Starting phenix.real_space_refine on Fri Dec 8 15:49:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/12_2023/6v7b_21094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/12_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_21094/12_2023/6v7b_21094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/12_2023/6v7b_21094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/12_2023/6v7b_21094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v7b_21094/12_2023/6v7b_21094.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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. 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 21.37, per 1000 atoms: 0.37 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: 18.68 Conformation dependent library (CDL) restraints added in 5.8 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: 15.84 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: 20.49 Time building geometry restraints manager: 20.49 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: 31680 22.09 - 44.18: 3057 44.18 - 66.28: 1092 66.28 - 88.37: 107 88.37 - 110.46: 8 Dihedral angle restraints: 35944 sinusoidal: 19522 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 35941 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 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: 1.200 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: 8.630 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 122.910 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 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 : 18.333 110.462 25249 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 % Allowed : 7.21 % Favored : 92.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP i 43 HIS 0.006 0.002 HIS B 18 PHE 0.008 0.002 PHE d 46 TYR 0.022 0.003 TYR e 6 ARG 0.016 0.001 ARG L 38 *********************** 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 : 5.119 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: 0.7229 time to fit residues: 2326.4592 Evaluate side-chains 1739 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1735 time to evaluate : 4.232 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4022 time to fit residues: 8.5802 ------------------------------------------------------------------------------- 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 56 GLN C 116 GLN 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 60649 Z= 0.262 Angle : 0.613 9.361 84634 Z= 0.355 Chirality : 0.037 0.147 9392 Planarity : 0.005 0.061 8420 Dihedral : 16.675 113.054 14048 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.67 % Allowed : 15.93 % Favored : 81.40 % 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: -2.57 (0.10), residues: 5543 helix: -1.69 (0.06), residues: 4347 sheet: None (None), residues: 0 loop : -0.83 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 121 HIS 0.005 0.002 HIS T 18 PHE 0.007 0.001 PHE R 107 TYR 0.020 0.002 TYR U 62 ARG 0.007 0.001 ARG n 27 *********************** 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 1988 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1864 time to evaluate : 4.317 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: 124 outliers final: 89 residues processed: 1901 average time/residue: 0.7229 time to fit residues: 2143.3857 Evaluate side-chains 1777 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1688 time to evaluate : 4.243 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.4720 time to fit residues: 84.0289 ------------------------------------------------------------------------------- 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: 6.9990 chunk 167 optimal weight: 2.9990 chunk 448 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 539 optimal weight: 5.9990 chunk 582 optimal weight: 7.9990 chunk 480 optimal weight: 3.9990 chunk 534 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 432 optimal weight: 0.0980 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 56 GLN C 18 HIS D 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 o 69 GLN ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 8 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 60649 Z= 0.229 Angle : 0.568 8.012 84634 Z= 0.329 Chirality : 0.036 0.153 9392 Planarity : 0.004 0.056 8420 Dihedral : 16.386 113.566 14048 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 19.65 % Favored : 78.50 % 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: -0.56 (0.11), residues: 5543 helix: -0.22 (0.08), residues: 4370 sheet: None (None), residues: 0 loop : -0.35 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP i 43 HIS 0.005 0.002 HIS K 18 PHE 0.007 0.001 PHE L 107 TYR 0.027 0.002 TYR I 62 ARG 0.008 0.001 ARG h 27 *********************** 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 1859 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1773 time to evaluate : 4.268 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: 86 outliers final: 53 residues processed: 1803 average time/residue: 0.6855 time to fit residues: 1918.9992 Evaluate side-chains 1738 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1685 time to evaluate : 4.199 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4405 time to fit residues: 48.5364 ------------------------------------------------------------------------------- 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: 2.9990 chunk 405 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 541 optimal weight: 6.9990 chunk 573 optimal weight: 9.9990 chunk 282 optimal weight: 0.0170 chunk 513 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 56 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 k 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: 0.8603 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 60649 Z= 0.191 Angle : 0.546 8.603 84634 Z= 0.317 Chirality : 0.035 0.143 9392 Planarity : 0.004 0.055 8420 Dihedral : 16.186 113.976 14048 