-> "OD2" Residue "T TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 106": "OD1" <-> "OD2" Residue "T TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 12": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 43": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "U ASP 57": "OD1" <-> "OD2" Residue "U TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 16": "OE1" <-> "OE2" Residue "V ASP 29": "OD1" <-> "OD2" Residue "V GLU 39": "OE1" <-> "OE2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V ASP 57": "OD1" <-> "OD2" Residue "V GLU 58": "OE1" <-> "OE2" Residue "V TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 113": "OE1" <-> "OE2" Residue "V TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 12": "OE1" <-> "OE2" Residue "W GLU 43": "OE1" <-> "OE2" Residue "W GLU 50": "OE1" <-> "OE2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "W TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W GLU 113": "OE1" <-> "OE2" Residue "W TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 28": "OE1" <-> "OE2" Residue "a PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 48": "OE1" <-> "OE2" Residue "a ASP 120": "OD1" <-> "OD2" Residue "a GLU 125": "OE1" <-> "OE2" Residue "b GLU 4": "OE1" <-> "OE2" Residue "b GLU 11": "OE1" <-> "OE2" Residue "b TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 28": "OE1" <-> "OE2" Residue "b PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 105": "OE1" <-> "OE2" Residue "c GLU 11": "OE1" <-> "OE2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 109": "OD1" <-> "OD2" Residue "c ASP 120": "OD1" <-> "OD2" Residue "d TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d GLU 48": "OE1" <-> "OE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "d ASP 120": "OD1" <-> "OD2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "e GLU 4": "OE1" <-> "OE2" Residue "e GLU 11": "OE1" <-> "OE2" Residue "e TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 28": "OE1" <-> "OE2" Residue "e GLU 40": "OE1" <-> "OE2" Residue "e ASP 120": "OD1" <-> "OD2" Residue "e GLU 125": "OE1" <-> "OE2" Residue "f GLU 4": "OE1" <-> "OE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 97": "OE1" <-> "OE2" Residue "f GLU 105": "OE1" <-> "OE2" Residue "f ASP 120": "OD1" <-> "OD2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "g TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 70": "OE1" <-> "OE2" Residue "g ASP 109": "OD1" <-> "OD2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "h GLU 4": "OE1" <-> "OE2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 28": "OE1" <-> "OE2" Residue "h GLU 31": "OE1" <-> "OE2" Residue "h GLU 40": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h GLU 105": "OE1" <-> "OE2" Residue "h ASP 120": "OD1" <-> "OD2" Residue "i GLU 20": "OE1" <-> "OE2" Residue "i TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 28": "OE1" <-> "OE2" Residue "i GLU 48": "OE1" <-> "OE2" Residue "i GLU 105": "OE1" <-> "OE2" Residue "i ASP 109": "OD1" <-> "OD2" Residue "i GLU 125": "OE1" <-> "OE2" Residue "j GLU 11": "OE1" <-> "OE2" Residue "j GLU 20": "OE1" <-> "OE2" Residue "j TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 28": "OE1" <-> "OE2" Residue "j GLU 31": "OE1" <-> "OE2" Residue "j GLU 40": "OE1" <-> "OE2" Residue "j PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 70": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j ASP 109": "OD1" <-> "OD2" Residue "j GLU 125": "OE1" <-> "OE2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k GLU 11": "OE1" <-> "OE2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 105": "OE1" <-> "OE2" Residue "k ASP 120": "OD1" <-> "OD2" Residue "l GLU 4": "OE1" <-> "OE2" Residue "l GLU 11": "OE1" <-> "OE2" Residue "l GLU 20": "OE1" <-> "OE2" Residue "l TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 40": "OE1" <-> "OE2" Residue "l GLU 48": "OE1" <-> "OE2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l GLU 105": "OE1" <-> "OE2" Residue "l ASP 120": "OD1" <-> "OD2" Residue "l GLU 125": "OE1" <-> "OE2" Residue "m GLU 4": "OE1" <-> "OE2" Residue "m GLU 11": "OE1" <-> "OE2" Residue "m TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 28": "OE1" <-> "OE2" Residue "m GLU 48": "OE1" <-> "OE2" Residue "m GLU 105": "OE1" <-> "OE2" Residue "m GLU 125": "OE1" <-> "OE2" Residue "n TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 105": "OE1" <-> "OE2" Residue "o GLU 20": "OE1" <-> "OE2" Residue "o TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 31": "OE1" <-> "OE2" Residue "o GLU 48": "OE1" <-> "OE2" Residue "o GLU 97": "OE1" <-> "OE2" Residue "o ASP 109": "OD1" <-> "OD2" Residue "o ASP 120": "OD1" <-> "OD2" Residue "p GLU 4": "OE1" <-> "OE2" Residue "p GLU 11": "OE1" <-> "OE2" Residue "p GLU 20": "OE1" <-> "OE2" Residue "p TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 31": "OE1" <-> "OE2" Residue "p GLU 40": "OE1" <-> "OE2" Residue "p PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 57": "OE1" <-> "OE2" Residue "p GLU 105": "OE1" <-> "OE2" Residue "p ASP 109": "OD1" <-> "OD2" Residue "p GLU 125": "OE1" <-> "OE2" Residue "q GLU 4": "OE1" <-> "OE2" Residue "q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 109": "OD1" <-> "OD2" Residue "q ASP 120": "OD1" <-> "OD2" Residue "q GLU 125": "OE1" <-> "OE2" Residue "r GLU 4": "OE1" <-> "OE2" Residue "r GLU 11": "OE1" <-> "OE2" Residue "r TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r GLU 40": "OE1" <-> "OE2" Residue "r PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 48": "OE1" <-> "OE2" Residue "r GLU 57": "OE1" <-> "OE2" Residue "r GLU 125": "OE1" <-> "OE2" Residue "s GLU 4": "OE1" <-> "OE2" Residue "s GLU 11": "OE1" <-> "OE2" Residue "s TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 70": "OE1" <-> "OE2" Residue "s ASP 109": "OD1" <-> "OD2" Residue "s GLU 125": "OE1" <-> "OE2" Residue "t GLU 4": "OE1" <-> "OE2" Residue "t GLU 11": "OE1" <-> "OE2" Residue "t GLU 20": "OE1" <-> "OE2" Residue "t TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 28": "OE1" <-> "OE2" Residue "t PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 57": "OE1" <-> "OE2" Residue "t GLU 105": "OE1" <-> "OE2" Residue "t ASP 120": "OD1" <-> "OD2" Residue "u GLU 20": "OE1" <-> "OE2" Residue "u TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 28": "OE1" <-> "OE2" Residue "u GLU 31": "OE1" <-> "OE2" Residue "u PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 48": "OE1" <-> "OE2" Residue "u GLU 57": "OE1" <-> "OE2" Residue "u ASP 120": "OD1" <-> "OD2" Residue "u GLU 125": "OE1" <-> "OE2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v GLU 20": "OE1" <-> "OE2" Residue "v TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 28": "OE1" <-> "OE2" Residue "v PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 109": "OD1" <-> "OD2" Residue "w GLU 11": "OE1" <-> "OE2" Residue "w TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 28": "OE1" <-> "OE2" Residue "w GLU 31": "OE1" <-> "OE2" Residue "w PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 97": "OE1" <-> "OE2" Residue "w ASP 109": "OD1" <-> "OD2" Residue "w ASP 120": "OD1" <-> "OD2" Residue "w GLU 125": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 58277 Number of models: 1 Model: "" Number of chains: 48 Chain: "1" Number of atoms: 6622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 6622 Classifications: {'DNA': 323} Link IDs: {'rna3p': 322} Chain: "2" Number of atoms: 6621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 6621 Classifications: {'DNA': 323} Link IDs: {'rna3p': 322} Chain: "A" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "O" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Q" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "R" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "S" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "T" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "U" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "V" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "a" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "b" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "c" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "d" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "e" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "f" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "g" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "h" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "i" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "j" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "k" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "l" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "m" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "n" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "o" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "p" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "q" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "r" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "s" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "t" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "u" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "v" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "w" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Time building chain proxies: 23.83, per 1000 atoms: 0.41 Number of scatterers: 58277 At special positions: 0 Unit cell: (211.4, 211.4, 127.4, 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 253 16.00 P 646 15.00 O 12064 8.00 N 10380 7.00 C 34934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS a 96 " - pdb=" SG CYS a 107 " distance=2.03 Simple disulfide: pdb=" SG CYS b 96 " - pdb=" SG CYS b 107 " distance=2.03 Simple disulfide: pdb=" SG CYS c 96 " - pdb=" SG CYS c 107 " distance=2.03 Simple disulfide: pdb=" SG CYS d 96 " - pdb=" SG CYS d 107 " distance=2.03 Simple disulfide: pdb=" SG CYS e 96 " - pdb=" SG CYS e 107 " distance=2.03 Simple disulfide: pdb=" SG CYS f 96 " - pdb=" SG CYS f 107 " distance=2.03 Simple disulfide: pdb=" SG CYS g 96 " - pdb=" SG CYS g 107 " distance=2.03 Simple disulfide: pdb=" SG CYS h 96 " - pdb=" SG CYS h 107 " distance=2.02 Simple disulfide: pdb=" SG CYS i 96 " - pdb=" SG CYS i 107 " distance=2.03 Simple disulfide: pdb=" SG CYS j 96 " - pdb=" SG CYS j 107 " distance=2.03 Simple disulfide: pdb=" SG CYS k 96 " - pdb=" SG CYS k 107 " distance=2.03 Simple disulfide: pdb=" SG CYS l 96 " - pdb=" SG CYS l 107 " distance=2.03 Simple disulfide: pdb=" SG CYS m 96 " - pdb=" SG CYS m 107 " distance=2.03 Simple disulfide: pdb=" SG CYS n 96 " - pdb=" SG CYS n 107 " distance=2.03 Simple disulfide: pdb=" SG CYS o 96 " - pdb=" SG CYS o 107 " distance=2.03 Simple disulfide: pdb=" SG CYS p 96 " - pdb=" SG CYS p 107 " distance=2.03 Simple disulfide: pdb=" SG CYS q 96 " - pdb=" SG CYS q 107 " distance=2.03 Simple disulfide: pdb=" SG CYS r 96 " - pdb=" SG CYS r 107 " distance=2.03 Simple disulfide: pdb=" SG CYS s 96 " - pdb=" SG CYS s 107 " distance=2.03 Simple disulfide: pdb=" SG CYS t 96 " - pdb=" SG CYS t 107 " distance=2.03 Simple disulfide: pdb=" SG CYS u 96 " - pdb=" SG CYS u 107 " distance=2.03 Simple disulfide: pdb=" SG CYS v 96 " - pdb=" SG CYS v 107 " distance=2.03 Simple disulfide: pdb=" SG CYS w 96 " - pdb=" SG CYS w 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.46 Conformation dependent library (CDL) restraints added in 5.4 seconds 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10626 Finding SS restraints... Secondary structure from input PDB file: 366 helices and 0 sheets defined 83.1% alpha, 0.0% beta 250 base pairs and 551 stacking pairs defined. Time for finding SS restraints: 13.