Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 04:16:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bt6_30170/10_2023/7bt6_30170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bt6_30170/10_2023/7bt6_30170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bt6_30170/10_2023/7bt6_30170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bt6_30170/10_2023/7bt6_30170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bt6_30170/10_2023/7bt6_30170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bt6_30170/10_2023/7bt6_30170_updated.pdb" } resolution = 3.12 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.009 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3247 5.49 5 Mg 2 5.21 5 S 166 5.16 5 C 71447 2.51 5 N 24376 2.21 5 O 34058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 230": "OD1" <-> "OD2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ASP 219": "OD1" <-> "OD2" Residue "G PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 130": "OD1" <-> "OD2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "H ASP 190": "OD1" <-> "OD2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J GLU 38": "OE1" <-> "OE2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J ASP 93": "OD1" <-> "OD2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J ASP 170": "OD1" <-> "OD2" Residue "L PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "N ARG 193": "NH1" <-> "NH2" Residue "N TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 4": "OE1" <-> "OE2" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 100": "OE1" <-> "OE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q ASP 22": "OD1" <-> "OD2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 148": "OE1" <-> "OE2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R GLU 72": "OE1" <-> "OE2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ASP 111": "OD1" <-> "OD2" Residue "R ASP 148": "OD1" <-> "OD2" Residue "R GLU 152": "OE1" <-> "OE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S GLU 57": "OE1" <-> "OE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 82": "OD1" <-> "OD2" Residue "S ASP 96": "OD1" <-> "OD2" Residue "S TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 38": "OD1" <-> "OD2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "T TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 91": "OD1" <-> "OD2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 27": "OD1" <-> "OD2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 97": "OD1" <-> "OD2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "W GLU 82": "OE1" <-> "OE2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "W TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "X GLU 104": "OE1" <-> "OE2" Residue "X ASP 106": "OD1" <-> "OD2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 30": "OD1" <-> "OD2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ASP 88": "OD1" <-> "OD2" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "Z PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "a PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 76": "OD1" <-> "OD2" Residue "a GLU 84": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 136": "OE1" <-> "OE2" Residue "b ASP 7": "OD1" <-> "OD2" Residue "b ASP 19": "OD1" <-> "OD2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 73": "OD1" <-> "OD2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ASP 83": "OD1" <-> "OD2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ASP 111": "OD1" <-> "OD2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 151": "OE1" <-> "OE2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b ASP 191": "OD1" <-> "OD2" Residue "b ASP 193": "OD1" <-> "OD2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 220": "OD1" <-> "OD2" Residue "b ASP 226": "OD1" <-> "OD2" Residue "b ASP 255": "OD1" <-> "OD2" Residue "b PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 296": "OE1" <-> "OE2" Residue "b ASP 299": "OD1" <-> "OD2" Residue "b ARG 302": "NH1" <-> "NH2" Residue "b GLU 311": "OE1" <-> "OE2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "b GLU 337": "OE1" <-> "OE2" Residue "b ASP 371": "OD1" <-> "OD2" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 389": "OD1" <-> "OD2" Residue "b ASP 418": "OD1" <-> "OD2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 423": "OE1" <-> "OE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 460": "OE1" <-> "OE2" Residue "b PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 479": "OD1" <-> "OD2" Residue "b GLU 482": "OE1" <-> "OE2" Residue "b GLU 485": "OE1" <-> "OE2" Residue "b ASP 487": "OD1" <-> "OD2" Residue "b ASP 488": "OD1" <-> "OD2" Residue "b GLU 491": "OE1" <-> "OE2" Residue "b ARG 510": "NH1" <-> "NH2" Residue "c TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "c TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "d TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 83": "OE1" <-> "OE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 3": "OE1" <-> "OE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "h ASP 23": "OD1" <-> "OD2" Residue "h ASP 79": "OD1" <-> "OD2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k ASP 7": "OD1" <-> "OD2" Residue "k PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 58": "OD1" <-> "OD2" Residue "m ASP 32": "OD1" <-> "OD2" Residue "m PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 49": "NH1" <-> "NH2" Residue "m PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 63": "OD1" <-> "OD2" Residue "m ASP 74": "OD1" <-> "OD2" Residue "m ARG 76": "NH1" <-> "NH2" Residue "m ARG 82": "NH1" <-> "NH2" Residue "m ASP 102": "OD1" <-> "OD2" Residue "m TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 110": "NH1" <-> "NH2" Residue "m TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 139": "OD1" <-> "OD2" Residue "m PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 147": "NH1" <-> "NH2" Residue "m ARG 149": "NH1" <-> "NH2" Residue "m GLU 166": "OE1" <-> "OE2" Residue "m ASP 167": "OD1" <-> "OD2" Residue "m ASP 178": "OD1" <-> "OD2" Residue "m GLU 200": "OE1" <-> "OE2" Residue "m PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 233": "OD1" <-> "OD2" Residue "m ARG 238": "NH1" <-> "NH2" Residue "m GLU 243": "OE1" <-> "OE2" Residue "m GLU 244": "OE1" <-> "OE2" Residue "m TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 379": "OE1" <-> "OE2" Residue "m PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 413": "OE1" <-> "OE2" Residue "m GLU 417": "OE1" <-> "OE2" Residue "m ASP 423": "OD1" <-> "OD2" Residue "m GLU 426": "OE1" <-> "OE2" Residue "m ARG 437": "NH1" <-> "NH2" Residue "m ASP 456": "OD1" <-> "OD2" Residue "m ARG 459": "NH1" <-> "NH2" Residue "m PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "p ASP 38": "OD1" <-> "OD2" Residue "p PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ASP 19": "OD1" <-> "OD2" Residue "r GLU 22": "OE1" <-> "OE2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 57": "OE1" <-> "OE2" Residue "r ASP 85": "OD1" <-> "OD2" Residue "r TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 95": "OE1" <-> "OE2" Residue "r ARG 126": "NH1" <-> "NH2" Residue "r GLU 131": "OE1" <-> "OE2" Residue "r ARG 149": "NH1" <-> "NH2" Residue "r PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 159": "OE1" <-> "OE2" Residue "r PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 188": "OE1" <-> "OE2" Residue "r GLU 248": "OE1" <-> "OE2" Residue "r ARG 251": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ASP 25": "OD1" <-> "OD2" Residue "u PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u GLU 97": "OE1" <-> "OE2" Residue "u GLU 98": "OE1" <-> "OE2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ASP 119": "OD1" <-> "OD2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "u GLU 128": "OE1" <-> "OE2" Residue "u GLU 138": "OE1" <-> "OE2" Residue "v PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 56": "OD1" <-> "OD2" Residue "v ASP 83": "OD1" <-> "OD2" Residue "v TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 112": "OD1" <-> "OD2" Residue "v GLU 115": "OE1" <-> "OE2" Residue "v PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 127": "OD1" <-> "OD2" Residue "v PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 149": "OD1" <-> "OD2" Residue "v TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 163": "OD1" <-> "OD2" Residue "v PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 168": "OE1" <-> "OE2" Residue "v ASP 171": "OD1" <-> "OD2" Residue "v ASP 189": "OD1" <-> "OD2" Residue "v GLU 194": "OE1" <-> "OE2" Residue "v ASP 212": "OD1" <-> "OD2" Residue "v ASP 243": "OD1" <-> "OD2" Residue "v ASP 281": "OD1" <-> "OD2" Residue "v PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 22": "OD1" <-> "OD2" Residue "w ASP 38": "OD1" <-> "OD2" Residue "w ASP 40": "OD1" <-> "OD2" Residue "w GLU 48": "OE1" <-> "OE2" Residue "w ASP 94": "OD1" <-> "OD2" Residue "w ASP 98": "OD1" <-> "OD2" Residue "w ARG 101": "NH1" <-> "NH2" Residue "w GLU 127": "OE1" <-> "OE2" Residue "w ARG 128": "NH1" <-> "NH2" Residue "w GLU 136": "OE1" <-> "OE2" Residue "w ASP 155": "OD1" <-> "OD2" Residue "w ASP 175": "OD1" <-> "OD2" Residue "w GLU 183": "OE1" <-> "OE2" Residue "x ASP 28": "OD1" <-> "OD2" Residue "x PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 40": "OD1" <-> "OD2" Residue "x PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 165": "OD1" <-> "OD2" Residue "x GLU 199": "OE1" <-> "OE2" Residue "x ASP 207": "OD1" <-> "OD2" Residue "x ASP 214": "OD1" <-> "OD2" Residue "x ASP 264": "OD1" <-> "OD2" Residue "x TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 305": "OD1" <-> "OD2" Residue "x ASP 331": "OD1" <-> "OD2" Residue "x PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 350": "OE1" <-> "OE2" Residue "x TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 423": "OD1" <-> "OD2" Residue "x GLU 488": "OE1" <-> "OE2" Residue "x TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 8": "OE1" <-> "OE2" Residue "y PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y GLU 98": "OE1" <-> "OE2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 120": "OD1" <-> "OD2" Residue "y GLU 172": "OE1" <-> "OE2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 209": "OD1" <-> "OD2" Residue "y ASP 226": "OD1" <-> "OD2" Residue "y GLU 230": "OE1" <-> "OE2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 27": "OD1" <-> "OD2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 30": "OE1" <-> "OE2" Residue "z GLU 39": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 133299 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1377 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 168} Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "C" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2559 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 318} Chain breaks: 1 Chain: "D" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2176 Classifications: {'peptide': 271} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 152} Chain: "H" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1510 Classifications: {'peptide': 190} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 183} Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 131} Chain: "N" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1570 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1442 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 161} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 943 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Chain: "U" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 812 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "V" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 997 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "W" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1885 Classifications: {'peptide': 234} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 222} Chain: "X" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "b" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4146 Classifications: {'peptide': 510} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 485} Chain breaks: 1 Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 819 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 750 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "j" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 603 Classifications: {'peptide': 77} Link IDs: {'PCIS': 1, 'TRANS': 75} Chain breaks: 1 Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "m" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3639 Classifications: {'peptide': 452} Link IDs: {'CIS': 5, 'PTRANS': 22, 'TRANS': 424} Chain breaks: 1 Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "r" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1860 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "u" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1216 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "v" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2318 Classifications: {'peptide': 287} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Chain: "w" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1448 Classifications: {'peptide': 182} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 168} Chain breaks: 1 Chain: "x" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3807 Classifications: {'peptide': 488} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 461} Chain breaks: 5 Chain: "y" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1849 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 234} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "1" Number of atoms: 63385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2962, 63385 Classifications: {'RNA': 2962} Modifications used: {'rna2p_pur': 331, 'rna2p_pyr': 241, 'rna3p_pur': 1322, 'rna3p_pyr': 1068} Link IDs: {'rna2p': 572, 'rna3p': 2389} Chain breaks: 11 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 32, 'rna3p': 125} Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 107} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45481 SG CYS j 19 160.920 119.235 181.385 1.00 4.81 S ATOM 45506 SG CYS j 22 162.392 116.640 178.964 1.00 6.69 S ATOM 45606 SG CYS j 34 158.715 118.104 178.606 1.00 4.37 S ATOM 45624 SG CYS j 37 159.804 115.714 181.346 1.00 4.26 S ATOM 50587 SG CYS p 39 117.792 172.133 190.974 1.00 16.33 S ATOM 50610 SG CYS p 42 119.940 175.127 192.109 1.00 16.73 S ATOM 50719 SG CYS p 57 120.924 172.272 189.490 1.00 18.24 S ATOM 50737 SG CYS p 60 120.929 172.185 193.531 1.00 21.96 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 49.49, per 1000 atoms: 0.37 Number of scatterers: 133299 At special positions: 0 Unit cell: (236.225, 236.225, 269.186, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 166 16.00 P 3247 15.00 Mg 2 11.99 O 34058 8.00 N 24376 7.00 C 71447 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.04 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.04 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.02 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.04 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 9 " distance=2.02 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.04 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: 45.84 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb=" ZN p 501 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 60 " Number of angles added : 12 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15076 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 267 helices and 82 sheets defined 41.3% alpha, 14.6% beta 829 base pairs and 1623 stacking pairs defined. Time for finding SS restraints: 64.98 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 removed outlier: 3.720A pdb=" N ARG A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 33 through 39' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.770A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.181A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.598A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 5.844A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.729A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.929A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 352 removed outlier: 4.158A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.893A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.761A pdb=" N ALA C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 removed outlier: 3.720A pdb=" N LEU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 4.678A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.637A pdb=" N VAL C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 4.014A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.136A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 262 removed outlier: 4.262A pdb=" N THR C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.536A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.854A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 removed outlier: 4.219A pdb=" N ASN C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.501A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.657A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 360 " --> pdb=" O THR C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.110A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.812A pdb=" N LYS D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 4.066A pdb=" N TYR D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 114 removed outlier: 3.639A pdb=" N GLY D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 4.141A pdb=" N GLY D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.696A pdb=" N LEU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 4.907A pdb=" N ASP D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 removed outlier: 3.631A pdb=" N LEU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 230 removed outlier: 3.999A pdb=" N ALA D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP D 229 " --> pdb=" O GLY D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.808A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.962A pdb=" N TYR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 292 removed outlier: 3.989A pdb=" N ARG D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 286 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 4.489A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 85' Processing helix chain 'E' and resid 102 through 107 removed outlier: 4.471A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 107' Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.894A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.696A pdb=" N SER E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 73 removed outlier: 5.174A pdb=" N ARG F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 42 " --> pdb=" O LYS F 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.538A pdb=" N LEU F 103 " --> pdb=" O PRO F 99 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN F 104 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 4.202A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.952A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 3.671A pdb=" N LEU F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 3.620A pdb=" N LEU F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.688A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 removed outlier: 4.600A pdb=" N ALA G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 77' Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.551A pdb=" N LYS G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 4.616A pdb=" N ALA G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 removed outlier: 4.643A pdb=" N GLU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 removed outlier: 4.688A pdb=" N VAL G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix removed outlier: 3.595A pdb=" N LYS G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 191 removed outlier: 4.777A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 229 removed outlier: 3.792A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR G 226 " --> pdb=" O PHE G 222 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.805A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.291A pdb=" N GLN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 5.768A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 41 removed outlier: 3.697A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 88 removed outlier: 4.020A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE J 79 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.929A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 168 removed outlier: 3.545A pdb=" N THR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 166 " --> pdb=" O TRP J 162 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR J 167 " --> pdb=" O PHE J 163 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP J 168 " --> pdb=" O LYS J 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.763A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 67 removed outlier: 3.915A pdb=" N ASN L 66 " --> pdb=" O THR L 62 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 62 through 67' Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.671A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 94 removed outlier: 4.055A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE L 93 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 123 removed outlier: 4.246A pdb=" N GLU L 118 " --> pdb=" O GLN L 114 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 146 removed outlier: 3.754A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.941A pdb=" N THR L 169 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 193 removed outlier: 4.299A pdb=" N GLU L 192 " --> pdb=" O ARG L 188 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.103A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.722A pdb=" N ALA M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 removed outlier: 4.015A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 removed outlier: 3.983A pdb=" N ALA M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU M 112 " --> pdb=" O ARG M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 