Starting phenix.real_space_refine on Fri Dec 8 09:56:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l20_23121/12_2023/7l20_23121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l20_23121/12_2023/7l20_23121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l20_23121/12_2023/7l20_23121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l20_23121/12_2023/7l20_23121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l20_23121/12_2023/7l20_23121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l20_23121/12_2023/7l20_23121_updated.pdb" } resolution = 3.15 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= -0.004 sd= 0.126 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 1586 5.49 5 Mg 102 5.21 5 S 312 5.16 5 C 63730 2.51 5 N 19983 2.21 5 O 24518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 191": "OD1" <-> "OD2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K ASP 136": "OD1" <-> "OD2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K GLU 174": "OE1" <-> "OE2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "M ASP 14": "OD1" <-> "OD2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ASP 111": "OD1" <-> "OD2" Residue "M ASP 117": "OD1" <-> "OD2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "M TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "O TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R ASP 134": "OD1" <-> "OD2" Residue "R GLU 137": "OE1" <-> "OE2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S GLU 126": "OE1" <-> "OE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 85": "OD1" <-> "OD2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ASP 115": "OD1" <-> "OD2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 111": "OE1" <-> "OE2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ASP 180": "OD1" <-> "OD2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X ASP 189": "OD1" <-> "OD2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "X GLU 198": "OE1" <-> "OE2" Residue "X GLU 199": "OE1" <-> "OE2" Residue "X GLU 209": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 65": "OE1" <-> "OE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "Z GLU 51": "OE1" <-> "OE2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 84": "OD1" <-> "OD2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "0 ASP 108": "OD1" <-> "OD2" Residue "0 GLU 112": "OE1" <-> "OE2" Residue "0 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 167": "OE1" <-> "OE2" Residue "0 ASP 178": "OD1" <-> "OD2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "2 ARG 49": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ASP 174": "OD1" <-> "OD2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "4 ASP 78": "OD1" <-> "OD2" Residue "4 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 97": "NH1" <-> "NH2" Residue "8 GLU 86": "OE1" <-> "OE2" Residue "8 PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 96": "OD1" <-> "OD2" Residue "8 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 134": "OD1" <-> "OD2" Residue "8 ARG 137": "NH1" <-> "NH2" Residue "8 GLU 145": "OE1" <-> "OE2" Residue "8 GLU 148": "OE1" <-> "OE2" Residue "8 GLU 149": "OE1" <-> "OE2" Residue "8 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 172": "OE1" <-> "OE2" Residue "8 GLU 174": "OE1" <-> "OE2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b GLU 45": "OE1" <-> "OE2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b GLU 50": "OE1" <-> "OE2" Residue "b TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 96": "OE1" <-> "OE2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "e TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e ASP 119": "OD1" <-> "OD2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "e GLU 177": "OE1" <-> "OE2" Residue "e GLU 189": "OE1" <-> "OE2" Residue "e TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 242": "OD1" <-> "OD2" Residue "e PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 258": "OD1" <-> "OD2" Residue "e GLU 259": "OE1" <-> "OE2" Residue "e ASP 262": "OD1" <-> "OD2" Residue "e TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "g ASP 154": "OD1" <-> "OD2" Residue "g GLU 163": "OE1" <-> "OE2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ASP 105": "OD1" <-> "OD2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j GLU 100": "OE1" <-> "OE2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "m ARG 72": "NH1" <-> "NH2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 69": "OE1" <-> "OE2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "o PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 34": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "q GLU 84": "OE1" <-> "OE2" Residue "q GLU 86": "OE1" <-> "OE2" Residue "q GLU 91": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 111": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q GLU 116": "OE1" <-> "OE2" Residue "q ASP 149": "OD1" <-> "OD2" Residue "q GLU 151": "OE1" <-> "OE2" Residue "r GLU 40": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "r GLU 117": "OE1" <-> "OE2" Residue "r ARG 134": "NH1" <-> "NH2" Residue "r GLU 137": "OE1" <-> "OE2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "r ARG 182": "NH1" <-> "NH2" Residue "r ARG 189": "NH1" <-> "NH2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J ASP 127": "OD1" <-> "OD2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 206": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 201": "OD1" <-> "OD2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N GLU 206": "OE1" <-> "OE2" Residue "N GLU 216": "OE1" <-> "OE2" Residue "N TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 40": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "P PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P ASP 156": "OD1" <-> "OD2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 125": "OD1" <-> "OD2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 132": "OE1" <-> "OE2" Residue "U GLU 133": "OE1" <-> "OE2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ASP 181": "OD1" <-> "OD2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "5 ARG 71": "NH1" <-> "NH2" Residue "5 ASP 78": "OD1" <-> "OD2" Residue "5 ARG 79": "NH1" <-> "NH2" Residue "5 ASP 83": "OD1" <-> "OD2" Residue "5 ARG 85": "NH1" <-> "NH2" Residue "5 ASP 100": "OD1" <-> "OD2" Residue "5 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 