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 66 removed outlier: 4.113A pdb=" N GLU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.548A pdb=" N ILE A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.783A pdb=" N TYR A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 removed outlier: 3.710A pdb=" N LYS B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.013A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 66 removed outlier: 4.109A pdb=" N ASN B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 66 " --> pdb=" O TYR B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.520A pdb=" N TRP B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.667A pdb=" N ILE B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 96 " --> pdb=" O GLN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.501A pdb=" N SER B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 29 removed outlier: 3.529A pdb=" N LYS C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 37 Processing helix chain 'C' and resid 42 through 66 removed outlier: 3.974A pdb=" N ASN C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 66 " --> pdb=" O TYR C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 89 through 100 removed outlier: 3.677A pdb=" N ILE C 93 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'D' and resid 13 through 29 removed outlier: 3.829A pdb=" N LYS D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 37 Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 43 through 66 removed outlier: 3.539A pdb=" N ARG D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 66 " --> pdb=" O TYR D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.617A pdb=" N TRP D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 100 removed outlier: 3.829A pdb=" N ILE D 93 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'E' and resid 13 through 29 removed outlier: 3.543A pdb=" N LYS E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 37 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 43 through 66 removed outlier: 3.542A pdb=" N ARG E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 66 " --> pdb=" O TYR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 removed outlier: 3.515A pdb=" N ILE E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.615A pdb=" N ILE E 93 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'F' and resid 13 through 24 removed outlier: 3.842A pdb=" N LYS F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 31 through 37 Processing helix chain 'F' and resid 42 through 66 removed outlier: 4.078A pdb=" N ASN F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.627A pdb=" N ILE F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL F 96 " --> pdb=" O GLN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 104 through 113 Processing helix chain 'F' and resid 115 through 127 removed outlier: 3.971A pdb=" N TYR F 121 " --> pdb=" O MET F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 29 removed outlier: 3.507A pdb=" N THR G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 37 Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 43 through 66 Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 89 through 100 removed outlier: 3.833A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G 96 " --> pdb=" O GLN G 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG G 98 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 103 No H-bonds generated for 'chain 'G' and resid 101 through 103' Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 117 through 127 removed outlier: 3.803A pdb=" N TYR G 121 " --> pdb=" O MET G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 29 removed outlier: 3.618A pdb=" N LYS H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 37 Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 43 through 66 removed outlier: 3.587A pdb=" N ARG H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU H 58 " --> pdb=" O ARG H 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 66 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 88 Processing helix chain 'H' and resid 89 through 100 removed outlier: 3.898A pdb=" N ILE H 93 " --> pdb=" O TYR H 89 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG H 98 " --> pdb=" O ASN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 113 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'I' and resid 13 through 29 removed outlier: 3.510A pdb=" N HIS I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 37 Processing helix chain 'I' and resid 42 through 67 removed outlier: 4.073A pdb=" N ASN I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS I 66 " --> pdb=" O TYR I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 88 removed outlier: 3.574A pdb=" N ARG I 83 " --> pdb=" O TRP I 79 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 100 removed outlier: 3.573A pdb=" N ILE I 93 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL I 96 " --> pdb=" O GLN I 92 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG I 98 " --> pdb=" O ASN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 103 No H-bonds generated for 'chain 'I' and resid 101 through 103' Processing helix chain 'I' and resid 104 through 113 Processing helix chain 'I' and resid 115 through 127 removed outlier: 3.533A pdb=" N SER I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR I 121 " --> pdb=" O MET I 117 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 29 removed outlier: 3.724A pdb=" N LYS J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 37 removed outlier: 4.082A pdb=" N VAL J 33 " --> pdb=" O ASP J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 66 removed outlier: 4.122A pdb=" N ASN J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG J 53 " --> pdb=" O ALA J 49 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 61 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS J 66 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.660A pdb=" N ILE J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 98 removed outlier: 3.509A pdb=" N ASN J 94 " --> pdb=" O THR J 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL J 96 " --> pdb=" O GLN J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 103 No H-bonds generated for 'chain 'J' and resid 101 through 103' Processing helix chain 'J' and resid 104 through 113 removed outlier: 3.525A pdb=" N LEU J 108 " --> pdb=" O TRP J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 127 removed outlier: 4.141A pdb=" N TYR J 121 " --> pdb=" O MET J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 29 removed outlier: 3.629A pdb=" N THR K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 37 Processing helix chain 'K' and resid 42 through 66 removed outlier: 4.127A pdb=" N ASN K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 89 through 100 removed outlier: 3.872A pdb=" N VAL K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL K 96 " --> pdb=" O GLN K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 103 No H-bonds generated for 'chain 'K' and resid 101 through 103' Processing helix chain 'K' and resid 104 through 113 removed outlier: 3.587A pdb=" N MET K 112 " --> pdb=" O LEU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 127 removed outlier: 3.950A pdb=" N TYR K 121 " --> pdb=" O MET K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 29 removed outlier: 3.806A pdb=" N VAL L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 37 Processing helix chain 'L' and resid 42 through 66 removed outlier: 3.935A pdb=" N ASN L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS L 66 " --> pdb=" O TYR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 88 removed outlier: 3.534A pdb=" N ILE L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 98 removed outlier: 3.628A pdb=" N ILE L 93 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL L 96 " --> pdb=" O GLN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 103 No H-bonds generated for 'chain 'L' and resid 101 through 103' Processing helix chain 'L' and resid 104 through 113 Processing helix chain 'L' and resid 115 through 127 removed outlier: 4.393A pdb=" N TYR L 121 " --> pdb=" O MET L 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 29 removed outlier: 3.730A pdb=" N LYS M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 37 Processing helix chain 'M' and resid 42 through 66 removed outlier: 4.139A pdb=" N ASN M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 88 removed outlier: 3.559A pdb=" N ILE M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 100 removed outlier: 3.662A pdb=" N VAL M 95 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M 96 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG M 98 " --> pdb=" O ASN M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 113 removed outlier: 3.558A pdb=" N MET M 112 " --> pdb=" O LEU M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 127 Processing helix chain 'N' and resid 13 through 29 removed outlier: 3.857A pdb=" N VAL N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 36 removed outlier: 3.898A pdb=" N VAL N 33 " --> pdb=" O ASP N 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 35 " --> pdb=" O TRP N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 67 removed outlier: 4.056A pdb=" N ASN N 46 " --> pdb=" O LEU N 42 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG N 53 " --> pdb=" O ALA N 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS N 66 " --> pdb=" O TYR N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 88 Processing helix chain 'N' and resid 89 through 98 removed outlier: 3.692A pdb=" N ILE N 93 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL N 95 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL N 96 " --> pdb=" O GLN N 92 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG N 98 " --> pdb=" O ASN N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 113 removed outlier: 3.502A pdb=" N LEU N 108 " --> pdb=" O TRP N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 128 removed outlier: 4.265A pdb=" N TYR N 121 " --> pdb=" O MET N 117 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG N 128 " --> pdb=" O LEU N 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 29 removed outlier: 3.584A pdb=" N LYS O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 37 Processing helix chain 'O' and resid 40 through 42 No H-bonds generated for 'chain 'O' and resid 40 through 42' Processing helix chain 'O' and resid 43 through 66 removed outlier: 3.601A pdb=" N GLU O 58 " --> pdb=" O ARG O 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 88 Processing helix chain 'O' and resid 89 through 97 removed outlier: 4.073A pdb=" N VAL O 95 " --> pdb=" O ASP O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 103 No H-bonds generated for 'chain 'O' and resid 101 through 103' Processing helix chain 'O' and resid 104 through 113 removed outlier: 3.558A pdb=" N MET O 112 " --> pdb=" O LEU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 127 Processing helix chain 'P' and resid 13 through 29 removed outlier: 3.879A pdb=" N VAL P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 36 removed outlier: 3.801A pdb=" N VAL P 33 " --> pdb=" O ASP P 29 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE P 35 " --> pdb=" O TRP P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 67 removed outlier: 4.011A pdb=" N ASN P 46 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS P 66 " --> pdb=" O TYR P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 88 removed outlier: 3.541A pdb=" N ILE P 77 " --> pdb=" O GLY P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 97 Processing helix