136 removed outlier: 3.758A pdb=" N MET M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 3.974A pdb=" N LEU N 10 " --> pdb=" O TYR N 6 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.810A pdb=" N LEU N 22 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG N 31 " --> pdb=" O VAL N 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.585A pdb=" N ARG N 50 " --> pdb=" O ASP N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.753A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG N 108 " --> pdb=" O GLU N 104 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG N 109 " --> pdb=" O ARG N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 removed outlier: 5.112A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.512A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 183 through 196 removed outlier: 3.971A pdb=" N LYS N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS N 192 " --> pdb=" O ARG N 188 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 153 removed outlier: 5.289A pdb=" N TRP N 150 " --> pdb=" O ARG N 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.855A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN O 29 " --> pdb=" O LYS O 25 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 4.528A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 4.107A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 4.096A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 102 removed outlier: 3.709A pdb=" N LYS O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU O 100 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 8.244A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.572A pdb=" N THR O 143 " --> pdb=" O GLY O 139 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER O 144 " --> pdb=" O LYS O 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL O 145 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 184 removed outlier: 4.217A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER O 180 " --> pdb=" O LYS O 176 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 removed outlier: 4.268A pdb=" N LEU O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY O 198 " --> pdb=" O LEU O 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.922A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 3.566A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP P 53 " --> pdb=" O GLU P 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.880A pdb=" N GLN P 96 " --> pdb=" O GLN P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 184 removed outlier: 5.337A pdb=" N ALA P 183 " --> pdb=" O GLN P 179 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA P 184 " --> pdb=" O LYS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.902A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE P 76 " --> pdb=" O GLY P 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 70 through 76' Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 54 removed outlier: 3.916A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS Q 50 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 removed outlier: 3.501A pdb=" N ARG Q 59 " --> pdb=" O SER Q 55 " (cutoff:3.500A) Proline residue: Q 60 - end of helix No H-bonds generated for 'chain 'Q' and resid 55 through 60' Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.942A pdb=" N ILE Q 67 " --> pdb=" O SER Q 63 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 68 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.544A pdb=" N GLY Q 118 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 132 Proline residue: Q 132 - end of helix Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.509A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 82 removed outlier: 4.020A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 7.067A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY R 113 " --> pdb=" O TYR R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 removed outlier: 4.070A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.512A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 122 removed outlier: 3.709A pdb=" N ILE S 121 " --> pdb=" O ARG S 117 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 117 through 122' Processing helix chain 'S' and resid 137 through 145 removed outlier: 5.001A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 123 removed outlier: 4.138A pdb=" N LEU T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 26 removed outlier: 4.124A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY U 26 " --> pdb=" O PRO U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 removed outlier: 4.049A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 88 removed outlier: 3.612A pdb=" N LEU U 76 " --> pdb=" O SER U 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 71 removed outlier: 3.920A pdb=" N ARG V 70 " --> pdb=" O LYS V 66 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 66 through 71' Processing helix chain 'V' and resid 119 through 127 removed outlier: 4.852A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 removed outlier: 3.601A pdb=" N ASN V 132 " --> pdb=" O ARG V 128 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 4.112A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 4.414A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 96 removed outlier: 5.236A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 120 removed outlier: 3.878A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR W 119 " --> pdb=" O TYR W 115 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL W 120 " --> pdb=" O PHE W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 155 removed outlier: 3.707A pdb=" N ASP W 154 " --> pdb=" O PRO W 150 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 150 through 155' Processing helix chain 'W' and resid 161 through 167 removed outlier: 3.867A pdb=" N MET W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 207 removed outlier: 3.996A pdb=" N ALA W 200 " --> pdb=" O ASP W 196 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU W 201 " --> pdb=" O VAL W 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE W 206 " --> pdb=" O ILE W 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY W 207 " --> pdb=" O LEU W 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.186A pdb=" N ILE X 63 " --> pdb=" O SER X 59 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 4.207A pdb=" N LYS X 74 " --> pdb=" O GLU X 70 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 removed outlier: 3.834A pdb=" N LYS X 96 " --> pdb=" O LYS X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 140 Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.834A pdb=" N ALA Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 32 removed outlier: 4.344A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.096A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 5.149A pdb=" N VAL Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR Z 66 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 58 through 67' Processing helix chain 'Z' and resid 76 through 81 removed outlier: 4.218A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 4.159A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 103 through 125 removed outlier: 5.037A pdb=" N ARG Z 107 " --> pdb=" O GLN Z 103 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL Z 113 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.965A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Proline residue: a 83 - end of helix No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 94 removed outlier: 4.597A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER a 93 " --> pdb=" O GLN a 89 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA a 94 " --> pdb=" O TYR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 removed outlier: 3.971A pdb=" N ALA a 107 " --> pdb=" O ASP a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.828A pdb=" N ILE a 138 " --> pdb=" O ALA a 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 29 removed outlier: 3.877A pdb=" N ASP b 19 " --> pdb=" O ASN b 15 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR b 29 " --> pdb=" O THR b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 66 removed outlier: 3.804A pdb=" N TYR b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 removed outlier: 3.847A pdb=" N ASP b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 119 removed outlier: 3.544A pdb=" N LEU b 95 " --> pdb=" O TYR b 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU b 106 " --> pdb=" O LYS b 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL b 113 " --> pdb=" O ALA b 109 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.954A pdb=" N LYS b 142 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.643A pdb=" N GLU b 151 " --> pdb=" O LEU b 147 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN b 152 " --> pdb=" O ALA b 148 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.806A pdb=" N MET b 237 " --> pdb=" O ASN b 233 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU b 246 " --> pdb=" O ALA b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 removed outlier: 4.171A pdb=" N LYS b 269 " --> pdb=" O GLU b 265 " (cutoff:3.500A) Proline residue: b 276 - end of helix removed outlier: 4.687A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 289 through 294 removed outlier: 4.679A pdb=" N ILE b 293 " --> pdb=" O LYS b 289 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 311 removed outlier: 4.046A pdb=" N VAL b 309 " --> pdb=" O LEU b 305 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS b 310 " --> pdb=" O LEU b 306 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 351 removed outlier: 4.487A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N MET b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU b 330 " --> pdb=" O GLU b 326 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL b 331 " --> pdb=" O ASN b 327 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG b 332 " --> pdb=" O VAL b 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU b 345 " --> pdb=" O ALA b 341 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN b 351 " --> pdb=" O LYS b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 352 through 362 removed outlier: 3.662A pdb=" N ASN b 356 " --> pdb=" O SER b 352 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN b 359 " --> pdb=" O ASN b 355 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE b 361 " --> pdb=" O VAL b 357 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS b 362 " --> pdb=" O LEU b 358 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.831A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 406 removed outlier: 4.071A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.998A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 4.477A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 483 through 512 removed outlier: 3.872A pdb=" N ASP b 487 " --> pdb=" O ALA b 483 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE b 489 " --> pdb=" O GLU b 485 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA b 494 " --> pdb=" O LYS b 490 