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.48 % Allowed : 20.62 % Favored : 76.90 % 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: 0.31 (0.11), residues: 5543 helix: 0.39 (0.08), residues: 4416 sheet: None (None), residues: 0 loop : 0.01 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 121 HIS 0.004 0.002 HIS E 18 PHE 0.007 0.001 PHE n 46 TYR 0.022 0.002 TYR C 62 ARG 0.010 0.001 ARG h 27 *********************** 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 1898 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1783 time to evaluate : 4.326 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: 115 outliers final: 77 residues processed: 1820 average time/residue: 0.6834 time to fit residues: 1931.1048 Evaluate side-chains 1757 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1680 time to evaluate : 4.194 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.4441 time to fit residues: 68.5551 ------------------------------------------------------------------------------- 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: 3.9990 chunk 325 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 426 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 489 optimal weight: 0.5980 chunk 396 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 292 optimal weight: 1.9990 chunk 514 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN K 56 GLN L 75 ASN Q 94 ASN ** 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** p 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 60649 Z= 0.164 Angle : 0.538 8.033 84634 Z= 0.311 Chirality : 0.034 0.133 9392 Planarity : 0.004 0.054 8420 Dihedral : 16.067 114.906 14048 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.53 % Allowed : 22.13 % Favored : 76.35 % 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: 0.91 (0.11), residues: 5543 helix: 0.78 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.37 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP j 121 HIS 0.003 0.001 HIS G 18 PHE 0.006 0.001 PHE q 46 TYR 0.026 0.001 TYR e 19 ARG 0.015 0.000 ARG V 125 *********************** 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 1830 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1759 time to evaluate : 4.307 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: 71 outliers final: 36 residues processed: 1779 average time/residue: 0.7004 time to fit residues: 1943.4863 Evaluate side-chains 1714 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1678 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4796 time to fit residues: 37.3033 ------------------------------------------------------------------------------- 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: 8.9990 chunk 113 optimal weight: 9.9990 chunk 336 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 573 optimal weight: 7.9990 chunk 476 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** H 46 ASN I 18 HIS Q 46 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 81 ASN k 8 GLN m 8 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 60649 Z= 0.184 Angle : 0.554 9.110 84634 Z= 0.318 Chirality : 0.035 0.156 9392 Planarity : 0.004 0.051 8420 Dihedral : 16.044 114.301 14048 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.70 % Allowed : 22.51 % Favored : 75.79 % 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: 1.18 (0.12), residues: 5543 helix: 1.00 (0.08), residues: 4416 sheet: None (None), residues: 0 loop : 0.31 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 79 HIS 0.003 0.002 HIS E 18 PHE 0.006 0.001 PHE f 46 TYR 0.030 0.002 TYR e 19 ARG 0.011 0.000 ARG h 27 *********************** 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 1801 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1722 time to evaluate : 5.648 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: 79 outliers final: 51 residues processed: 1752 average time/residue: 0.7015 time to fit residues: 1923.3712 Evaluate side-chains 1710 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1659 time to evaluate : 4.248 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4445 time to fit residues: 47.8564 ------------------------------------------------------------------------------- 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: 9.9990 chunk 64 optimal weight: 4.9990 chunk 326 optimal weight: 7.9990 chunk 418 optimal weight: 0.6980 chunk 324 optimal weight: 6.9990 chunk 482 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 571 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 L 92 GLN ** 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 k 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: 0.8617 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 60649 Z= 0.243 Angle : 0.588 7.150 84634 Z= 0.336 Chirality : 0.036 0.137 9392 Planarity : 0.004 0.051 8420 Dihedral : 16.157 110.802 14048 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.42 % Allowed : 23.27 % Favored : 75.31 % 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: 1.29 (0.12), residues: 5543 helix: 1.06 (0.08), residues: 4416 sheet: None (None), residues: 0 loop : 0.44 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 79 HIS 0.005 0.002 HIS E 18 PHE 0.007 0.001 PHE j 46 TYR 0.023 0.002 TYR e 19 ARG 0.011 0.001 ARG h 27 *********************** 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 1756 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1690 time to evaluate : 4.217 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 outliers start: 66 outliers final: 37 residues processed: 1710 average time/residue: 0.7042 time to fit residues: 1899.7592 Evaluate side-chains 1676 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1639 time to evaluate : 4.278 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4888 time to fit residues: 38.3756 ------------------------------------------------------------------------------- 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: 9.9990 chunk 228 