chain 'P' and resid 101 through 103 No H-bonds generated for 'chain 'P' and resid 101 through 103' Processing helix chain 'P' and resid 104 through 113 Processing helix chain 'P' and resid 118 through 127 Processing helix chain 'Q' and resid 13 through 29 removed outlier: 3.784A pdb=" N LYS Q 24 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR Q 28 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 37 removed outlier: 3.903A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 43 through 66 removed outlier: 3.501A pdb=" N LYS Q 66 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 88 Processing helix chain 'Q' and resid 89 through 100 removed outlier: 3.591A pdb=" N VAL Q 95 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL Q 96 " --> pdb=" O GLN Q 92 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG Q 98 " --> pdb=" O ASN Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 113 removed outlier: 3.544A pdb=" N MET Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 128 removed outlier: 3.559A pdb=" N TYR Q 121 " --> pdb=" O MET Q 117 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 29 removed outlier: 3.804A pdb=" N THR R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 25 " --> pdb=" O GLY R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 37 removed outlier: 3.895A pdb=" N VAL R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE R 35 " --> pdb=" O TRP R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 66 removed outlier: 3.894A pdb=" N ASN R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS R 66 " --> pdb=" O TYR R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 88 Processing helix chain 'R' and resid 89 through 98 removed outlier: 3.914A pdb=" N VAL R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG R 98 " --> pdb=" O ASN R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 113 Processing helix chain 'R' and resid 118 through 127 Processing helix chain 'S' and resid 13 through 29 removed outlier: 3.721A pdb=" N VAL S 25 " --> pdb=" O GLY S 21 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR S 28 " --> pdb=" O LYS S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 37 Processing helix chain 'S' and resid 42 through 66 removed outlier: 4.165A pdb=" N ASN S 46 " --> pdb=" O LEU S 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU S 58 " --> pdb=" O ARG S 54 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN S 65 " --> pdb=" O ALA S 61 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS S 66 " --> pdb=" O TYR S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 88 removed outlier: 3.606A pdb=" N ILE S 77 " --> pdb=" O GLY S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 100 removed outlier: 3.761A pdb=" N VAL S 95 " --> pdb=" O ASP S 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL S 96 " --> pdb=" O GLN S 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG S 98 " --> pdb=" O ASN S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 113 removed outlier: 3.674A pdb=" N MET S 112 " --> pdb=" O LEU S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 127 Processing helix chain 'T' and resid 13 through 29 removed outlier: 3.522A pdb=" N LYS T 24 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL T 25 " --> pdb=" O GLY T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 37 removed outlier: 3.711A pdb=" N VAL T 33 " --> pdb=" O ASP T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 42 No H-bonds generated for 'chain 'T' and resid 40 through 42' Processing helix chain 'T' and resid 43 through 66 removed outlier: 3.517A pdb=" N ARG T 53 " --> pdb=" O ALA T 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU T 58 " --> pdb=" O ARG T 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE T 60 " --> pdb=" O GLN T 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN T 65 " --> pdb=" O ALA T 61 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS T 66 " --> pdb=" O TYR T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 88 removed outlier: 3.633A pdb=" N TRP T 86 " --> pdb=" O LEU T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 98 removed outlier: 4.122A pdb=" N VAL T 95 " --> pdb=" O ASP T 91 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL T 96 " --> pdb=" O GLN T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 103 No H-bonds generated for 'chain 'T' and resid 101 through 103' Processing helix chain 'T' and resid 104 through 113 removed outlier: 3.537A pdb=" N THR T 109 " --> pdb=" O ARG T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 127 Processing helix chain 'U' and resid 13 through 29 removed outlier: 3.709A pdb=" N LYS U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL U 25 " --> pdb=" O GLY U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 37 Processing helix chain 'U' and resid 42 through 66 removed outlier: 4.175A pdb=" N ASN U 46 " --> pdb=" O LEU U 42 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE U 60 " --> pdb=" O GLN U 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS U 66 " --> pdb=" O TYR U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 88 removed outlier: 3.663A pdb=" N ILE U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 89 through 100 removed outlier: 3.983A pdb=" N VAL U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL U 96 " --> pdb=" O GLN U 92 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG U 98 " --> pdb=" O ASN U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 113 removed outlier: 3.557A pdb=" N LEU U 108 " --> pdb=" O TRP U 104 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET U 112 " --> pdb=" O LEU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 128 removed outlier: 3.534A pdb=" N TYR U 121 " --> pdb=" O MET U 117 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG U 128 " --> pdb=" O LEU U 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 29 removed outlier: 3.609A pdb=" N LYS V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL V 25 " --> pdb=" O GLY V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 37 removed outlier: 3.746A pdb=" N VAL V 33 " --> pdb=" O ASP V 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE V 35 " --> pdb=" O TRP V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 42 No H-bonds generated for 'chain 'V' and resid 40 through 42' Processing helix chain 'V' and resid 43 through 66 removed outlier: 3.597A pdb=" N GLU V 58 " --> pdb=" O ARG V 54 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS V 66 " --> pdb=" O TYR V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 88 removed outlier: 3.537A pdb=" N ILE V 77 " --> pdb=" O GLY V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 89 through 98 removed outlier: 4.044A pdb=" N VAL V 95 " --> pdb=" O ASP V 91 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL V 96 " --> pdb=" O GLN V 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG V 98 " --> pdb=" O ASN V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 103 No H-bonds generated for 'chain 'V' and resid 101 through 103' Processing helix chain 'V' and resid 104 through 113 removed outlier: 3.540A pdb=" N THR V 109 " --> pdb=" O ARG V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 127 removed outlier: 4.212A pdb=" N TYR V 121 " --> pdb=" O MET V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 29 removed outlier: 3.552A pdb=" N LYS W 24 " --> pdb=" O LEU W 20 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL W 25 " --> pdb=" O GLY W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 37 Processing helix chain 'W' and resid 42 through 67 removed outlier: 4.220A pdb=" N ASN W 46 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE W 47 " --> pdb=" O GLU W 43 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU W 58 " --> pdb=" O ARG W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 88 removed outlier: 3.564A pdb=" N ILE W 77 " --> pdb=" O GLY W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 100 removed outlier: 3.723A pdb=" N VAL W 95 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL W 96 " --> pdb=" O GLN W 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG W 98 " --> pdb=" O ASN W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 103 No H-bonds generated for 'chain 'W' and resid 101 through 103' Processing helix chain 'W' and resid 104 through 113 removed outlier: 3.577A pdb=" N MET W 112 " --> pdb=" O LEU W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 127 removed outlier: 4.013A pdb=" N TYR W 121 " --> pdb=" O MET W 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 11 removed outlier: 3.690A pdb=" N LYS a 9 " --> pdb=" O VAL a 5 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 27 removed outlier: 3.585A pdb=" N ALA a 17 " --> pdb=" O GLY a 13 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 52 removed outlier: 3.579A pdb=" N SER a 41 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA a 42 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER a 44 " --> pdb=" O GLU a 40 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS a 45 " --> pdb=" O SER a 41 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE a 46 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU a 48 " --> pdb=" O SER a 44 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA a 49 " --> pdb=" O LYS a 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL a 50 " --> pdb=" O PHE a 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS a 51 " --> pdb=" O GLY a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 76 removed outlier: 3.810A pdb=" N TYR a 74 " --> pdb=" O GLU a 70 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 97 removed outlier: 3.536A pdb=" N ALA a 88 " --> pdb=" O LEU a 84 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN a 91 " --> pdb=" O ALA a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 116 removed outlier: 3.549A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) Processing helix chain 'a' and resid 118 through 127 removed outlier: 4.239A pdb=" N ILE a 122 " --> pdb=" O ALA a 118 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU a 125 " --> pdb=" O TRP a 121 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET a 126 " --> pdb=" O ILE a 122 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR a 127 " --> pdb=" O ARG a 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.627A pdb=" N GLN b 8 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS b 9 " --> pdb=" O VAL b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 27 Processing helix chain 'b' and resid 33 through 51 removed outlier: 3.559A pdb=" N SER b 41 " --> pdb=" O SER b 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA b 42 " --> pdb=" O ARG b 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER b 44 " --> pdb=" O GLU b 40 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS b 45 " --> pdb=" O SER b 41 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N PHE b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU b 48 " --> pdb=" O SER b 44 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL b 50 " --> pdb=" O PHE b 46 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS b 51 " --> pdb=" O GLY b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 54 No H-bonds generated for 'chain 'b' and resid 52 through 54' Processing helix chain 'b' and resid 61 through 76 removed outlier: 3.756A pdb=" N TYR b 74 " --> pdb=" O GLU b 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET b 75 " --> pdb=" O ALA b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 97 removed outlier: 3.598A pdb=" N ALA b 88 " --> pdb=" O LEU b 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN b 91 " --> pdb=" O