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR b 502 " --> pdb=" O ASN b 498 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA b 505 " --> pdb=" O LYS b 501 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER b 512 " --> pdb=" O ARG b 508 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 20 removed outlier: 3.996A pdb=" N LYS c 13 " --> pdb=" O SER c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 removed outlier: 3.507A pdb=" N GLY c 82 " --> pdb=" O GLY c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 99 through 104 removed outlier: 3.514A pdb=" N THR c 103 " --> pdb=" O ASP c 99 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU c 104 " --> pdb=" O ILE c 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 99 through 104' Processing helix chain 'd' and resid 15 through 21 removed outlier: 4.417A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU d 20 " --> pdb=" O LEU d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 45 removed outlier: 3.687A pdb=" N ARG d 28 " --> pdb=" O SER d 24 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA d 29 " --> pdb=" O PHE d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 3.856A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 61 removed outlier: 3.588A pdb=" N ASN d 56 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN d 57 " --> pdb=" O PRO d 53 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 26 removed outlier: 3.801A pdb=" N TYR e 25 " --> pdb=" O HIS e 21 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 21 through 26' Processing helix chain 'e' and resid 40 through 45 removed outlier: 3.609A pdb=" N ARG e 45 " --> pdb=" O VAL e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 86 removed outlier: 3.888A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.268A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 3.574A pdb=" N GLN f 42 " --> pdb=" O PRO f 38 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.710A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 105 removed outlier: 5.966A pdb=" N VAL g 85 " --> pdb=" O CYS g 81 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS g 86 " --> pdb=" O ALA g 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU g 87 " --> pdb=" O ASN g 83 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.741A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 36 removed outlier: 4.606A pdb=" N ALA h 18 " --> pdb=" O LYS h 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.055A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS h 49 " --> pdb=" O LYS h 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL h 57 " --> pdb=" O CYS h 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 3.691A pdb=" N ARG h 81 " --> pdb=" O PRO h 77 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 77 through 82' Processing helix chain 'h' and resid 85 through 91 removed outlier: 3.549A pdb=" N ARG h 90 " --> pdb=" O ARG h 86 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA h 91 " --> pdb=" O ALA h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 99 removed outlier: 3.616A pdb=" N GLN h 99 " --> pdb=" O PHE h 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 removed outlier: 3.725A pdb=" N ILE h 109 " --> pdb=" O ARG h 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.922A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU i 60 " --> pdb=" O ARG i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 77 removed outlier: 3.725A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL i 72 " --> pdb=" O ARG i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 98 removed outlier: 3.731A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE i 94 " --> pdb=" O MET i 90 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA i 95 " --> pdb=" O ASN i 91 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA i 96 " --> pdb=" O ASN i 92 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER i 97 " --> pdb=" O ILE i 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.710A pdb=" N LYS j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 77 removed outlier: 4.105A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY j 77 " --> pdb=" O ARG j 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.539A pdb=" N ARG k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 removed outlier: 3.537A pdb=" N ALA k 62 " --> pdb=" O ASP k 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 44 removed outlier: 4.064A pdb=" N MET m 41 " --> pdb=" O LYS m 37 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 75 through 80 removed outlier: 3.785A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ASN m 80 " --> pdb=" O ARG m 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 75 through 80' Processing helix chain 'm' and resid 85 through 99 removed outlier: 3.529A pdb=" N LEU m 96 " --> pdb=" O PHE m 92 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY m 97 " --> pdb=" O ARG m 93 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU m 98 " --> pdb=" O SER m 94 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR m 99 " --> pdb=" O ALA m 95 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 120 removed outlier: 4.119A pdb=" N LEU m 118 " --> pdb=" O PRO m 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU m 119 " --> pdb=" O MET m 115 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU m 120 " --> pdb=" O SER m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 114 through 120' Processing helix chain 'm' and resid 136 through 141 removed outlier: 5.698A pdb=" N ALA m 140 " --> pdb=" O SER m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 156 through 182 removed outlier: 3.791A pdb=" N LYS m 162 " --> pdb=" O GLU m 158 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR m 169 " --> pdb=" O ASN m 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS m 174 " --> pdb=" O LYS m 170 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 193 removed outlier: 3.839A pdb=" N ASP m 189 " --> pdb=" O GLY m 185 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 4.931A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS m 205 " --> pdb=" O ALA m 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 200 through 205' Processing helix chain 'm' and resid 208 through 222 removed outlier: 4.401A pdb=" N TRP m 212 " --> pdb=" O SER m 208 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU m 214 " --> pdb=" O ARG m 210 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR m 216 " --> pdb=" O TRP m 212 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS m 217 " --> pdb=" O ASN m 213 " (cutoff:3.500A) Processing helix chain 'm' and resid 233 through 238 removed outlier: 3.859A pdb=" N THR m 237 " --> pdb=" O ASP m 233 " (cutoff:3.500A) Processing helix chain 'm' and resid 240 through 250 removed outlier: 4.625A pdb=" N GLU m 244 " --> pdb=" O LYS m 240 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR m 245 " --> pdb=" O SER m 241 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 266 removed outlier: 4.761A pdb=" N VAL m 265 " --> pdb=" O LYS m 261 " (cutoff:3.500A) Proline residue: m 266 - end of helix No H-bonds generated for 'chain 'm' and resid 261 through 266' Processing helix chain 'm' and resid 267 through 279 removed outlier: 4.074A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) Processing helix chain 'm' and resid 295 through 311 removed outlier: 3.525A pdb=" N LEU m 302 " --> pdb=" O SER m 298 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN m 305 " --> pdb=" O GLN m 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS m 310 " --> pdb=" O PHE m 306 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR m 311 " --> pdb=" O SER m 307 " (cutoff:3.500A) Processing helix chain 'm' and resid 327 through 337 removed outlier: 3.502A pdb=" N ILE m 332 " --> pdb=" O LYS m 328 " (cutoff:3.500A) Processing helix chain 'm' and resid 378 through 386 removed outlier: 5.571A pdb=" N ILE m 382 " --> pdb=" O SER m 378 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU m 383 " --> pdb=" O GLU m 379 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE m 384 " --> pdb=" O GLU m 380 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 395 through 407 removed outlier: 4.871A pdb=" N TYR m 399 " --> pdb=" O HIS m 395 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE m 400 " --> pdb=" O PRO m 396 " (cutoff:3.500A) Proline residue: m 401 - end of helix Processing helix chain 'm' and resid 408 through 417 removed outlier: 3.865A pdb=" N ARG m 414 " --> pdb=" O LYS m 410 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR m 415 " --> pdb=" O HIS m 411 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR m 416 " --> pdb=" O LEU m 412 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU m 417 " --> pdb=" O GLU m 413 " (cutoff:3.500A) Processing helix chain 'm' and resid 423 through 436 removed outlier: 4.057A pdb=" N PHE m 427 " --> pdb=" O ASP m 423 " (cutoff:3.500A) Processing helix chain 'm' and resid 445 through 460 removed outlier: 4.193A pdb=" N VAL m 449 " --> pdb=" O ASP m 445 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN m 452 " --> pdb=" O GLY m 448 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY m 460 " --> pdb=" O ASP m 456 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.502A pdb=" N ARG p 23 " --> pdb=" O GLY p 19 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS p 28 " --> pdb=" O ARG p 24 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA p 35 " --> pdb=" O ILE p 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 91 removed outlier: 4.163A pdb=" N GLU p 88 " --> pdb=" O ARG p 84 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET p 89 " --> pdb=" O ARG p 85 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL p 90 " --> pdb=" O LEU p 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 20 through 34 removed outlier: 4.256A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 6.273A pdb=" N LYS r 48 " --> pdb=" O GLY r 44 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE r 50 " --> pdb=" O LYS r 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS r 53 " --> pdb=" O GLN r 49 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS r 58 " --> pdb=" O ARG r 54 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS r 72 " --> pdb=" O HIS r 68 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL r 73 " --> pdb=" O GLU r 69 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 93 removed outlier: 5.519A pdb=" N ASP r 93 " --> pdb=" O THR r 89 " (cutoff:3.500A) Processing helix chain 'r' and resid 129 through 134 removed outlier: 4.752A pdb=" N MET r 133 " --> pdb=" O SER r 129 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE r 134 " --> pdb=" O GLU r 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 129 through 134' Processing helix chain 'r' and resid 206 through 213 removed outlier: 3.915A pdb=" N THR r 210 " --> pdb=" O SER r 206 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 253 removed outlier: 3.999A pdb=" N ASP r 252 " --> pdb=" O GLU r 248 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY r 253 " --> pdb=" O PRO r 