133": "OE1" <-> "OE2" Residue "5 GLU 147": "OE1" <-> "OE2" Residue "5 ASP 150": "OD1" <-> "OD2" Residue "5 GLU 151": "OE1" <-> "OE2" Residue "5 GLU 167": "OE1" <-> "OE2" Residue "5 ASP 181": "OD1" <-> "OD2" Residue "5 ARG 222": "NH1" <-> "NH2" Residue "5 ARG 241": "NH1" <-> "NH2" Residue "5 GLU 243": "OE1" <-> "OE2" Residue "5 GLU 245": "OE1" <-> "OE2" Residue "5 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 271": "OD1" <-> "OD2" Residue "5 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 294": "OD1" <-> "OD2" Residue "5 ASP 306": "OD1" <-> "OD2" Residue "5 ASP 331": "OD1" <-> "OD2" Residue "5 ASP 347": "OD1" <-> "OD2" Residue "5 PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 362": "OD1" <-> "OD2" Residue "5 GLU 367": "OE1" <-> "OE2" Residue "5 ASP 376": "OD1" <-> "OD2" Residue "5 ASP 378": "OD1" <-> "OD2" Residue "5 TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 394": "NH1" <-> "NH2" Residue "5 GLU 398": "OE1" <-> "OE2" Residue "6 ASP 39": "OD1" <-> "OD2" Residue "6 ASP 41": "OD1" <-> "OD2" Residue "6 GLU 46": "OE1" <-> "OE2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 118": "OE1" <-> "OE2" Residue "6 GLU 120": "OE1" <-> "OE2" Residue "6 ARG 126": "NH1" <-> "NH2" Residue "6 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 207": "OE1" <-> "OE2" Residue "6 GLU 209": "OE1" <-> "OE2" Residue "6 GLU 210": "OE1" <-> "OE2" Residue "6 GLU 227": "OE1" <-> "OE2" Residue "6 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 276": "OD1" <-> "OD2" Residue "6 ASP 280": "OD1" <-> "OD2" Residue "6 PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 336": "OD1" <-> "OD2" Residue "6 GLU 343": "OE1" <-> "OE2" Residue "6 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 39": "OE1" <-> "OE2" Residue "7 ARG 44": "NH1" <-> "NH2" Residue "7 ASP 46": "OD1" <-> "OD2" Residue "7 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 ASP 190": "OD1" <-> "OD2" Residue "7 ARG 200": "NH1" <-> "NH2" Residue "7 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 217": "OE1" <-> "OE2" Residue "7 GLU 222": "OE1" <-> "OE2" Residue "7 ASP 238": "OD1" <-> "OD2" Residue "7 GLU 242": "OE1" <-> "OE2" Residue "7 GLU 249": "OE1" <-> "OE2" Residue "7 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 314": "OD1" <-> "OD2" Residue "7 GLU 326": "OE1" <-> "OE2" Residue "7 ASP 327": "OD1" <-> "OD2" Residue "9 ARG 31": "NH1" <-> "NH2" Residue "9 ARG 33": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 GLU 82": "OE1" <-> "OE2" Residue "9 GLU 83": "OE1" <-> "OE2" Residue "9 GLU 94": "OE1" <-> "OE2" Residue "9 GLU 101": "OE1" <-> "OE2" Residue "9 GLU 115": "OE1" <-> "OE2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "9 ARG 133": "NH1" <-> "NH2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "a ASP 79": "OD1" <-> "OD2" Residue "a ARG 95": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "c GLU 102": "OE1" <-> "OE2" Residue "c GLU 113": "OE1" <-> "OE2" Residue "c ASP 143": "OD1" <-> "OD2" Residue "c TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 151": "OE1" <-> "OE2" Residue "c GLU 163": "OE1" <-> "OE2" Residue "c GLU 182": "OE1" <-> "OE2" Residue "c GLU 209": "OE1" <-> "OE2" Residue "c PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 217": "OD1" <-> "OD2" Residue "c GLU 227": "OE1" <-> "OE2" Residue "c PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d ASP 94": "OD1" <-> "OD2" Residue "d ASP 136": "OD1" <-> "OD2" Residue "d ASP 143": "OD1" <-> "OD2" Residue "d ASP 175": "OD1" <-> "OD2" Residue "d PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ARG 219": "NH1" <-> "NH2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 244": "OE1" <-> "OE2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 104": "OE1" <-> "OE2" Residue "f GLU 122": "OE1" <-> "OE2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f GLU 172": "OE1" <-> "OE2" Residue "f ARG 183": "NH1" <-> "NH2" Residue "f GLU 188": "OE1" <-> "OE2" Residue "f GLU 191": "OE1" <-> "OE2" Residue "h TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "h ASP 88": "OD1" <-> "OD2" Residue "h GLU 92": "OE1" <-> "OE2" Residue "h ASP 93": "OD1" <-> "OD2" Residue "h ASP 107": "OD1" <-> "OD2" Residue "h ASP 136": "OD1" <-> "OD2" Residue "h PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ASP 58": "OD1" <-> "OD2" Residue "k GLU 61": "OE1" <-> "OE2" Residue "k PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "l TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 89": "OD1" <-> "OD2" Residue "l GLU 94": "OE1" <-> "OE2" Residue "l ARG 120": "NH1" <-> "NH2" Residue "p ASP 56": "OD1" <-> "OD2" Residue "p ASP 75": "OD1" <-> "OD2" Residue "p GLU 138": "OE1" <-> "OE2" Residue "p ASP 156": "OD1" <-> "OD2" Residue "p GLU 160": "OE1" <-> "OE2" Residue "p ASP 172": "OD1" <-> "OD2" Residue "s TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s GLU 78": "OE1" <-> "OE2" Residue "s ARG 104": "NH1" <-> "NH2" Residue "s ASP 138": "OD1" <-> "OD2" Residue "s TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 203": "NH1" <-> "NH2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ASP 254": "OD1" <-> "OD2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s ASP 290": "OD1" <-> "OD2" Residue "s ARG 307": "NH1" <-> "NH2" Residue "s GLU 309": "OE1" <-> "OE2" Residue "s ARG 310": "NH1" <-> "NH2" Residue "s ARG 313": "NH1" <-> "NH2" Residue "s TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 407": "OD1" <-> "OD2" Residue "s PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ASP 98": "OD1" <-> "OD2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q GLU 210": "OE1" <-> "OE2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 251": "OE1" <-> "OE2" Residue "Q ASP 274": "OD1" <-> "OD2" Residue "Q ARG 291": "NH1" <-> "NH2" Residue "w TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 110234 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 32395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 32395 Classifications: {'RNA': 1527} Modifications used: {'rna2p_pur': 166, 'rna2p_pyr': 118, 'rna3p_pur': 636, 'rna3p_pyr': 606} Link IDs: {'rna2p': 284, 'rna3p': 1242} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "D" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1866 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 13, 'TRANS': 225} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 105} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 135} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "W" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "X" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2027 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 17, 'TRANS': 225} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 342 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 836 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 9, 'TRANS': 89} Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "e" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1762 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "g" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 115} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 740 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "q" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 151} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "r" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 142} Chain: "J" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1330 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Chain: "I" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1435 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 17, 'TRANS': 161} Chain: "N" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1786 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "P" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1165 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 136} Chain: "U" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1222 Classifications: {'peptide': 152} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 138} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "V" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1682 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 187} Chain: "E" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2410 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain: "5" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3205 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 360} Chain: "6" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2948 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 319} Chain: "7" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2410 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 17, 'TRANS': 279} Chain: "9" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "a" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 896 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2322 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 17, 'TRANS': 271} Chain: "d" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2075 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 236} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "f" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1126 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 141} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "h" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 894 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "k" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "l" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 619 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 6, 'TRANS': 65} Chain: "p" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1227 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "s" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3178 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 361} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1834 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 205} Chain: "u" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 325 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'TRANS': 64} Chain breaks: 4 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "TA" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 345 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "TB" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "TC" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 352 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "z" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1525 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain: "w" Number of atoms: 5422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5422 Classifications: {'peptide': 696} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 661} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Unusual residues: {' MG': 97} Classifications: {'undetermined': 97} Link IDs: {None: 96} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 53590 SG CYS 0 110 177.534 49.053 121.192 1.00 70.81 S ATOM 53612 SG CYS 0 113 180.796 49.135 124.535 1.00 72.77 S ATOM 53692 SG CYS 0 123 179.252 52.272 122.303 1.00 66.60 S ATOM 53715 SG CYS 0 126 181.443 49.508 120.914 1.00 68.95 S ATOM 55940 SG CYS 4 76 97.088 121.076 84.654 1.00 72.65 S ATOM 55963 SG CYS 4 79 98.832 119.651 87.465 1.00 68.81 S ATOM 56087 SG CYS 4 92 99.085 117.607 84.147 1.00 67.32 S ATOM 65362 SG CYS r 70 77.614 108.671 114.808 1.00 75.27 S ATOM 65383 SG CYS r 73 77.301 108.272 118.390 1.00 76.72 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' GCP w 801 " occ=0.69 ... (30 atoms not shown) pdb=" PG GCP w 801 " occ=0.69 Time building chain proxies: 41.17, per 1000 atoms: 0.37 Number of scatterers: 110234 At special positions: 0 Unit cell: (287.631, 258.653, 248.994, 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 312 16.00 P 1586 15.00 Mg 102 11.99 O 24518 8.00 N 19983 7.00 C 63730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 19247 O4' C A2577 .*. O " rejected from bonding due to valence issues. Atom "ATOM 10740 O5' C A2175 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.84 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb=" ZN r 200 " pdb="ZN ZN r 200 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 200 " - pdb=" SG CYS r 73 " Number of angles added : 9 18668 Ramachandran restraints generated. 9334 Oldfield, 0 Emsley, 9334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17968 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 304 helices and 82 sheets defined 41.0% alpha, 13.1% beta 399 base pairs and 700 stacking pairs defined. Time for finding SS restraints: 62.76 Creating SS restraints... Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.696A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.934A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.790A pdb=" N HIS D 252 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN D 253 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 109 removed outlier: 3.562A pdb=" N LEU F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 4.136A pdb=" N ASP F 185 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.659A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.834A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.270A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.476A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.010A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 133 through 149 removed outlier: 3.779A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU H 149 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 removed outlier: 3.906A pdb=" N MET K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.544A pdb=" N LYS K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 116 through 126 removed outlier: 4.801A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.764A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 167 removed outlier: 4.557A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.732A pdb=" N ASN L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 removed outlier: 4.593A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 125 through 131' Processing helix chain 'L' and resid 134 through 142 removed outlier: 4.580A pdb=" N LEU L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 20 removed outlier: 3.984A pdb=" N ASP M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 73 through 78 removed outlier: 4.044A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 removed outlier: 4.008A pdb=" N GLY M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 125 removed outlier: 3.552A pdb=" N LEU M 121 " --> pdb=" O ASP M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 4.268A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.899A pdb=" N LYS M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 197 removed outlier: 3.633A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 215 Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 225 through 241 removed outlier: 4.189A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.654A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.712A pdb=" N THR M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.987A pdb=" N LEU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 removed outlier: 3.542A pdb=" N ARG O 25 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.244A pdb=" N LYS O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 82 through 98 removed outlier: 6.606A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.659A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix removed outlier: 3.683A pdb=" N LYS O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 160 removed outlier: 3.610A pdb=" N GLN O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.990A pdb=" N ARG R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 80 removed outlier: 4.539A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.641A pdb=" N CYS R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.930A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 49 through 55 removed outlier: 4.565A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.707A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.914A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.329A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.712A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 removed outlier: 3.743A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.976A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 34 Processing helix chain 'X' and resid 72 through 79 removed outlier: 3.737A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 removed outlier: 3.588A pdb=" N LEU X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS X 154 " --> pdb=" O GLY X 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 149 through 154' Processing helix chain 'X' and resid 155 through 172 removed outlier: 3.563A pdb=" N MET X 159 " --> pdb=" O SER X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 192 removed outlier: 3.576A pdb=" N ARG X 184 " --> pdb=" O ASP X 180 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS X 192 " --> pdb=" O TYR X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 3.802A pdb=" N GLU X 202 " --> pdb=" O GLU X 198 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 removed outlier: 3.546A pdb=" N GLU X 220 " --> pdb=" O ARG X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.890A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER X 244 " --> pdb=" O GLN X 240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 5.048A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 3.922A pdb=" N TRP Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 75' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.735A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.703A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 removed outlier: 4.020A pdb=" N ARG Y 196 " --> pdb=" O LYS Y 192 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 238 Processing helix chain 'Z' and resid 49 through 57 removed outlier: 4.760A pdb=" N GLY Z 57 " --> pdb=" O HIS Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.752A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 removed outlier: 3.601A pdb=" N ARG 0 95 " --> pdb=" O ARG 0 91 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 removed outlier: 3.849A pdb=" N GLY 0 146 " --> pdb=" O GLY 0 142 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 73 removed outlier: 4.527A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Proline residue: 2 73 - end of helix Processing helix chain '2' and resid 74 through 86 Processing helix chain '3' and resid 107 through 114 removed outlier: 3.825A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.038A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 146 removed outlier: 4.142A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.340A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.127A pdb=" N HIS 3 181 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 177 through 182' Processing helix chain '8' and resid 107 through 154 removed outlier: 3.672A pdb=" N