ALA b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 116 removed outlier: 3.533A pdb=" N ALA b 110 " --> pdb=" O ARG b 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA b 112 " --> pdb=" O LEU b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 125 removed outlier: 4.276A pdb=" N ILE b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU b 125 " --> pdb=" O TRP b 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 11 removed outlier: 3.609A pdb=" N GLN c 8 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS c 9 " --> pdb=" O VAL c 5 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 27 removed outlier: 3.512A pdb=" N ALA c 17 " --> pdb=" O GLY c 13 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR c 19 " --> pdb=" O TYR c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 51 removed outlier: 3.605A pdb=" N SER c 37 " --> pdb=" O LEU c 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA c 42 " --> pdb=" O ARG c 38 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER c 44 " --> pdb=" O GLU c 40 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS c 45 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE c 46 " --> pdb=" O ALA c 42 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA c 49 " --> pdb=" O LYS c 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL c 50 " --> pdb=" O PHE c 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS c 51 " --> pdb=" O GLY c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 52 through 54 No H-bonds generated for 'chain 'c' and resid 52 through 54' Processing helix chain 'c' and resid 61 through 76 removed outlier: 3.883A pdb=" N TYR c 74 " --> pdb=" O GLU c 70 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET c 75 " --> pdb=" O ALA c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 98 removed outlier: 3.790A pdb=" N ALA c 88 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN c 91 " --> pdb=" O ALA c 87 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN c 98 " --> pdb=" O ARG c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 116 removed outlier: 3.534A pdb=" N ALA c 110 " --> pdb=" O ARG c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 125 removed outlier: 4.292A pdb=" N ILE c 122 " --> pdb=" O ALA c 118 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU c 125 " --> pdb=" O TRP c 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 11 removed outlier: 3.637A pdb=" N GLN d 8 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS d 9 " --> pdb=" O VAL d 5 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 27 Processing helix chain 'd' and resid 33 through 51 removed outlier: 3.513A pdb=" N SER d 37 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER d 41 " --> pdb=" O SER d 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA d 42 " --> pdb=" O ARG d 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER d 44 " --> pdb=" O GLU d 40 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS d 45 " --> pdb=" O SER d 41 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE d 46 " --> pdb=" O ALA d 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA d 49 " --> pdb=" O LYS d 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL d 50 " --> pdb=" O PHE d 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS d 51 " --> pdb=" O GLY d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 54 No H-bonds generated for 'chain 'd' and resid 52 through 54' Processing helix chain 'd' and resid 61 through 76 removed outlier: 3.616A pdb=" N MET d 75 " --> pdb=" O ALA d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 98 removed outlier: 3.595A pdb=" N MET d 86 " --> pdb=" O MET d 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA d 87 " --> pdb=" O LYS d 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN d 98 " --> pdb=" O ARG d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 116 removed outlier: 3.621A pdb=" N CYS d 107 " --> pdb=" O ASN d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 127 removed outlier: 4.329A pdb=" N ILE d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU d 125 " --> pdb=" O TRP d 121 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR d 127 " --> pdb=" O ARG d 123 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 11 removed outlier: 3.596A pdb=" N GLN e 8 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS e 9 " --> pdb=" O VAL e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 13 through 27 Processing helix chain 'e' and resid 33 through 52 removed outlier: 3.688A pdb=" N SER e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA e 42 " --> pdb=" O ARG e 38 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER e 44 " --> pdb=" O GLU e 40 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS e 45 " --> pdb=" O SER e 41 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU e 48 " --> pdb=" O SER e 44 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA e 49 " --> pdb=" O LYS e 45 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL e 50 " --> pdb=" O PHE e 46 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS e 51 " --> pdb=" O GLY e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 61 through 76 removed outlier: 3.867A pdb=" N TYR e 74 " --> pdb=" O GLU e 70 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET e 75 " --> pdb=" O ALA e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 98 removed outlier: 3.710A pdb=" N ALA e 88 " --> pdb=" O LEU e 84 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN e 91 " --> pdb=" O ALA e 87 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN e 98 " --> pdb=" O ARG e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 116 Processing helix chain 'e' and resid 119 through 127 removed outlier: 4.209A pdb=" N GLU e 125 " --> pdb=" O TRP e 121 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 11 removed outlier: 3.651A pdb=" N GLN f 8 " --> pdb=" O GLU f 4 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS f 9 " --> pdb=" O VAL f 5 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE f 10 " --> pdb=" O TYR f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 27 Processing helix chain 'f' and resid 33 through 51 removed outlier: 3.530A pdb=" N SER f 37 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER f 41 " --> pdb=" O SER f 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA f 42 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS f 45 " --> pdb=" O SER f 41 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE f 46 " --> pdb=" O ALA f 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA f 49 " --> pdb=" O LYS f 45 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS f 51 " --> pdb=" O GLY f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 54 No H-bonds generated for 'chain 'f' and resid 52 through 54' Processing helix chain 'f' and resid 61 through 76 removed outlier: 3.684A pdb=" N TYR f 74 " --> pdb=" O GLU f 70 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET f 75 " --> pdb=" O ALA f 71 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 97 removed outlier: 3.512A pdb=" N ALA f 88 " --> pdb=" O LEU f 84 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN f 91 " --> pdb=" O ALA f 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 116 Processing helix chain 'f' and resid 118 through 127 removed outlier: 4.348A pdb=" N ILE f 122 " --> pdb=" O ALA f 118 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU f 125 " --> pdb=" O TRP f 121 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR f 127 " --> pdb=" O ARG f 123 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 11 removed outlier: 3.811A pdb=" N GLN g 8 " --> pdb=" O GLU g 4 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS g 9 " --> pdb=" O VAL g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 27 removed outlier: 3.553A pdb=" N ALA g 17 " --> pdb=" O GLY g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 52 removed outlier: 3.507A pdb=" N SER g 37 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER g 44 " --> pdb=" O GLU g 40 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS g 45 " --> pdb=" O SER g 41 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA g 49 " --> pdb=" O LYS g 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL g 50 " --> pdb=" O PHE g 46 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS g 51 " --> pdb=" O GLY g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 76 removed outlier: 3.530A pdb=" N TYR g 74 " --> pdb=" O GLU g 70 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET g 75 " --> pdb=" O ALA g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 98 removed outlier: 3.816A pdb=" N GLN g 91 " --> pdb=" O ALA g 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA g 92 " --> pdb=" O ALA g 88 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN g 98 " --> pdb=" O ARG g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 116 Processing helix chain 'g' and resid 118 through 127 removed outlier: 4.406A pdb=" N ILE g 122 " --> pdb=" O ALA g 118 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU g 125 " --> pdb=" O TRP g 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR g 127 " --> pdb=" O ARG g 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 11 removed outlier: 3.908A pdb=" N LYS h 9 " --> pdb=" O VAL h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 27 Processing helix chain 'h' and resid 33 through 52 removed outlier: 3.580A pdb=" N SER h 41 " --> pdb=" O SER h 37 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA h 42 " --> pdb=" O ARG h 38 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS h 45 " --> pdb=" O SER h 41 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA h 49 " --> pdb=" O LYS h 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL h 50 " --> pdb=" O PHE h 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS h 51 " --> pdb=" O GLY h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 76 removed outlier: 3.707A pdb=" N MET h 75 " --> pdb=" O ALA h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 98 removed outlier: 3.644A pdb=" N ALA h 88 " --> pdb=" O LEU h 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN h 91 " --> pdb=" O ALA h 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN h 98 " --> pdb=" O ARG h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 116 Processing helix chain 'h' and resid 118 through 127 removed outlier: 4.275A pdb=" N ILE h 122 " --> pdb=" O ALA h 118 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU h 125 " --> pdb=" O TRP h 121 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR h 127 " --> pdb=" O ARG h 123 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 11 removed outlier: 3.544A pdb=" N GLN i 8 " --> pdb=" O GLU i 4 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS i 9 " --> pdb=" O VAL i 5 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE i 10 " --> pdb=" O TYR i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 27 Processing helix chain 'i' and resid 33 through 51 removed outlier: 3.649A pdb=" N SER i 37 " --> pdb=" O LEU i 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA i 42 " --> pdb=" O ARG i 38 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER i 44 " --> pdb=" O GLU i 40 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS i 45 " --> pdb=" O SER i 41 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU i 48 " --> pdb=" O SER i 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA i 49 " --> pdb=" O LYS i 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL i 50 " --> pdb=" O PHE i 46 " (cutoff:3.500A) Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 61 through 76 removed