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 248 through 253' Processing helix chain 'u' and resid 33 through 43 removed outlier: 3.513A pdb=" N LYS u 41 " --> pdb=" O HIS u 37 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG u 43 " --> pdb=" O ALA u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 removed outlier: 3.584A pdb=" N ALA u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY u 60 " --> pdb=" O ARG u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 71 removed outlier: 4.702A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'u' and resid 83 through 131 removed outlier: 4.063A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA u 92 " --> pdb=" O THR u 88 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU u 97 " --> pdb=" O MET u 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP u 119 " --> pdb=" O ASN u 115 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE u 120 " --> pdb=" O LYS u 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN u 130 " --> pdb=" O LEU u 126 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 144 Processing helix chain 'v' and resid 9 through 21 removed outlier: 4.170A pdb=" N LYS v 13 " --> pdb=" O ASN v 9 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA v 15 " --> pdb=" O ARG v 11 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG v 19 " --> pdb=" O ALA v 15 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU v 20 " --> pdb=" O LEU v 16 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA v 21 " --> pdb=" O VAL v 17 " (cutoff:3.500A) Processing helix chain 'v' and resid 39 through 54 removed outlier: 3.893A pdb=" N ILE v 45 " --> pdb=" O ASN v 41 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET v 46 " --> pdb=" O LEU v 42 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL v 47 " --> pdb=" O HIS v 43 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP v 48 " --> pdb=" O ASP v 44 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU v 52 " --> pdb=" O ASP v 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS v 53 " --> pdb=" O LEU v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 72 through 83 Processing helix chain 'v' and resid 124 through 129 removed outlier: 6.036A pdb=" N LYS v 129 " --> pdb=" O LEU v 125 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 151 removed outlier: 4.054A pdb=" N THR v 150 " --> pdb=" O ALA v 146 " (cutoff:3.500A) Processing helix chain 'v' and resid 152 through 166 removed outlier: 3.552A pdb=" N LYS v 158 " --> pdb=" O TYR v 154 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP v 163 " --> pdb=" O SER v 159 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG v 166 " --> pdb=" O LEU v 162 " (cutoff:3.500A) Processing helix chain 'v' and resid 174 through 179 removed outlier: 4.467A pdb=" N LEU v 178 " --> pdb=" O ASP v 174 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLN v 179 " --> pdb=" O VAL v 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 174 through 179' Processing helix chain 'v' and resid 241 through 250 removed outlier: 5.387A pdb=" N LYS v 250 " --> pdb=" O THR v 246 " (cutoff:3.500A) Processing helix chain 'v' and resid 290 through 295 removed outlier: 3.946A pdb=" N LYS v 294 " --> pdb=" O MET v 290 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER v 295 " --> pdb=" O LYS v 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 290 through 295' Processing helix chain 'w' and resid 35 through 40 removed outlier: 4.056A pdb=" N LEU w 39 " --> pdb=" O ASP w 35 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP w 40 " --> pdb=" O LYS w 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 35 through 40' Processing helix chain 'w' and resid 45 through 68 removed outlier: 4.741A pdb=" N LYS w 49 " --> pdb=" O ARG w 45 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER w 52 " --> pdb=" O GLU w 48 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN w 57 " --> pdb=" O LEU w 53 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER w 67 " --> pdb=" O ASN w 63 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU w 68 " --> pdb=" O GLN w 64 " (cutoff:3.500A) Processing helix chain 'w' and resid 112 through 122 removed outlier: 6.155A pdb=" N LYS w 116 " --> pdb=" O THR w 112 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA w 119 " --> pdb=" O GLU w 115 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) Processing helix chain 'w' and resid 149 through 157 removed outlier: 4.034A pdb=" N LYS w 153 " --> pdb=" O GLY w 149 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU w 154 " --> pdb=" O ALA w 150 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP w 155 " --> pdb=" O ASN w 151 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP w 156 " --> pdb=" O LYS w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 175 through 201 removed outlier: 3.540A pdb=" N LEU w 187 " --> pdb=" O GLU w 183 " (cutoff:3.500A) Processing helix chain 'x' and resid 9 through 18 removed outlier: 4.157A pdb=" N GLN x 17 " --> pdb=" O LYS x 13 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU x 18 " --> pdb=" O LYS x 14 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 69 removed outlier: 4.085A pdb=" N GLU x 61 " --> pdb=" O GLU x 57 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU x 62 " --> pdb=" O LYS x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 102 through 108 removed outlier: 4.850A pdb=" N LYS x 107 " --> pdb=" O SER x 103 " (cutoff:3.500A) Proline residue: x 108 - end of helix Processing helix chain 'x' and resid 239 through 244 removed outlier: 3.785A pdb=" N VAL x 243 " --> pdb=" O PRO x 239 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYS x 244 " --> pdb=" O ILE x 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 239 through 244' Processing helix chain 'x' and resid 330 through 337 removed outlier: 3.943A pdb=" N ARG x 335 " --> pdb=" O ASP x 331 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE x 336 " --> pdb=" O TYR x 332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY x 337 " --> pdb=" O ALA x 333 " (cutoff:3.500A) Processing helix chain 'x' and resid 348 through 365 Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.859A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 4.417A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 4.216A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR y 63 " --> pdb=" O ILE y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 58 through 63' Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.595A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 removed outlier: 3.667A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS y 152 " --> pdb=" O VAL y 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 147 through 152' Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.635A pdb=" N GLY y 196 " --> pdb=" O VAL y 192 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 192 through 197' Processing helix chain 'y' and resid 211 through 223 removed outlier: 3.768A pdb=" N VAL y 217 " --> pdb=" O PRO y 213 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE y 222 " --> pdb=" O ILE y 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG y 223 " --> pdb=" O GLU y 219 " (cutoff:3.500A) Processing helix chain 'y' and resid 231 through 244 removed outlier: 4.592A pdb=" N ASN y 235 " --> pdb=" O SER y 231 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR y 239 " --> pdb=" O ASN y 235 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 54 removed outlier: 3.926A pdb=" N SER z 15 " --> pdb=" O LEU z 11 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL z 16 " --> pdb=" O ASN z 12 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG z 19 " --> pdb=" O SER z 15 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA z 25 " --> pdb=" O VAL z 21 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG z 29 " --> pdb=" O ALA z 25 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU z 39 " --> pdb=" O ASP z 35 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN z 44 " --> pdb=" O ASP z 40 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.793A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.364A pdb=" N ASN A 100 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.116A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 5, first strand: chain 'B' and resid 45 through 50 removed outlier: 3.585A pdb=" N PHE B 46 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 338 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 53 through 57 removed outlier: 5.312A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 321 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.805A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL B 87 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 107 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 177 through 182 removed outlier: 5.242A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 87 through 93 Processing sheet with id= 10, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.234A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 224 through 229 removed outlier: 3.567A pdb=" N GLU C 226 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.641A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 145 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 60 through 64 removed outlier: 6.412A pdb=" N ILE D 60 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D 76 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 37 through 43 removed outlier: 4.033A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.893A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 176 through 181 removed outlier: 3.865A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU G 200 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.215A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.534A pdb=" N ARG H 23 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.271A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 132 through 137 removed outlier: 4.975A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR H 92 " --> pdb=" O ASP H 142 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 16 through 23 removed outlier: 3.785A pdb=" N VAL J 69 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 23 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS J 68 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL J 46 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 101 through 107 removed outlier: 4.237A pdb=" N PHE J 104 " --> pdb=" O PHE J 127 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 24, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.850A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 36 through 39 removed outlier: 6.324A pdb=" N LYS M 43 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.457A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.577A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 29, first strand: chain 'P' and resid 14 through 20 removed outlier: 6.509A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 31, first strand: chain 'P' and resid 124 through 127 removed outlier: 3.793A pdb=" N