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 363 optimal weight: 6.9990 chunk 389 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 449 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN L 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** a 98 GLN d 8 GLN e 8 GLN f 103 ASN j 81 ASN k 8 GLN ** p 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 60649 Z= 0.240 Angle : 0.595 10.182 84634 Z= 0.338 Chirality : 0.036 0.167 9392 Planarity : 0.004 0.052 8420 Dihedral : 16.127 109.900 14048 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.33 % Allowed : 23.55 % Favored : 75.12 % 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: 1.49 (0.12), residues: 5543 helix: 1.15 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.77 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 79 HIS 0.005 0.002 HIS E 18 PHE 0.008 0.001 PHE f 46 TYR 0.026 0.002 TYR e 19 ARG 0.011 0.001 ARG d 123 *********************** 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 1723 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1661 time to evaluate : 4.437 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: 62 outliers final: 42 residues processed: 1675 average time/residue: 0.6781 time to fit residues: 1778.8511 Evaluate side-chains 1696 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1654 time to evaluate : 4.179 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4666 time to fit residues: 41.1868 ------------------------------------------------------------------------------- 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: 1.9990 chunk 547 optimal weight: 9.9990 chunk 499 optimal weight: 6.9990 chunk 532 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 418 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 481 optimal weight: 1.9990 chunk 503 optimal weight: 5.9990 chunk 530 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 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 k 8 GLN ** p 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 60649 Z= 0.216 Angle : 0.595 11.657 84634 Z= 0.337 Chirality : 0.036 0.174 9392 Planarity : 0.004 0.051 8420 Dihedral : 16.095 110.023 14048 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.82 % Allowed : 24.30 % Favored : 74.88 % 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: 1.55 (0.12), residues: 5543 helix: 1.19 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.81 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 79 HIS 0.005 0.002 HIS Q 18 PHE 0.007 0.001 PHE p 46 TYR 0.035 0.002 TYR o 19 ARG 0.014 0.000 ARG h 27 *********************** 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: 38 poor density : 1676 time to evaluate : 4.252 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: 38 outliers final: 27 residues processed: 1688 average time/residue: 0.6956 time to fit residues: 1847.5921 Evaluate side-chains 1664 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1637 time to evaluate : 4.245 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4885 time to fit residues: 29.8682 ------------------------------------------------------------------------------- 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: 2.9990 chunk 343 optimal weight: 0.5980 chunk 267 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 590 optimal weight: 7.9990 chunk 543 optimal weight: 5.9990 chunk 470 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 ** p 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 60649 Z= 0.227 Angle : 0.605 12.327 84634 Z= 0.342 Chirality : 0.036 0.186 9392 Planarity : 0.004 0.051 8420 Dihedral : 16.110 109.748 14048 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.58 % Allowed : 24.90 % Favored : 74.52 % 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: 1.58 (0.12), residues: 5543 helix: 1.21 (0.08), residues: 4393 sheet: None (None), residues: 0 loop : 0.83 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 79 HIS 0.004 0.002 HIS E 18 PHE 0.008 0.001 PHE f 46 TYR 0.038 0.002 TYR o 19 ARG 0.014 0.001 ARG h 27 ********************** 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 1683 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1656 time to evaluate : 4.288 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: 27 outliers final: 16 residues processed: 1661 average time/residue: 0.6793 time to fit residues: 1765.2761 Evaluate side-chains 1665 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1649 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5224 time to fit residues: 19.9882 ------------------------------------------------------------------------------- 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: 20.0000 chunk 501 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 471 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 483 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN D 116 GLN E 92 GLN L 110 GLN N 18 HIS O 65 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 e 8 GLN k 8 GLN ** p 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.078071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.070481 restraints weight = 136878.223| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.81 r_work: 0.2713 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 60649 Z= 0.350 Angle : 0.669 12.029 84634 Z= 0.375 Chirality : 0.040 0.182 9392 Planarity : 0.004 0.051 8420 Dihedral : 16.377 108.816 14048 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.75 % Allowed : 25.23 % Favored : 74.02 % 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: 4416 sheet: None (None), residues: 0 loop : 0.58 (0.20), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 79 HIS 0.007 0.003 HIS E 18 PHE 0.007 0.001 PHE f 46 TYR 0.038 0.002 TYR o 19 ARG 0.014 0.001 ARG h 27 =============================================================================== Job complete usr+sys time: 24074.43 seconds wall clock time: 415 minutes 58.88 seconds (24958.88 seconds total)