outlier: 3.759A pdb=" N TYR i 74 " --> pdb=" O GLU i 70 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 98 removed outlier: 3.534A pdb=" N ALA i 87 " --> pdb=" O LYS i 83 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA i 88 " --> pdb=" O LEU i 84 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN i 91 " --> pdb=" O ALA i 87 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN i 98 " --> pdb=" O ARG i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 116 Processing helix chain 'i' and resid 118 through 127 removed outlier: 4.411A pdb=" N ILE i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU i 125 " --> pdb=" O TRP i 121 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR i 127 " --> pdb=" O ARG i 123 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 11 removed outlier: 3.866A pdb=" N LYS j 9 " --> pdb=" O VAL j 5 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 27 Processing helix chain 'j' and resid 33 through 51 removed outlier: 3.518A pdb=" N SER j 37 " --> pdb=" O LEU j 33 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER j 41 " --> pdb=" O SER j 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA j 42 " --> pdb=" O ARG j 38 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS j 45 " --> pdb=" O SER j 41 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU j 48 " --> pdb=" O SER j 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA j 49 " --> pdb=" O LYS j 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL j 50 " --> pdb=" O PHE j 46 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS j 51 " --> pdb=" O GLY j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 54 No H-bonds generated for 'chain 'j' and resid 52 through 54' Processing helix chain 'j' and resid 61 through 76 removed outlier: 3.557A pdb=" N TYR j 74 " --> pdb=" O GLU j 70 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET j 75 " --> pdb=" O ALA j 71 " (cutoff:3.500A) Processing helix chain 'j' and resid 81 through 98 removed outlier: 3.644A pdb=" N ALA j 88 " --> pdb=" O LEU j 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN j 91 " --> pdb=" O ALA j 87 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN j 98 " --> pdb=" O ARG j 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 116 Processing helix chain 'j' and resid 118 through 125 removed outlier: 4.233A pdb=" N ILE j 122 " --> pdb=" O ALA j 118 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU j 125 " --> pdb=" O TRP j 121 " (cutoff:3.500A) Processing helix chain 'k' and resid 3 through 11 removed outlier: 3.506A pdb=" N GLN k 8 " --> pdb=" O GLU k 4 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS k 9 " --> pdb=" O VAL k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 27 Processing helix chain 'k' and resid 33 through 50 removed outlier: 3.591A pdb=" N ALA k 42 " --> pdb=" O ARG k 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER k 44 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS k 45 " --> pdb=" O SER k 41 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU k 48 " --> pdb=" O SER k 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA k 49 " --> pdb=" O LYS k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 54 removed outlier: 3.634A pdb=" N GLY k 54 " --> pdb=" O LYS k 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 51 through 54' Processing helix chain 'k' and resid 61 through 76 removed outlier: 3.520A pdb=" N VAL k 68 " --> pdb=" O VAL k 64 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR k 74 " --> pdb=" O GLU k 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 98 removed outlier: 3.551A pdb=" N ALA k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN k 91 " --> pdb=" O ALA k 87 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN k 98 " --> pdb=" O ARG k 94 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 116 Processing helix chain 'k' and resid 118 through 127 removed outlier: 4.109A pdb=" N ILE k 122 " --> pdb=" O ALA k 118 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU k 125 " --> pdb=" O TRP k 121 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET k 126 " --> pdb=" O ILE k 122 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR k 127 " --> pdb=" O ARG k 123 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 3.518A pdb=" N GLN l 8 " --> pdb=" O GLU l 4 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS l 9 " --> pdb=" O VAL l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 27 removed outlier: 3.511A pdb=" N ALA l 17 " --> pdb=" O GLY l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 51 removed outlier: 3.511A pdb=" N ARG l 38 " --> pdb=" O SER l 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER l 41 " --> pdb=" O SER l 37 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA l 42 " --> pdb=" O ARG l 38 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LYS l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU l 48 " --> pdb=" O SER l 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA l 49 " --> pdb=" O LYS l 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL l 50 " --> pdb=" O PHE l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 52 through 54 No H-bonds generated for 'chain 'l' and resid 52 through 54' Processing helix chain 'l' and resid 61 through 76 removed outlier: 3.570A pdb=" N ALA l 73 " --> pdb=" O GLN l 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR l 74 " --> pdb=" O GLU l 70 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 81 through 98 removed outlier: 3.507A pdb=" N ALA l 88 " --> pdb=" O LEU l 84 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN l 91 " --> pdb=" O ALA l 87 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN l 98 " --> pdb=" O ARG l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 103 through 116 Processing helix chain 'l' and resid 118 through 127 removed outlier: 4.186A pdb=" N ILE l 122 " --> pdb=" O ALA l 118 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU l 125 " --> pdb=" O TRP l 121 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR l 127 " --> pdb=" O ARG l 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 11 removed outlier: 3.528A pdb=" N GLN m 8 " --> pdb=" O GLU m 4 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS m 9 " --> pdb=" O VAL m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 27 Processing helix chain 'm' and resid 33 through 51 removed outlier: 3.614A pdb=" N SER m 37 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG m 38 " --> pdb=" O SER m 34 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER m 41 " --> pdb=" O SER m 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA m 42 " --> pdb=" O ARG m 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER m 44 " --> pdb=" O GLU m 40 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS m 45 " --> pdb=" O SER m 41 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU m 48 " --> pdb=" O SER m 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA m 49 " --> pdb=" O LYS m 45 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL m 50 " --> pdb=" O PHE m 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS m 51 " --> pdb=" O GLY m 47 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 54 No H-bonds generated for 'chain 'm' and resid 52 through 54' Processing helix chain 'm' and resid 61 through 76 removed outlier: 3.752A pdb=" N TYR m 74 " --> pdb=" O GLU m 70 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET m 75 " --> pdb=" O ALA m 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER m 76 " --> pdb=" O LEU m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 81 through 98 removed outlier: 3.653A pdb=" N GLN m 91 " --> pdb=" O ALA m 87 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN m 98 " --> pdb=" O ARG m 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 103 through 116 Processing helix chain 'm' and resid 118 through 127 removed outlier: 4.297A pdb=" N ILE m 122 " --> pdb=" O ALA m 118 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU m 125 " --> pdb=" O TRP m 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET m 126 " --> pdb=" O ILE m 122 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR m 127 " --> pdb=" O ARG m 123 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 11 removed outlier: 3.518A pdb=" N GLN n 8 " --> pdb=" O GLU n 4 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS n 9 " --> pdb=" O VAL n 5 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 27 removed outlier: 3.551A pdb=" N ALA n 17 " --> pdb=" O GLY n 13 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 51 removed outlier: 3.740A pdb=" N SER n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA n 42 " --> pdb=" O ARG n 38 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS n 45 " --> pdb=" O SER n 41 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU n 48 " --> pdb=" O SER n 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA n 49 " --> pdb=" O LYS n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 54 No H-bonds generated for 'chain 'n' and resid 52 through 54' Processing helix chain 'n' and resid 61 through 76 removed outlier: 3.541A pdb=" N ALA n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR n 74 " --> pdb=" O GLU n 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET n 75 " --> pdb=" O ALA n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 81 through 98 removed outlier: 3.638A pdb=" N ALA n 88 " --> pdb=" O LEU n 84 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA n 89 " --> pdb=" O ALA n 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN n 98 " --> pdb=" O ARG n 94 " (cutoff:3.500A) Processing helix chain 'n' and resid 103 through 116 Processing helix chain 'n' and resid 119 through 127 removed outlier: 4.249A pdb=" N GLU n 125 " --> pdb=" O TRP n 121 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR n 127 " --> pdb=" O ARG n 123 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 11 removed outlier: 3.552A pdb=" N GLN o 8 " --> pdb=" O GLU o 4 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS o 9 " --> pdb=" O VAL o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 13 through 27 removed outlier: 3.509A pdb=" N THR o 22 " --> pdb=" O ALA o 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 33 through 50 removed outlier: 3.664A pdb=" N SER o 41 " --> pdb=" O SER o 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA o 42 " --> pdb=" O ARG o 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER o 44 " --> pdb=" O GLU o 40 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS o 45 " --> pdb=" O SER o 41 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N PHE o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU o 48 " --> pdb=" O SER o 44 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA o 49 " --> pdb=" O LYS o 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 54 removed outlier: 3.682A pdb=" N GLY o 54 " --> pdb=" O LYS o 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 51 through 54' Processing helix chain 'o' and resid 61 through 76 removed outlier: 3.744A pdb=" N TYR o 74 " --> pdb=" O GLU o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 81 through 98 removed outlier: 3.690A pdb=" N GLN o 91 " --> pdb=" O ALA o 87 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN o 98 " --> pdb=" O ARG o 94 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 116 Processing helix chain 'o' and resid 119 through 127 removed outlier: 4.103A pdb=" N GLU o 125 " --> pdb=" O TRP o 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET o 126 " --> pdb=" O ILE o 122 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR o 127 " --> pdb=" O