THR 8 111 " --> pdb=" O THR 8 107 " (cutoff:3.500A) Processing helix chain '8' and resid 156 through 164 removed outlier: 3.908A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 91 through 96 removed outlier: 3.970A pdb=" N LEU 8 95 " --> pdb=" O LEU 8 92 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP 8 96 " --> pdb=" O LYS 8 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 7 Proline residue: b 7 - end of helix Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.427A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 50 removed outlier: 4.392A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 removed outlier: 3.560A pdb=" N ASN b 58 " --> pdb=" O PHE b 54 " (cutoff:3.500A) Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 3.501A pdb=" N ILE b 97 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 85 through 104 removed outlier: 4.570A pdb=" N GLU e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 132 removed outlier: 4.576A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 137 through 143 removed outlier: 4.935A pdb=" N ASP e 141 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 197 removed outlier: 3.594A pdb=" N SER e 196 " --> pdb=" O LEU e 192 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU e 197 " --> pdb=" O ALA e 193 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 265 removed outlier: 6.282A pdb=" N LYS e 265 " --> pdb=" O GLY e 261 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 4.631A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL e 276 " --> pdb=" O VAL e 272 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 52 removed outlier: 4.590A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 133 removed outlier: 3.740A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'i' and resid 48 through 54 removed outlier: 3.892A pdb=" N ALA i 52 " --> pdb=" O ASN i 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET i 53 " --> pdb=" O GLU i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 64 removed outlier: 4.051A pdb=" N LEU i 63 " --> pdb=" O ASN i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 74 removed outlier: 4.182A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 25 through 32 removed outlier: 5.285A pdb=" N LEU j 29 " --> pdb=" O GLY j 25 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN j 30 " --> pdb=" O GLN j 26 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN j 31 " --> pdb=" O TRP j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 41 removed outlier: 5.409A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLY j 41 " --> pdb=" O PRO j 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 36 through 41' Processing helix chain 'j' and resid 60 through 108 removed outlier: 3.835A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) Processing helix chain 'm' and resid 35 through 40 removed outlier: 4.749A pdb=" N SER m 39 " --> pdb=" O SER m 35 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU m 40 " --> pdb=" O SER m 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 35 through 40' Processing helix chain 'o' and resid 28 through 51 removed outlier: 3.695A pdb=" N LYS o 32 " --> pdb=" O SER o 28 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 6.154A pdb=" N GLU o 59 " --> pdb=" O THR o 55 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 55 through 60' Processing helix chain 'o' and resid 63 through 81 removed outlier: 4.923A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 97 removed outlier: 4.077A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.212A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 78 through 93 removed outlier: 4.136A pdb=" N LEU q 82 " --> pdb=" O SER q 78 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 127 Processing helix chain 'q' and resid 129 through 159 removed outlier: 3.635A pdb=" N LEU q 156 " --> pdb=" O ARG q 152 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN q 157 " --> pdb=" O ARG q 153 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA q 158 " --> pdb=" O ALA q 154 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU q 159 " --> pdb=" O ARG q 155 " (cutoff:3.500A) Processing helix chain 'q' and resid 166 through 192 Proline residue: q 170 - end of helix removed outlier: 3.731A pdb=" N GLU q 192 " --> pdb=" O LYS q 188 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 76 removed outlier: 3.581A pdb=" N SER q 74 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU q 75 " --> pdb=" O PRO q 72 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP q 76 " --> pdb=" O GLY q 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.567A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.345A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 removed outlier: 3.537A pdb=" N ARG r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS r 114 " --> pdb=" O GLU r 110 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS r 120 " --> pdb=" O GLU r 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY r 126 " --> pdb=" O ALA r 122 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.004A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 'r' and resid 137 through 142 removed outlier: 3.787A pdb=" N VAL r 140 " --> pdb=" O GLU r 137 " (cutoff:3.500A) Proline residue: r 141 - end of helix No H-bonds generated for 'chain 'r' and resid 137 through 142' Processing helix chain 'J' and resid 33 through 43 Proline residue: J 37 - end of helix Processing helix chain 'J' and resid 45 through 59 removed outlier: 3.877A pdb=" N PHE J 49 " --> pdb=" O SER J 45 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.549A pdb=" N VAL J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 134 removed outlier: 4.458A pdb=" N LEU J 132 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN J 133 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP J 134 " --> pdb=" O PHE J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 3.642A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY J 152 " --> pdb=" O ALA J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 192 removed outlier: 4.915A pdb=" N ALA J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 4.469A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 Proline residue: I 66 - end of helix Processing helix chain 'I' and resid 76 through 93 removed outlier: 4.312A pdb=" N