GLN P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 33, first strand: chain 'R' and resid 21 through 25 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.645A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N SER S 55 " --> pdb=" O LEU S 14 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 89 through 96 removed outlier: 5.247A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.779A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 71 through 79 removed outlier: 3.714A pdb=" N VAL T 72 " --> pdb=" O LEU T 91 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 54 through 58 removed outlier: 6.111A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR U 16 " --> pdb=" O ASN U 101 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 79 through 82 removed outlier: 3.991A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN V 98 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 84 through 88 removed outlier: 4.023A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 75 through 78 Processing sheet with id= 42, first strand: chain 'W' and resid 38 through 42 removed outlier: 8.191A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.917A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.408A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 10 through 14 removed outlier: 4.058A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 27 through 30 removed outlier: 3.645A pdb=" N HIS Z 40 " --> pdb=" O HIS Z 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Z 73 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'a' and resid 123 through 126 Processing sheet with id= 48, first strand: chain 'b' and resid 204 through 210 removed outlier: 5.010A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS b 173 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE b 253 " --> pdb=" O CYS b 173 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.502A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA c 46 " --> pdb=" O PHE c 70 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 48 through 51 removed outlier: 4.725A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL d 8 " --> pdb=" O ARG d 77 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL d 107 " --> pdb=" O GLU d 11 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 52, first strand: chain 'f' and resid 11 through 15 removed outlier: 6.832A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE f 49 " --> pdb=" O GLY f 69 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 8 through 14 removed outlier: 4.041A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.742A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 15 through 18 removed outlier: 8.436A pdb=" N SER j 15 " --> pdb=" O HIS j 28 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS j 28 " --> pdb=" O SER j 15 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR j 17 " --> pdb=" O SER j 26 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.559A pdb=" N THR k 53 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER k 50 " --> pdb=" O GLY k 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'm' and resid 282 through 286 removed outlier: 6.093A pdb=" N TYR m 257 " --> pdb=" O PRO m 282 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS m 254 " --> pdb=" O ASP m 223 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL m 225 " --> pdb=" O HIS m 254 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN m 260 " --> pdb=" O LEU m 229 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 53 through 57 removed outlier: 4.608A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 60, first strand: chain 'r' and resid 191 through 196 removed outlier: 4.490A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL r 255 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA r 199 " --> pdb=" O GLU r 222 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 18 through 23 removed outlier: 4.315A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 56 through 60 removed outlier: 3.701A pdb=" N ALA v 30 " --> pdb=" O ASP v 56 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N SER v 92 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N SER v 85 " --> pdb=" O THR v 105 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP v 112 " --> pdb=" O ARG v 104 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG v 236 " --> pdb=" O GLU v 115 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 139 through 145 removed outlier: 3.653A pdb=" N ILE v 182 " --> pdb=" O MET v 140 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE v 186 " --> pdb=" O GLN v 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL v 181 " --> pdb=" O TYR v 204 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR v 185 " --> pdb=" O LEU v 200 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 262 through 266 removed outlier: 6.503A pdb=" N ASN v 262 " --> pdb=" O ARG v 274 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP v 270 " --> pdb=" O ASP v 266 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 198 through 202 Processing sheet with id= 66, first strand: chain 'w' and resid 17 through 23 removed outlier: 5.679A pdb=" N SER w 31 " --> pdb=" O PRO w 18 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'w' and resid 69 through 72 removed outlier: 3.786A pdb=" N LEU w 89 " --> pdb=" O LYS w 71 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'x' and resid 50 through 53 removed outlier: 3.976A pdb=" N ARG x 50 " --> pdb=" O ILE x 34 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE x 117 " --> pdb=" O SER x 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS x 35 " --> pdb=" O ILE x 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR x 121 " --> pdb=" O GLN x 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG x 124 " --> pdb=" O PRO x 76 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 136 through 140 removed outlier: 4.812A pdb=" N SER x 137 " --> pdb=" O LEU x 512 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU x 512 " --> pdb=" O SER x 137 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N MET x 509 " --> pdb=" O GLY x 505 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY x 505 " --> pdb=" O MET x 509 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG x 500 " --> pdb=" O SER x 495 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY x 504 " --> pdb=" O THR x 491 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'x' and resid 147 through 151 removed outlier: 6.743A pdb=" N SER x 157 " --> pdb=" O CYS x 173 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'x' and resid 190 through 195 removed outlier: 5.687A pdb=" N VAL x 200 " --> pdb=" O SER x 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG x 211 " --> pdb=" O THR x 203 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 234 through 238 removed outlier: 3.957A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP x 263 " --> pdb=" O LEU x 251 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE x 262 " --> pdb=" O TYR x 272 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 291 through 295 removed outlier: 3.923A pdb=" N LEU x 292 " --> pdb=" O TRP x 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN x 314 " --> pdb=" O VAL x 303 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 326 through 329 removed outlier: 6.417A pdb=" N MET x 373 " --> pdb=" O SER x 329 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA x 396 " --> pdb=" O LEU x 385 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 406 through 411 removed outlier: 3.744A pdb=" N HIS x 407 " --> pdb=" O ALA x 420 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER x 421 " --> pdb=" O SER x 425 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER x 425 " --> pdb=" O SER x 421 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE x 426 " --> pdb=" O PHE x 440 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 448 through 453 removed outlier: 3.647A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER x 453 " --> pdb=" O LEU x 458 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER x 463 " --> pdb=" O THR x 467 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N THR x 467 " --> pdb=" O SER x 463 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'x' and resid 167 through 170 removed outlier: 3.543A pdb=" N ALA x 168 " --> pdb=" O LEU x 182 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE x 170 " --> pdb=" O HIS x 180 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N HIS x 180 " --> pdb=" O ILE x 170 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'y' and resid 1 through 4 Processing sheet with id= 79, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 80, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 81, first strand: chain 'y' and resid 114 through 117 Processing sheet with id= 82, first strand: chain 'y' and resid 158 through 161 removed outlier: 3.822A pdb=" N VAL y 182 " --> pdb=" O GLY y 159 " (cutoff:3.500A) 2207 hydrogen bonds defined for protein. 6576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2056 hydrogen bonds 3300 hydrogen bond angles 0 basepair planarities 829 basepair parallelities 1623 stacking parallelities Total time for adding SS restraints: 160.81 Time building geometry restraints manager: 50.11 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: 26077 1.33 - 1.46: 56714 1.46 - 1.59: 54606 1.59 - 1.72: 5029 1.72 - 1.85: 267 Bond restraints: 142693 Sorted by residual: bond pdb=" C ASN J 132 " pdb=" N ARG J 133 " ideal model delta sigma weight residual 1.330 1.263 0.067 1.47e-02 4.63e+03 2.11e+01 bond pdb=" C ASP b 220 " pdb=" N THR b 221 " ideal model delta sigma weight residual 1.333 1.426 -0.094 2.74e-02 1.33e+03 1.17e+01 bond pdb=" C SER k 68 " pdb=" N LEU k 69 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.47e-02 4.63e+03 6.39e+00 bond pdb=" C LEU i 50 " pdb=" N SER i 51 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.07e-02 2.33e+03 4.65e+00 bond pdb=" CB CYS g 81 " pdb=" SG CYS g 81 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.88e+00 ... (remaining 142688 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.00: 18581 106.00 - 113.41: 84533 113.41 - 120.83: 61795 120.83 - 128.25: 38393 128.25 - 135.67: 5186 Bond angle restraints: 208488 Sorted by residual: angle pdb=" N TYR i 28 " pdb=" CA TYR i 28 " pdb=" C TYR i 28 " ideal model delta sigma weight residual 114.62 108.23 6.39 1.14e+00 7.69e-01 3.14e+01 angle pdb=" C3' A 1 720 " pdb=" O3' A 1 720 " pdb=" P G 1 721 " ideal model delta sigma weight residual 120.20 128.09 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" O3' G 1 160 " pdb=" C3' G 1 160 " pdb=" C2' G 1 160 " ideal model delta sigma weight residual 109.50 117.23 -7.73 1.50e+00 4.44e-01 2.65e+01 angle pdb=" C2' A 1 646 " pdb=" C1' A 1 646 " pdb=" N9 A 1 646 " ideal model delta sigma weight residual 114.00 121.66 -7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" C GLY r 15 " pdb=" N LYS r 16 " pdb=" CA LYS r 16 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 ... (remaining 208483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 