ARG o 123 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 11 removed outlier: 3.646A pdb=" N LYS p 9 " --> pdb=" O VAL p 5 " (cutoff:3.500A) Processing helix chain 'p' and resid 13 through 27 Processing helix chain 'p' and resid 33 through 50 removed outlier: 3.514A pdb=" N SER p 37 " --> pdb=" O LEU p 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER p 41 " --> pdb=" O SER p 37 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA p 42 " --> pdb=" O ARG p 38 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS p 45 " --> pdb=" O SER p 41 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE p 46 " --> pdb=" O ALA p 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU p 48 " --> pdb=" O SER p 44 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA p 49 " --> pdb=" O LYS p 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL p 50 " --> pdb=" O PHE p 46 " (cutoff:3.500A) Processing helix chain 'p' and resid 51 through 54 removed outlier: 3.686A pdb=" N GLY p 54 " --> pdb=" O LYS p 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 51 through 54' Processing helix chain 'p' and resid 61 through 76 removed outlier: 3.627A pdb=" N TYR p 74 " --> pdb=" O GLU p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 81 through 98 removed outlier: 3.614A pdb=" N ALA p 88 " --> pdb=" O LEU p 84 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA p 89 " --> pdb=" O ALA p 85 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN p 91 " --> pdb=" O ALA p 87 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN p 98 " --> pdb=" O ARG p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 116 Processing helix chain 'p' and resid 118 through 125 removed outlier: 4.146A pdb=" N ILE p 122 " --> pdb=" O ALA p 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU p 125 " --> pdb=" O TRP p 121 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 removed outlier: 3.564A pdb=" N GLN q 8 " --> pdb=" O GLU q 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS q 9 " --> pdb=" O VAL q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 13 through 27 removed outlier: 3.501A pdb=" N TYR q 19 " --> pdb=" O TYR q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 33 through 51 removed outlier: 3.619A pdb=" N SER q 41 " --> pdb=" O SER q 37 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA q 42 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER q 44 " --> pdb=" O GLU q 40 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS q 45 " --> pdb=" O SER q 41 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE q 46 " --> pdb=" O ALA q 42 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU q 48 " --> pdb=" O SER q 44 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA q 49 " --> pdb=" O LYS q 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL q 50 " --> pdb=" O PHE q 46 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS q 51 " --> pdb=" O GLY q 47 " (cutoff:3.500A) Processing helix chain 'q' and resid 52 through 54 No H-bonds generated for 'chain 'q' and resid 52 through 54' Processing helix chain 'q' and resid 61 through 76 removed outlier: 3.628A pdb=" N TYR q 74 " --> pdb=" O GLU q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 98 removed outlier: 3.557A pdb=" N ALA q 88 " --> pdb=" O LEU q 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN q 91 " --> pdb=" O ALA q 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN q 98 " --> pdb=" O ARG q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 103 through 116 Processing helix chain 'q' and resid 118 through 127 removed outlier: 4.343A pdb=" N ILE q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU q 125 " --> pdb=" O TRP q 121 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR q 127 " --> pdb=" O ARG q 123 " (cutoff:3.500A) Processing helix chain 'r' and resid 3 through 11 removed outlier: 3.850A pdb=" N LYS r 9 " --> pdb=" O VAL r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 27 removed outlier: 3.656A pdb=" N ALA r 17 " --> pdb=" O GLY r 13 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 51 removed outlier: 3.698A pdb=" N SER r 41 " --> pdb=" O SER r 37 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA r 42 " --> pdb=" O ARG r 38 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS r 45 " --> pdb=" O SER r 41 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE r 46 " --> pdb=" O ALA r 42 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA r 49 " --> pdb=" O LYS r 45 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL r 50 " --> pdb=" O PHE r 46 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS r 51 " --> pdb=" O GLY r 47 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 54 No H-bonds generated for 'chain 'r' and resid 52 through 54' Processing helix chain 'r' and resid 61 through 76 removed outlier: 3.691A pdb=" N TYR r 74 " --> pdb=" O GLU r 70 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET r 75 " --> pdb=" O ALA r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 81 through 98 removed outlier: 3.704A pdb=" N ALA r 88 " --> pdb=" O LEU r 84 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN r 91 " --> pdb=" O ALA r 87 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN r 98 " --> pdb=" O ARG r 94 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 116 Processing helix chain 'r' and resid 118 through 127 removed outlier: 4.060A pdb=" N ILE r 122 " --> pdb=" O ALA r 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU r 125 " --> pdb=" O TRP r 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET r 126 " --> pdb=" O ILE r 122 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR r 127 " --> pdb=" O ARG r 123 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 3.909A pdb=" N LYS s 9 " --> pdb=" O VAL s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 27 Processing helix chain 's' and resid 33 through 51 removed outlier: 3.505A pdb=" N SER s 37 " --> pdb=" O LEU s 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER s 41 " --> pdb=" O SER s 37 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA s 42 " --> pdb=" O ARG s 38 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER s 44 " --> pdb=" O GLU s 40 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LYS s 45 " --> pdb=" O SER s 41 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE s 46 " --> pdb=" O ALA s 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU s 48 " --> pdb=" O SER s 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA s 49 " --> pdb=" O LYS s 45 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL s 50 " --> pdb=" O PHE s 46 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS s 51 " --> pdb=" O GLY s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 61 through 76 removed outlier: 3.661A pdb=" N TYR s 74 " --> pdb=" O GLU s 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET s 75 " --> pdb=" O ALA s 71 " (cutoff:3.500A) Processing helix chain 's' and resid 81 through 98 removed outlier: 3.779A pdb=" N ALA s 88 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN s 91 " --> pdb=" O ALA s 87 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN s 98 " --> pdb=" O ARG s 94 " (cutoff:3.500A) Processing helix chain 's' and resid 103 through 116 Processing helix chain 's' and resid 119 through 127 removed outlier: 4.090A pdb=" N GLU s 125 " --> pdb=" O TRP s 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR s 127 " --> pdb=" O ARG s 123 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 11 removed outlier: 3.750A pdb=" N LYS t 9 " --> pdb=" O VAL t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 13 through 27 Processing helix chain 't' and resid 33 through 51 removed outlier: 3.697A pdb=" N SER t 41 " --> pdb=" O SER t 37 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA t 42 " --> pdb=" O ARG t 38 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS t 45 " --> pdb=" O SER t 41 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE t 46 " --> pdb=" O ALA t 42 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA t 49 " --> pdb=" O LYS t 45 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL t 50 " --> pdb=" O PHE t 46 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS t 51 " --> pdb=" O GLY t 47 " (cutoff:3.500A) Processing helix chain 't' and resid 52 through 54 No H-bonds generated for 'chain 't' and resid 52 through 54' Processing helix chain 't' and resid 61 through 76 Processing helix chain 't' and resid 81 through 98 removed outlier: 3.586A pdb=" N ALA t 87 " --> pdb=" O LYS t 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA t 88 " --> pdb=" O LEU t 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN t 91 " --> pdb=" O ALA t 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN t 98 " --> pdb=" O ARG t 94 " (cutoff:3.500A) Processing helix chain 't' and resid 103 through 116 Processing helix chain 't' and resid 118 through 125 removed outlier: 4.082A pdb=" N ILE t 122 " --> pdb=" O ALA t 118 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU t 125 " --> pdb=" O TRP t 121 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 11 removed outlier: 3.613A pdb=" N LYS u 9 " --> pdb=" O VAL u 5 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 27 Processing helix chain 'u' and resid 33 through 51 removed outlier: 3.594A pdb=" N SER u 37 " --> pdb=" O LEU u 33 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG u 38 " --> pdb=" O SER u 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER u 41 " --> pdb=" O SER u 37 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA u 42 " --> pdb=" O ARG u 38 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER u 44 " --> pdb=" O GLU u 40 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS u 45 " --> pdb=" O SER u 41 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE u 46 " --> pdb=" O ALA u 42 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU u 48 " --> pdb=" O SER u 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA u 49 " --> pdb=" O LYS u 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL u 50 " --> pdb=" O PHE u 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS u 51 " --> pdb=" O GLY u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 54 No H-bonds generated for 'chain 'u' and resid 52 through 54' Processing helix chain 'u' and resid 61 through 76 removed outlier: 3.561A pdb=" N LEU u 72 " --> pdb=" O VAL u 68 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR u 74 " --> pdb=" O GLU u 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET u 75 " --> pdb=" O ALA u 71 " (cutoff:3.500A) Processing helix chain 'u' and resid 81 through 98 removed outlier: 3.625A pdb=" N ALA u 88 " --> pdb=" O LEU u 84 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN u 98 " --> pdb=" O ARG u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 103 through 116 Processing helix chain 'u' and resid 118 through 127 removed outlier: 4.271A pdb=" N ILE u 122 " --> pdb=" O ALA u 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU u 125 " --> pdb=" O TRP u 121 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR u 127 " --> pdb=" O ARG u 123 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 removed outlier: 3.640A pdb=" N LYS v 9 " --> pdb=" O VAL v 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU v 11 " --> pdb=" O ARG v 7 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 27 Processing helix chain 'v' and resid 33 through 51 removed outlier: 3.604A pdb=" N ALA v 42 " --> pdb=" O ARG v 38 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS v 45 " --> pdb=" O SER v 41 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE v 46 " --> pdb=" O ALA v 42 