ASN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.786A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 140 through 145 removed outlier: 3.887A pdb=" N LEU I 144 " --> pdb=" O TYR I 140 " (cutoff:3.500A) Proline residue: I 145 - end of helix No H-bonds generated for 'chain 'I' and resid 140 through 145' Processing helix chain 'I' and resid 160 through 172 removed outlier: 4.188A pdb=" N MET I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 removed outlier: 3.996A pdb=" N LYS I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU I 197 " --> pdb=" O ASN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 207 removed outlier: 4.430A pdb=" N LEU I 207 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 4.101A pdb=" N ARG N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 69 through 74' Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 170 through 181 removed outlier: 3.525A pdb=" N VAL N 179 " --> pdb=" O PHE N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 209 removed outlier: 3.605A pdb=" N ASN N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 226 through 231 removed outlier: 5.028A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 5.052A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 116 removed outlier: 4.176A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 156 through 169 Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 122 through 138 removed outlier: 5.661A pdb=" N LEU U 126 " --> pdb=" O ALA U 122 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 116 through 121 removed outlier: 3.677A pdb=" N VAL V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 121' Processing helix chain 'V' and resid 178 through 184 removed outlier: 3.556A pdb=" N GLU V 184 " --> pdb=" O GLU V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 203 removed outlier: 3.659A pdb=" N GLY V 203 " --> pdb=" O MET V 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 removed outlier: 3.990A pdb=" N VAL E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.703A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.894A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.956A pdb=" N CYS E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 320 through 325 removed outlier: 3.983A pdb=" N ASP E 324 " --> pdb=" O PHE E 320 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU E 325 " --> pdb=" O PRO E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 320 through 325' Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.623A pdb=" N HIS E 197 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG E 199 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 53 removed outlier: 3.807A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 48 through 53' Processing helix chain '5' and resid 115 through 124 Processing helix chain '5' and resid 132 through 141 removed outlier: 3.617A pdb=" N LEU 5 136 " --> pdb=" O PRO 5 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP 5 141 " --> pdb=" O SER 5 137 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 162 Processing helix chain '5' and resid 171 through 195 Proline residue: 5 177 - end of helix removed outlier: 4.573A pdb=" N GLN 5 190 " --> pdb=" O LEU 5 186 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE 5 191 " --> pdb=" O CYS 5 187 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU 5 192 " --> pdb=" O LYS 5 188 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS 5 193 " --> pdb=" O SER 5 189 " (cutoff:3.500A) Proline residue: 5 195 - end of helix Processing helix chain '5' and resid 196 through 201 removed outlier: 5.210A pdb=" N ARG 5 200 " --> pdb=" O SER 5 196 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE 5 201 " --> pdb=" O LEU 5 197 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 196 through 201' Processing helix chain '5' and resid 240 through 250 removed outlier: 4.013A pdb=" N LYS 5 248 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASN 5 249 " --> pdb=" O GLU 5 245 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS 5 250 " --> pdb=" O ALA 5 246 " (cutoff:3.500A) Processing helix chain '5' and resid 298 through 303 removed outlier: 3.530A pdb=" N ARG 5 302 " --> pdb=" O LEU 5 298 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU 5 303 " --> pdb=" O ARG 5 299 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 298 through 303' Processing helix chain '5' and resid 304 through 328 Processing helix chain '5' and resid 406 through 419 removed outlier: 4.349A pdb=" N PHE 5 410 " --> pdb=" O LYS 5 406 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 3.769A pdb=" N LEU 6 48 " --> pdb=" O ASN 6 44 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 44 through 49' Processing helix chain '6' and resid 53 through 67 removed outlier: 4.339A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN 6 66 " --> pdb=" O GLU 6 62 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA 6 67 " --> pdb=" O GLN 6 63 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 79 removed outlier: 4.088A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE 6 78 " --> pdb=" O TYR 6 74 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY 6 79 " --> pdb=" O ARG 6 75 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 73 through 79' Processing helix chain '6' and resid 98 through 116 removed outlier: 4.112A pdb=" N ASN 6 116 " --> pdb=" O GLU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 126 Processing helix chain '6' and resid 131 through 143 removed outlier: 3.588A pdb=" N CYS 6 143 " --> pdb=" O TRP 6 139 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 removed outlier: 3.623A pdb=" N GLY 6 156 " --> pdb=" O ALA 6 152 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 281 through 286 removed outlier: 4.455A pdb=" N ALA 6 285 " --> pdb=" O PHE 6 281 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG 6 286 " --> pdb=" O SER 6 282 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 281 through 286' Processing helix chain '6' and resid 292 through 297 removed outlier: 3.623A pdb=" N ARG 6 296 " --> pdb=" O GLN 6 292 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR 6 297 " --> pdb=" O LEU 6 293 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 292 through 297' Processing helix chain '6' and resid 299 through 308 Processing helix chain '6' and resid 324 through 333 removed outlier: 