74902 35.91 - 71.81: 3735 71.81 - 107.72: 290 107.72 - 143.63: 39 143.63 - 179.53: 81 Dihedral angle restraints: 79047 sinusoidal: 55744 harmonic: 23303 Sorted by residual: dihedral pdb=" C5' G 1 160 " pdb=" C4' G 1 160 " pdb=" C3' G 1 160 " pdb=" O3' G 1 160 " ideal model delta sinusoidal sigma weight residual 147.00 72.62 74.38 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" C5' A 11102 " pdb=" C4' A 11102 " pdb=" C3' A 11102 " pdb=" O3' A 11102 " ideal model delta sinusoidal sigma weight residual 147.00 74.97 72.03 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C4' G 1 160 " pdb=" C3' G 1 160 " pdb=" C2' G 1 160 " pdb=" C1' G 1 160 " ideal model delta sinusoidal sigma weight residual -35.00 35.34 -70.34 1 8.00e+00 1.56e-02 9.95e+01 ... (remaining 79044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 24230 0.085 - 0.170: 1598 0.170 - 0.255: 92 0.255 - 0.340: 16 0.340 - 0.425: 3 Chirality restraints: 25939 Sorted by residual: chirality pdb=" C3' G 1 160 " pdb=" C4' G 1 160 " pdb=" O3' G 1 160 " pdb=" C2' G 1 160 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C3' A 11102 " pdb=" C4' A 11102 " pdb=" O3' A 11102 " pdb=" C2' A 11102 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1' A 1 646 " pdb=" O4' A 1 646 " pdb=" C2' A 1 646 " pdb=" N9 A 1 646 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 25936 not shown) Planarity restraints: 14367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 13016 " -0.054 2.00e-02 2.50e+03 2.46e-02 1.66e+01 pdb=" N9 A 13016 " 0.057 2.00e-02 2.50e+03 pdb=" C8 A 13016 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 13016 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 13016 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 13016 " -0.011 2.00e-02 2.50e+03 pdb=" N6 A 13016 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A 13016 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A 13016 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 13016 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A 13016 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 835 " 0.055 2.00e-02 2.50e+03 2.34e-02 1.64e+01 pdb=" N9 G 1 835 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G 1 835 " -0.009 2.00e-02 2.50e+03 pdb=" N7 G 1 835 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 835 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 835 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G 1 835 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G 1 835 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 1 835 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G 1 835 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 1 835 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G 1 835 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 646 " 0.046 2.00e-02 2.50e+03 2.34e-02 1.51e+01 pdb=" N9 A 1 646 " -0.061 2.00e-02 2.50e+03 pdb=" C8 A 1 646 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 1 646 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 1 646 " 0.009 2.00e-02 2.50e+03 pdb=" C6 A 1 646 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A 1 646 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A 1 646 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 646 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A 1 646 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A 1 646 " 0.002 2.00e-02 2.50e+03 ... (remaining 14364 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 467 2.42 - 3.04: 73805 3.04 - 3.66: 212110 3.66 - 4.28: 341332 4.28 - 4.90: 497531 Nonbonded interactions: 1125245 Sorted by model distance: nonbonded pdb=" O1G GTP m 501 " pdb="MG MG m 502 " model vdw 1.797 2.170 nonbonded pdb=" O2B GTP m 501 " pdb="MG MG m 502 " model vdw 1.901 2.170 nonbonded pdb=" O2' C 13092 " pdb=" OP2 A 13094 " model vdw 1.944 2.440 nonbonded pdb=" NH1 ARG u 33 " pdb="ZN ZN u 201 " model vdw 1.954 2.310 nonbonded pdb=" O2' U 12723 " pdb=" O2 U 12724 " model vdw 1.971 2.440 ... (remaining 1125240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.21 max=1.00 mean=0.99 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: 0.970 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: 0.070 Extract box with map and model: 11.480 Check model and map are aligned: 1.480 Set scattering table: 0.910 Process input model: 432.870 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 453.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.006 0.094 142693 Z= 0.370 Angle : 0.765 13.383 208488 Z= 0.411 Chirality : 0.045 0.425 25939 Planarity : 0.005 0.083 14367 Dihedral : 18.447 179.534 63953 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.48 % Favored : 90.14 % Rotamer: Outliers : 9.89 % Allowed : 21.29 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.08), residues: 7910 helix: -2.13 (0.08), residues: 2610 sheet: -2.10 (0.13), residues: 1279 loop : -3.47 (0.08), residues: 4021 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 678 poor density : 1047 time to evaluate : 7.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 678 outliers final: 534 residues processed: 1635 average time/residue: 1.2172 time to fit residues: 3460.2328 Evaluate side-chains 1424 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 534 poor density : 890 time to evaluate : 7.393 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 534 outliers final: 1 residues processed: 534 average time/residue: 1.0138 time to fit residues: 1035.9652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 933 optimal weight: 10.0000 chunk 838 optimal weight: 10.0000 chunk 465 optimal weight: 5.9990 chunk 286 optimal weight: 0.0470 chunk 565 optimal weight: 6.9990 chunk 447 optimal weight: 3.9990 chunk 866 optimal weight: 20.0000 chunk 335 optimal weight: 8.9990 chunk 527 optimal weight: 6.9990 chunk 645 optimal weight: 0.9990 chunk 1004 optimal weight: 30.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 13 HIS B 256 HIS C 221 ASN C 296 GLN C 307 GLN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 45 ASN D 90 HIS D 264 GLN E 80 ASN E 138 GLN E 167 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS G 77 GLN G 95 ASN H 49 ASN H 157 ASN H 183 HIS ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS L 120 GLN M 62 GLN M 126 GLN N 37 HIS O 50 ASN R 75 HIS S 46 GLN S 89 ASN S 122 HIS S 138 GLN ** S 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 131 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 109 GLN V 81 GLN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 110 ASN W 148 GLN Y 4 GLN Z 36 HIS Z 57 HIS a 74 ASN b 89 ASN b 120 GLN b 124 GLN b 280 ASN b 333 ASN b 440 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 HIS e 104 ASN g 52 GLN h 62 GLN h 68 GLN i 12 ASN i 63 ASN ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 13 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN m 146 GLN r 4 ASN r 10 HIS r 14 HIS u 37 HIS v 29 GLN v 173 GLN v 249 HIS ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 83 GLN w 194 GLN w 195 GLN ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 31 ASN x 154 HIS x 208 ASN x 241 HIS x 321 HIS x 401 HIS x 515 HIS y 9 ASN y 11 ASN y 33 ASN y 106 ASN y 140 GLN y 168 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 142693 Z= 0.227 Angle : 0.655 12.169 208488 Z= 0.338 Chirality : 0.040 0.370 25939 Planarity : 0.005 0.080 14367 Dihedral : 16.934 179.957 47745 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.80 % Favored : 91.01 % Rotamer: Outliers : 2.83 % Allowed : 25.39 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.97 (0.08), residues: 7910 helix: -0.86 (0.10), residues: 2614 sheet: -1.60 (0.14), residues: 1254 loop : -2.95 (0.08), residues: 4042 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 978 time to evaluate : 7.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 90 residues processed: 1124 average time/residue: 1.2209 time to fit residues: 2398.1986 Evaluate side-chains 1003 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 913 time to evaluate : 7.323 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 90 outliers final: 1 residues processed: 90 average time/residue: 1.0709 time to fit residues: 187.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 558 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 835 optimal weight: 10.0000 chunk 683 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 chunk 1006 optimal weight: 30.0000 chunk 1086 optimal weight: 20.0000 chunk 896 optimal weight: 20.0000 chunk 997 optimal weight: 50.0000 chunk 343 optimal weight: 8.9990 chunk 807 optimal weight: 40.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 83 HIS B 109 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 ASN H 125 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN N 181 ASN S 138 GLN U 25 ASN V 4 ASN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN j 13 ASN v 187 GLN v 276 HIS ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 83 GLN ** w 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 235 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 142693 Z= 0.503 Angle : 0.831 16.142 208488 Z= 0.418 Chirality : 0.049 0.417 25939 Planarity : 0.007 0.115 14367 Dihedral : 17.271 179.519 47745 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.34 % Favored : 89.34 % Rotamer: Outliers : 5.01 % Allowed : 26.20 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.87 (0.09), residues: 7910 helix: -0.80 (0.10), residues: 2609 sheet: -1.51 (0.14), residues: 1270 loop : -2.87 (0.08), residues: 4031 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 887 time to evaluate : 7.