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU v 48 " --> pdb=" O SER v 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA v 49 " --> pdb=" O LYS v 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL v 50 " --> pdb=" O PHE v 46 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS v 51 " --> pdb=" O GLY v 47 " (cutoff:3.500A) Processing helix chain 'v' and resid 52 through 54 No H-bonds generated for 'chain 'v' and resid 52 through 54' Processing helix chain 'v' and resid 61 through 76 Processing helix chain 'v' and resid 81 through 98 removed outlier: 3.514A pdb=" N ALA v 87 " --> pdb=" O LYS v 83 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA v 88 " --> pdb=" O LEU v 84 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN v 91 " --> pdb=" O ALA v 87 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN v 98 " --> pdb=" O ARG v 94 " (cutoff:3.500A) Processing helix chain 'v' and resid 103 through 116 removed outlier: 3.559A pdb=" N ALA v 110 " --> pdb=" O ARG v 106 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 127 removed outlier: 4.256A pdb=" N ILE v 122 " --> pdb=" O ALA v 118 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU v 125 " --> pdb=" O TRP v 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET v 126 " --> pdb=" O ILE v 122 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR v 127 " --> pdb=" O ARG v 123 " (cutoff:3.500A) Processing helix chain 'w' and resid 3 through 11 removed outlier: 3.909A pdb=" N LYS w 9 " --> pdb=" O VAL w 5 " (cutoff:3.500A) Processing helix chain 'w' and resid 13 through 27 removed outlier: 3.507A pdb=" N TYR w 19 " --> pdb=" O TYR w 15 " (cutoff:3.500A) Processing helix chain 'w' and resid 33 through 51 removed outlier: 3.587A pdb=" N SER w 37 " --> pdb=" O LEU w 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG w 38 " --> pdb=" O SER w 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA w 42 " --> pdb=" O ARG w 38 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER w 44 " --> pdb=" O GLU w 40 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS w 45 " --> pdb=" O SER w 41 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE w 46 " --> pdb=" O ALA w 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU w 48 " --> pdb=" O SER w 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA w 49 " --> pdb=" O LYS w 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL w 50 " --> pdb=" O PHE w 46 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS w 51 " --> pdb=" O GLY w 47 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 54 No H-bonds generated for 'chain 'w' and resid 52 through 54' Processing helix chain 'w' and resid 61 through 76 removed outlier: 3.547A pdb=" N VAL w 68 " --> pdb=" O VAL w 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR w 74 " --> pdb=" O GLU w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 81 through 98 removed outlier: 3.621A pdb=" N ALA w 88 " --> pdb=" O LEU w 84 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN w 91 " --> pdb=" O ALA w 87 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN w 98 " --> pdb=" O ARG w 94 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 116 removed outlier: 3.557A pdb=" N ALA w 112 " --> pdb=" O LEU w 108 " (cutoff:3.500A) Processing helix chain 'w' and resid 118 through 127 removed outlier: 4.346A pdb=" N ILE w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU w 125 " --> pdb=" O TRP w 121 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR w 127 " --> pdb=" O ARG w 123 " (cutoff:3.500A) 2596 hydrogen bonds defined for protein. 7788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 500 hydrogen bonds 1000 hydrogen bond angles 0 basepair planarities 250 basepair parallelities 551 stacking parallelities Total time for adding SS restraints: 19.55 Time building geometry restraints manager: 20.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10835 1.33 - 1.45: 17490 1.45 - 1.57: 30575 1.57 - 1.70: 1289 1.70 - 1.82: 460 Bond restraints: 60649 Sorted by residual: bond pdb=" C3' DT 2 240 " pdb=" O3' DT 2 240 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.43e+00 bond pdb=" CA GLU V 12 " pdb=" CB GLU V 12 " ideal model delta sigma weight residual 1.527 1.551 -0.024 1.39e-02 5.18e+03 2.98e+00 bond pdb=" C ALA c 59 " pdb=" N PRO c 60 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" O4' DT 1 188 " pdb=" C1' DT 1 188 " ideal model delta sigma weight residual 1.414 1.380 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C ALA f 59 " pdb=" N PRO f 60 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.70e+00 ... (remaining 60644 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.65: 3707 105.65 - 112.75: 32645 112.75 - 119.85: 21151 119.85 - 126.96: 24536 126.96 - 134.06: 2595 Bond angle restraints: 84634 Sorted by residual: angle pdb=" N VAL M 127 " pdb=" CA VAL M 127 " pdb=" C VAL M 127 " ideal model delta sigma weight residual 112.80 106.96 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" C ARG L 38 " pdb=" N GLU L 39 " pdb=" CA GLU L 39 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 angle pdb=" N VAL I 127 " pdb=" CA VAL I 127 " pdb=" C VAL I 127 " ideal model delta sigma weight residual 113.07 107.85 5.22 1.36e+00 5.41e-01 1.48e+01 angle pdb=" N GLU W 12 " pdb=" CA GLU W 12 " pdb=" C GLU W 12 " ideal model delta sigma weight residual 110.61 115.37 -4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" C GLY u 58 " pdb=" N ALA u 59 " pdb=" CA ALA u 59 " ideal model delta sigma weight residual 122.29 127.89 -5.60 1.48e+00 4.57e-01 1.43e+01 ... (remaining 84629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 31505 22.09 - 44.18: 2576 44.18 - 66.28: 456 66.28 - 88.37: 107 88.37 - 110.46: 8 Dihedral angle restraints: 34652 sinusoidal: 18230 harmonic: 16422 Sorted by residual: dihedral pdb=" CA ASP H 91 " pdb=" C ASP H 91 " pdb=" N GLN H 92 " pdb=" CA GLN H 92 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ALA p 59 " pdb=" C ALA p 59 " pdb=" N PRO p 60 " pdb=" CA PRO p 60 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA r 59 " pdb=" C ALA r 59 " pdb=" N PRO r 60 " pdb=" CA PRO r 60 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 34649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 6922 0.050 - 0.101: 2124 0.101 - 0.151: 298 0.151 - 0.201: 43 0.201 - 0.251: 5 Chirality restraints: 9392 Sorted by residual: chirality pdb=" C1' DT 1 188 " pdb=" O4' DT 1 188 " pdb=" C2' DT 1 188 " pdb=" N1 DT 1 188 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB THR C 115 " pdb=" CA THR C 115 " pdb=" OG1 THR C 115 " pdb=" CG2 THR C 115 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB THR A 115 " pdb=" CA THR A 115 " pdb=" OG1 THR A 115 " pdb=" CG2 THR A 115 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 9389 not shown) Planarity restraints: 8420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA v 59 " -0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO v 60 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO v 60 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO v 60 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA u 59 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO u 60 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO u 60 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO u 60 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA k 59 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO k 60 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO k 60 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO k 60 " 0.042 5.00e-02 4.00e+02 ... (remaining 8417 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 12919 2.77 - 3.30: 48807 3.30 - 3.83: 98085 3.83 - 4.37: 126803 4.37 - 4.90: 204926 Nonbonded interactions: 491540 Sorted by model distance: nonbonded pdb=" OE1 GLU I 16 " pdb=" OH TYR i 25 " model vdw 2.234 2.440 nonbonded pdb=" OE1 GLU W 16 " pdb=" OH TYR w 25 " model vdw 2.253 2.440 nonbonded pdb=" O VAL Q 33 " pdb=" OG SER Q 37 " model vdw 2.295 2.440 nonbonded pdb=" O VAL F 33 " pdb=" OG SER F 37 " model vdw 2.297 2.440 nonbonded pdb=" O VAL B 33 " pdb=" OG SER B 37 " model vdw 2.300 2.440 ... (remaining 491535 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 '1' and resid -27 through 294) selection = (chain '2' and resid 211 through 532) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } 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 646 5.49 5 S 253 5.16 5 C 34934 2.51 5 N 10380 2.21 5 O 12064 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 individual isotropic 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: 1.960 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: 11.870 Check model and map are aligned: 0.660 Process input model: 121.560 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Set scattering table: 0.410 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 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 : 0.008 0.056 60649 Z= 0.453 Angle : 0.841 8.015 84634 Z= 0.516 Chirality : 0.047 0.251 9392 Planarity : 0.006 0.080 8420 Dihedral : 16.159 110.462 23957 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.34 (0.06), residues: 5543 helix: -4.48 (0.03), residues: 4324 sheet: None (None), residues: 0 loop : -1.70 (0.16), residues: 1219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2117 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2112 time to evaluate : 4.703 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 outliers start: 5 outliers final: 4 residues processed: 2114 average time/residue: 0.7577 time to fit residues: 2442.7755 Evaluate side-chains 1739 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1735 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4082 time to fit residues: 8.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 500 optimal weight: 9.9990 chunk 449 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 153 optimal weight: 0.0770 chunk 303 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 464 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 538 optimal weight: 7.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 65 ASN B 18 HIS B 65 ASN C 18 HIS C 56 GLN C 116 GLN D 18 HIS D 65 ASN D 114 ASN E 18 HIS ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS F 94 ASN F 114 ASN G 65 ASN G 114 ASN H 18 HIS H 65 ASN I 65 ASN I 114 ASN J 18 HIS J 65 ASN J 114 ASN K 18 HIS K 65 ASN L 18 HIS ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN L 114 ASN ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 114 ASN N 94 ASN N 114 ASN O 18 HIS O 56 GLN O 65 ASN O 92 GLN P 18 HIS P 65 ASN P 114 ASN ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 HIS Q 65 ASN Q 92 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN Q 116 GLN R 18 HIS R 114 ASN S 18 HIS S 94 ASN S 114 ASN T 18 HIS T 92 GLN T 114 ASN U 18 HIS U 56 GLN ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 HIS V 65 ASN V 114 ASN W 18 HIS W 56 GLN W 65 ASN ** W 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 GLN d 103 ASN g 98 GLN m 8 GLN r 8 GLN t 8 GLN t 91 GLN v 98 GLN w 8 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 60649 Z= 0.264 Angle : 0.612 9.587 84634 Z= 0.354 Chirality : 0.037 0.150 9392 Planarity : 0.005 0.062 8420 Dihedral : 13.198 113.757 12756 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.10), residues: 5543 helix: -1.64 (0.07), residues: 4347 sheet: None (None), residues: 0 loop : -0.82 (0.17), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2003 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1873 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 94 residues processed: 1911 average time/residue: 0.7378 time to fit residues: 2203.4016 Evaluate side-chains 1784 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1690 time to evaluate : 4.554 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.4585 time to fit residues: 86.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 299 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 448 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 539 optimal weight: 6.9990 chunk 582 optimal weight: 7.9990 chunk 480 optimal weight: 3.9990 chunk 534 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 432 optimal weight: 0.0040 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS C 56 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS L 110 GLN M 18 HIS O 92 GLN ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 GLN ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN c 69 GLN d 8 GLN e 8 GLN k 8 GLN o 69 GLN r 8 GLN ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 60649 Z= 0.270 Angle : 0.585 7.898 84634 Z= 0.338 Chirality : 0.037 0.155 9392 Planarity : 0.004 0.056 8420 Dihedral : 13.036 113.628 12756 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 5543 helix: -0.23 (0.08), residues: 4370 sheet: None (None), residues: 0 loop : -0.33 (0.18), residues: 1173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1744 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 66 residues processed: 1785 average time/residue: 0.6794 time to fit residues: 1886.1741 Evaluate side-chains 1718 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1652 time to evaluate : 4.497 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.4314 time to fit residues: 58.9226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 533 optimal weight: 6.9990 chunk 405 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 362 optimal weight: 3.9990 chunk 541 optimal weight: 20.0000 chunk 573 optimal weight: 0.0770 chunk 282 optimal weight: 3.9990 chunk 513 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN L 110 GLN ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN d 8 GLN e 8 GLN k 8 GLN r 8 GLN ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 GLN ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 60649 Z= 0.206 Angle : 0.555 8.285 84634 Z= 0.321 Chirality : 0.035 0.142 9392 Planarity : 0.004 0.055 8420 Dihedral : 12.897 113.642 12756 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5543 helix: 0.36 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.04 (0.18), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1869 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1745 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 87 residues processed: 1787 average time/residue: 0.7303 time to fit residues: 2056.0401 Evaluate side-chains 1769 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1682 time to evaluate : 4.522 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.4666 time to fit residues: 82.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 477 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 489 optimal weight: 2.9990 chunk 396 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 514 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN K 56 GLN ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 65 ASN a 98 GLN d 8 GLN e 8 GLN ** f 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN j 81 ASN ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 60649 Z= 0.184 Angle : 0.548 8.278 84634 Z= 0.316 Chirality : 0.035 0.154 9392 Planarity : 0.004 0.054 8420 Dihedral : 12.809 113.967 12756 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 5543 helix: 0.74 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.44 (0.19), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1735 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 47 residues processed: 1766 average time/residue: 0.6998 time to fit residues: 1913.9824 Evaluate side-chains 1696 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1649 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4555 time to fit residues: 45.1242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 192 optimal weight: 10.0000 chunk 516 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 573 optimal weight: 0.0470 chunk 476 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN d 8 GLN e 8 GLN p 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 60649 Z= 0.165 Angle : 0.549 9.880 84634 Z= 0.315 Chirality : 0.034 0.133 9392 Planarity : 0.004 0.056 8420 Dihedral : 12.734 114.983 12756 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 5543 helix: 1.01 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.55 (0.19), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1817 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1747 time to evaluate : 4.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 42 residues processed: 1763 average time/residue: 0.6802 time to fit residues: 1871.1757 Evaluate side-chains 1698 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1656 time to evaluate : 4.567 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4691 time to fit residues: 41.2725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 553 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 326 optimal weight: 0.9980 chunk 418 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 482 optimal weight: 0.0050 chunk 320 optimal weight: 7.9990 chunk 571 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 348 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 56 GLN H 46 ASN L 92 GLN Q 46 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN d 8 GLN d 103 ASN e 8 GLN i 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 60649 Z= 0.169 Angle : 0.554 9.449 84634 Z= 0.317 Chirality : 0.034 0.130 9392 Planarity : 0.004 0.052 8420 Dihedral : 12.741 115.340 12756 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.12), residues: 5543 helix: 1.16 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.65 (0.19), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1753 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1700 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 33 residues processed: 1716 average time/residue: 0.6845 time to fit residues: 1837.6428 Evaluate side-chains 1680 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1647 time to evaluate : 4.491 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5002 time to fit residues: 34.8100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 353 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 389 optimal weight: 0.5980 chunk 282 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 449 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN I 65 ASN L 92 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN d 8 GLN e 8 GLN ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 60649 Z= 0.173 Angle : 0.568 10.493 84634 Z= 0.322 Chirality : 0.035 0.146 9392 Planarity : 0.004 0.050 8420 Dihedral : 12.800 115.401 12756 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.12), residues: 5543 helix: 1.26 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.73 (0.20), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1693 time to evaluate : 4.632 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 outliers start: 44 outliers final: 30 residues processed: 1705 average time/residue: 0.6807 time to fit residues: 1811.1883 Evaluate side-chains 1679 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1649 time to evaluate : 4.547 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4745 time to fit residues: 31.4605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 519 optimal weight: 7.9990 chunk 547 optimal weight: 6.9990 chunk 499 optimal weight: 9.9990 chunk 532 optimal weight: 0.4980 chunk 320 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 418 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 481 optimal weight: 4.9990 chunk 503 optimal weight: 5.9990 chunk 530 optimal weight: 1.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN L 110 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN d 8 GLN e 8 GLN f 103 ASN r 8 GLN w 8 GLN ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 60649 Z= 0.228 Angle : 0.601 10.933 84634 Z= 0.340 Chirality : 0.036 0.159 9392 Planarity : 0.004 0.052 8420 Dihedral : 12.804 112.111 12756 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.12), residues: 5543 helix: 1.28 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.81 (0.20), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1684 time to evaluate : 4.642 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 outliers start: 30 outliers final: 16 residues processed: 1693 average time/residue: 0.7114 time to fit residues: 1884.9837 Evaluate side-chains 1675 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1659 time to evaluate : 4.529 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5555 time to fit residues: 21.0586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 349 optimal weight: 20.0000 chunk 563 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 391 optimal weight: 8.9990 chunk 590 optimal weight: 4.9990 chunk 543 optimal weight: 4.9990 chunk 470 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 363 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 GLN L 110 GLN M 65 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 65 ASN d 8 GLN e 8 GLN ** p 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 GLN ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 60649 Z= 0.295 Angle : 0.643 11.823 84634 Z= 0.361 Chirality : 0.038 0.178 9392 Planarity : 0.004 0.052 8420 Dihedral : 12.820 108.899 12756 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.12), residues: 5543 helix: 1.20 (0.08), residues: 4416 sheet: None (None), residues: 0 loop : 0.89 (0.20), residues: 1127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1709 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1677 time to evaluate : 4.631 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 outliers start: 32 outliers final: 24 residues processed: 1684 average time/residue: 0.6840 time to fit residues: 1796.1958 Evaluate side-chains 1658 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1634 time to evaluate : 4.611 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5108 time to fit residues: 27.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 593 random chunks: chunk 373 optimal weight: 7.9990 chunk 501 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 433 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 471 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 483 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN E 92 GLN M 65 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 GLN e 8 GLN ** p 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 GLN ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 98 GLN ** 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 = 0.2993 r_free = 0.2993 target = 0.079752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.072108 restraints weight = 136065.885| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.81 r_work: 0.2746 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 60649 Z= 0.287 Angle : 0.645 11.041 84634 Z= 0.361 Chirality : 0.038 0.187 9392 Planarity : 0.004 0.051 8420 Dihedral : 12.793 109.022 12756 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.12), residues: 5543 helix: 1.18 (0.08), residues: 4416 sheet: None (None), residues: 0 loop : 0.91 (0.21), residues: 1127 =============================================================================== Job complete usr+sys time: 24166.99 seconds wall clock time: 417 minutes 8.00 seconds (25028.00 seconds total)