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 343 outliers final: 230 residues processed: 1152 average time/residue: 1.1805 time to fit residues: 2372.7483 Evaluate side-chains 1099 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 869 time to evaluate : 6.575 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 230 outliers final: 1 residues processed: 230 average time/residue: 0.9132 time to fit residues: 407.8518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 994 optimal weight: 10.0000 chunk 756 optimal weight: 1.9990 chunk 522 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 480 optimal weight: 30.0000 chunk 675 optimal weight: 7.9990 chunk 1009 optimal weight: 20.0000 chunk 1069 optimal weight: 7.9990 chunk 527 optimal weight: 6.9990 chunk 957 optimal weight: 5.9990 chunk 288 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS C 316 ASN C 320 ASN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN H 49 ASN H 157 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN S 138 GLN T 95 HIS ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN j 13 ASN j 76 ASN m 260 ASN m 310 HIS r 70 GLN ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 142693 Z= 0.287 Angle : 0.684 14.675 208488 Z= 0.352 Chirality : 0.042 0.361 25939 Planarity : 0.005 0.085 14367 Dihedral : 16.979 179.711 47745 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.03 % Favored : 90.72 % Rotamer: Outliers : 2.60 % Allowed : 27.98 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.49 (0.09), residues: 7910 helix: -0.41 (0.10), residues: 2640 sheet: -1.31 (0.14), residues: 1258 loop : -2.71 (0.08), residues: 4012 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 928 time to evaluate : 7.409 Fit side-chains revert: symmetry clash outliers start: 178 outliers final: 105 residues processed: 1053 average time/residue: 1.1875 time to fit residues: 2171.2673 Evaluate side-chains 999 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 894 time to evaluate : 7.347 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 105 outliers final: 1 residues processed: 105 average time/residue: 0.9530 time to fit residues: 199.1816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 890 optimal weight: 10.0000 chunk 606 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 795 optimal weight: 20.0000 chunk 441 optimal weight: 10.0000 chunk 912 optimal weight: 10.0000 chunk 738 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 545 optimal weight: 30.0000 chunk 959 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN N 181 ASN S 138 GLN T 95 HIS ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN i 12 ASN r 70 GLN ** v 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 142693 Z= 0.431 Angle : 0.776 14.257 208488 Z= 0.394 Chirality : 0.046 0.400 25939 Planarity : 0.006 0.108 14367 Dihedral : 17.135 179.451 47745 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.37 % Favored : 89.34 % Rotamer: Outliers : 3.63 % Allowed : 28.17 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.09), residues: 7910 helix: -0.48 (0.10), residues: 2636 sheet: -1.29 (0.14), residues: 1262 loop : -2.70 (0.08), residues: 4012 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 883 time to evaluate : 7.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 249 outliers final: 157 residues processed: 1068 average time/residue: 1.1754 time to fit residues: 2191.8603 Evaluate side-chains 1016 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 859 time to evaluate : 7.037 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 157 outliers final: 1 residues processed: 157 average time/residue: 0.9393 time to fit residues: 288.7075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 359 optimal weight: 0.9980 chunk 962 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 627 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 1070 optimal weight: 7.9990 chunk 888 optimal weight: 10.0000 chunk 495 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 353 optimal weight: 0.0870 chunk 561 optimal weight: 5.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 198 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 HIS ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 HIS ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN r 70 GLN v 280 GLN w 57 ASN ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 449 GLN y 235 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 142693 Z= 0.173 Angle : 0.608 12.949 208488 Z= 0.315 Chirality : 0.038 0.322 25939 Planarity : 0.005 0.076 14367 Dihedral : 16.677 179.929 47745 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.91 % Favored : 91.90 % Rotamer: Outliers : 1.44 % Allowed : 29.32 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.04 (0.09), residues: 7910 helix: -0.01 (0.10), residues: 2653 sheet: -1.03 (0.15), residues: 1247 loop : -2.48 (0.09), residues: 4010 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 974 time to evaluate : 7.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 43 residues processed: 1039 average time/residue: 1.2114 time to fit residues: 2211.0875 Evaluate side-chains 952 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 909 time to evaluate : 7.324 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 43 outliers final: 1 residues processed: 43 average time/residue: 0.9993 time to fit residues: 90.6083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 1031 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 609 optimal weight: 1.9990 chunk 781 optimal weight: 4.9990 chunk 605 optimal weight: 3.9990 chunk 900 optimal weight: 10.0000 chunk 597 optimal weight: 5.9990 chunk 1066 optimal weight: 20.0000 chunk 667 optimal weight: 20.0000 chunk 649 optimal weight: 3.9990 chunk 492 optimal weight: 0.0020 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN H 49 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 142693 Z= 0.195 Angle : 0.605 13.719 208488 Z= 0.312 Chirality : 0.038 0.316 25939 Planarity : 0.005 0.074 14367 Dihedral : 16.551 179.372 47745 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.56 % Favored : 91.25 % Rotamer: Outliers : 1.40 % Allowed : 29.99 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.86 (0.09), residues: 7910 helix: 0.12 (0.10), residues: 2666 sheet: -0.91 (0.15), residues: 1262 loop : -2.37 (0.09), residues: 3982 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 927 time to evaluate : 7.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 59 residues processed: 992 average time/residue: 1.2064 time to fit residues: 2070.9912 Evaluate side-chains 957 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 898 time to evaluate : 7.382 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 59 outliers final: 1 residues processed: 59 average time/residue: 0.9381 time to fit residues: 115.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 659 optimal weight: 5.9990 chunk 425 optimal weight: 9.9990 chunk 636 optimal weight: 0.7980 chunk 321 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 206 optimal weight: 0.0570 chunk 677 optimal weight: 20.0000 chunk 726 optimal weight: 8.9990 chunk 527 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 837 optimal weight: 10.0000 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 ASN r 70 GLN v 238 HIS ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 142693 Z= 0.152 Angle : 0.580 12.172 208488 Z= 0.299 Chirality : 0.036 0.296 25939 Planarity : 0.004 0.071 14367 Dihedral : 16.440 179.772 47745 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.88 % Favored : 91.97 % Rotamer: Outliers : 0.85 % Allowed : 30.39 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.66 (0.09), residues: 7910 helix: 0.30 (0.10), residues: 2657 sheet: -0.73 (0.15), residues: 1229 loop : -2.28 (0.09), residues: 4024 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 947 time to evaluate : 7.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 22 residues processed: 978 average time/residue: 1.2100 time to fit residues: 2052.2838 Evaluate side-chains 934 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 912 time to evaluate : 7.341 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.9457 time to fit residues: 48.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 969 optimal weight: 10.0000 chunk 1021 optimal weight: 20.0000 chunk 931 optimal weight: 10.0000 chunk 993 optimal weight: 10.0000 chunk 1020 optimal weight: 20.0000 chunk 597 optimal weight: 1.9990 chunk 432 optimal weight: 5.9990 chunk 780 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 897 optimal weight: 10.0000 chunk 939 optimal weight: 10.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN T 95 HIS ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 GLN W 159 HIS b 346 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 187 GLN ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 142693 Z= 0.283 Angle : 0.653 16.331 208488 Z= 0.334 Chirality : 0.040 0.315 25939 Planarity : 0.005 0.080 14367 Dihedral : 16.567 179.810 47745 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.13 % Favored : 90.68 % Rotamer: Outliers : 0.90 % Allowed : 30.55 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.76 (0.09), residues: 7910 helix: 0.19 (0.10), residues: 2663 sheet: -0.79 (0.15), residues: 1239 loop : -2.31 (0.09), residues: 4008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 904 time to evaluate : 6.693 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 938 average time/residue: 1.2117 time to fit residues: 1964.2735 Evaluate side-chains 929 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 885 time to evaluate : 7.384 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 1.0212 time to fit residues: 93.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 989 optimal weight: 10.0000 chunk 652 optimal weight: 0.0570 chunk 1050 optimal weight: 10.0000 chunk 641 optimal weight: 2.9990 chunk 498 optimal weight: 1.9990 chunk 730 optimal weight: 5.9990 chunk 1101 optimal weight: 40.0000 chunk 1014 optimal weight: 10.0000 chunk 877 optimal weight: 40.0000 chunk 91 optimal weight: 9.9990 chunk 677 optimal weight: 8.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN H 49 ASN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 HIS ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 142693 Z= 0.238 Angle : 0.636 16.976 208488 Z= 0.327 Chirality : 0.039 0.313 25939 Planarity : 0.005 0.150 14367 Dihedral : 16.543 179.263 47745 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.58 % Favored : 91.23 % Rotamer: Outliers : 0.44 % Allowed : 30.68 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.09), residues: 7910 helix: 0.21 (0.10), residues: 2663 sheet: -0.77 (0.15), residues: 1255 loop : -2.30 (0.09), residues: 3992 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15820 Ramachandran restraints generated. 7910 Oldfield, 0 Emsley, 7910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 901 time to evaluate : 7.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 919 average time/residue: 1.1964 time to fit residues: 1903.4811 Evaluate side-chains 908 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 885 time to evaluate : 7.347 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.9813 time to fit residues: 51.2669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 538 optimal weight: 5.9990 chunk 696 optimal weight: 0.3980 chunk 934 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 809 optimal weight: 30.0000 chunk 129 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 chunk 878 optimal weight: 50.0000 chunk 367 optimal weight: 0.9980 chunk 902 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 GLN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 70 GLN v 187 GLN ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN ** w 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124157 restraints weight = 186043.605| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.23 r_work: 0.3066 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 142693 Z= 0.216 Angle : 0.623 16.037 208488 Z= 0.321 Chirality : 0.038 0.547 25939 Planarity : 0.005 0.074 14367 Dihedral : 16.520 179.416 47745 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.79 % Favored : 91.01 % Rotamer: Outliers : 0.47 % Allowed : 30.78 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.70 (0.09), residues: 7910 helix: 0.24 (0.10), residues: 2662 sheet: -0.80 (0.15), residues: 1262 loop : -2.27 (0.09), residues: 3986 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34026.73 seconds wall clock time: 593 minutes 12.64 seconds (35592.64 seconds total)