4.532A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.684A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG 6 370 " --> pdb=" O LEU 6 366 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 364 through 371' Processing helix chain '6' and resid 157 through 163 removed outlier: 4.360A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS 6 163 " --> pdb=" O TYR 6 158 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 157 through 163' Processing helix chain '7' and resid 36 through 59 removed outlier: 3.682A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR 7 59 " --> pdb=" O GLN 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 removed outlier: 4.136A pdb=" N HIS 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU 7 95 " --> pdb=" O CYS 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 103 removed outlier: 3.812A pdb=" N SER 7 103 " --> pdb=" O TYR 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 158 removed outlier: 4.015A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA 7 157 " --> pdb=" O VAL 7 153 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 removed outlier: 3.505A pdb=" N LEU 7 199 " --> pdb=" O THR 7 195 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS 7 212 " --> pdb=" O ALA 7 208 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 removed outlier: 3.547A pdb=" N PHE 7 230 " --> pdb=" O ALA 7 226 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN 7 231 " --> pdb=" O LEU 7 227 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 248 removed outlier: 3.875A pdb=" N GLN 7 246 " --> pdb=" O GLU 7 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN 7 247 " --> pdb=" O LYS 7 243 " (cutoff:3.500A) Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 4.058A pdb=" N ARG 7 321 " --> pdb=" O LEU 7 317 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.808A pdb=" N ILE 7 274 " --> pdb=" O ARG 7 271 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 271 through 276' Processing helix chain '9' and resid 27 through 35 removed outlier: 5.394A pdb=" N GLY 9 32 " --> pdb=" O ARG 9 28 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG 9 33 " --> pdb=" O SER 9 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 9 34 " --> pdb=" O PHE 9 30 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.666A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 95 Processing helix chain '9' and resid 96 through 107 removed outlier: 3.650A pdb=" N GLY 9 107 " --> pdb=" O ASP 9 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 99 removed outlier: 6.006A pdb=" N LEU a 92 " --> pdb=" O HIS a 88 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS a 93 " --> pdb=" O ASP a 89 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU a 97 " --> pdb=" O LYS a 93 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU a 98 " --> pdb=" O THR a 94 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS a 99 " --> pdb=" O ARG a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 127 through 134 removed outlier: 3.706A pdb=" N ARG a 133 " --> pdb=" O TYR a 129 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS a 134 " --> pdb=" O HIS a 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.601A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.722A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 removed outlier: 3.876A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN c 80 " --> pdb=" O GLY c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 93 removed outlier: 3.903A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 109 Processing helix chain 'c' and resid 114 through 119 removed outlier: 4.934A pdb=" N ASN c 118 " --> pdb=" O ALA c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 4.753A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 4.019A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 Processing helix chain 'c' and resid 288 through 306 removed outlier: 3.624A pdb=" N TYR c 305 " --> pdb=" O LEU c 301 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 54 removed outlier: 4.832A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU d 53 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 48 through 54' Processing helix chain 'd' and resid 66 through 72 removed outlier: 3.974A pdb=" N GLU d 70 " --> pdb=" O VAL d 66 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS d 71 " --> pdb=" O ILE d 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER d 72 " --> pdb=" O PRO d 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 66 through 72' Processing helix chain 'd' and resid 93 through 98 Processing helix chain 'd' and resid 107 through 129 removed outlier: 4.527A pdb=" N ARG d 111 " --> pdb=" O GLU d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 removed outlier: 4.828A pdb=" N PHE d 137 " --> pdb=" O LYS d 133 " (cutoff:3.500A) Proline residue: d 138 - end of helix Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.545A pdb=" N LEU d 160 " --> pdb=" O ASP d 156 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 173 Proline residue: d 170 - end of helix Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.732A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 removed outlier: 3.905A pdb=" N ALA f 103 " --> pdb=" O ASP f 99 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.593A pdb=" N SER f 177 " --> pdb=" O ILE f 173 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 79 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 120 removed outlier: 4.366A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 133 removed outlier: 3.706A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN h 131 " --> pdb=" O LEU h 127 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Proline residue: h 133 - end of helix Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.462A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.557A pdb=" N ALA k 6 " --> pdb=" O ALA k 2 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY k 9 " --> pdb=" O LEU k 5 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.913A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 4.726A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU k 47 " --> pdb=" O ARG k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 97 removed outlier: 3.835A pdb=" N ARG k 97 " --> pdb=" O HIS k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 85 removed outlier: 3.561A pdb=" N GLN l 82 " --> pdb=" O TYR l 78 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP l 83 " --> pdb=" O LYS l 79 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL l 84 " --> pdb=" O GLU l 80 " (cutoff:3.500A) Proline residue: l 85 - end of helix No H-bonds generated for 'chain 'l' and resid 78 through 85' Processing helix chain 'l' and resid 88 through 93 removed outlier: 3.601A pdb=" N TYR l 92 " --> pdb=" O PRO l 88 " (cutoff:3.500A) Proline residue: l 93 - end of helix No H-bonds generated for 'chain 'l' and resid 88 through 93' Processing helix chain 'l' and resid 94 through 99 removed outlier: 4.715A pdb=" N GLU l 98 " --> pdb=" O GLU l 94 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N MET l 99 " --> pdb=" O TRP l 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 94 through 99' Processing helix chain 'l' and resid 106 through 111 removed outlier: 5.073A pdb=" N ASP l 111 " --> pdb=" O LEU l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 134 removed outlier: 4.034A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS l 134 " --> pdb=" O ASN l 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 removed outlier: 3.682A pdb=" N TYR p 49 " --> pdb=" O LEU p 45 " (cutoff:3.500A) Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 62 through 67 removed outlier: 3.726A pdb=" N LYS p 66 " --> pdb=" O PRO p 62 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN p 67 " --> pdb=" O ASN p 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 62 through 67' Processing helix chain 'p' and resid 73 through 78 removed outlier: 3.820A pdb=" N LEU p 77 " --> pdb=" O PRO p 73 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 73 through 78' Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 164 removed outlier: 3.600A pdb=" N ASN p 146 " --> pdb=" O TYR p 142 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN p 163 " --> pdb=" O THR p 159 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR p 164 " --> pdb=" O GLU p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 173 through 189 removed outlier: 5.262A pdb=" N ARG p 177 " --> pdb=" O VAL p 173 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU p 188 " --> pdb=" O ASN p 184 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 74 removed outlier: 3.688A pdb=" N ARG s 59 " --> pdb=" O SER s 55 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA s 73 " --> pdb=" O THR s 69 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU s 74 " --> pdb=" O VAL s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.571A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 154 removed outlier: 3.770A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 190 removed outlier: 3.925A pdb=" N GLU s 168 " --> pdb=" O HIS s 164 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER s 173 " --> pdb=" O SER s 169 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix removed outlier: 3.605A pdb=" N ASP s 178 " --> pdb=" O LEU s 174 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY s 186 " --> pdb=" O SER s 182 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER s 189 " --> pdb=" O VAL s 185 " (cutoff:3.500A) Proline residue: s 190 - end of helix Processing helix chain 's' and resid 192 through 199 removed outlier: 4.590A pdb=" N ALA s 196 " --> pdb=" O ASN s 192 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA s 197 " --> pdb=" O PRO s 193 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA s 198 " --> pdb=" O ALA s 194 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA s 199 " --> pdb=" O LEU s 195 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 192 through 199' Processing helix chain 's' and resid 267 through 272 removed outlier: 4.672A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 removed outlier: 3.795A pdb=" N ASN s 315 " --> pdb=" O LEU s 311 " (cutoff:3.500A) Processing helix chain 's' and resid 319 through 344 removed outlier: 3.667A pdb=" N VAL s 323 " --> pdb=" O GLN s 319 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN s 343 " --> pdb=" O GLN s 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY s 344 " --> pdb=" O ALA s 340 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 385 removed outlier: 4.000A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.777A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN s 427 " --> pdb=" O HIS s 423 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 107 removed outlier: 4.030A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 removed outlier: 5.368A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.064A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU Q 249 " --> pdb=" O PHE Q 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 244 through 249' Processing helix chain 'Q' and resid 250 through 261 removed outlier: 4.026A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 262 through 268 removed outlier: 4.457A pdb=" N GLU Q 266 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 removed outlier: 3.988A pdb=" N SER Q 292 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing helix chain 'TA' and resid 61 through 72 removed outlier: 3.843A pdb=" N GLNTA 65 " --> pdb=" O PROTA 61 " (cutoff:3.500A) Processing helix chain 'TA' and resid 75 through 90 removed outlier: 4.945A pdb=" N THRTA 89 " --> pdb=" O LEUTA 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEUTA 90 " --> pdb=" O LEUTA 86 " (cutoff:3.500A) Processing helix chain 'TB' and resid 64 through 75 removed outlier: 4.524A pdb=" N VALTB 68 " --> pdb=" O ILETB 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEUTB 74 " --> pdb=" O ASPTB 70 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THRTB 75 " --> pdb=" O ILETB 71 " (cutoff:3.500A) Processing helix chain 'TB' and resid 76 through 90 Processing helix chain 'TC' and resid 141 through 153 removed outlier: 3.802A pdb=" N LEUTC 145 " --> pdb=" O ASPTC 141 " (cutoff:3.500A) Processing helix chain 'TC' and resid 157 through 168 removed outlier: 4.679A pdb=" N LEUTC 168 " --> pdb=" O LEUTC 164 " (cutoff:3.500A) Processing helix chain 'TC' and resid 178 through 192 removed outlier: 3.892A pdb=" N GLYTC 192 " --> pdb=" O LEUTC 188 " (cutoff:3.500A) Processing helix chain 'z' and resid 76 through 83 removed outlier: 3.945A pdb=" N GLU z 80 " --> pdb=" O ALA z 76 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE z 82 " --> pdb=" O LEU z 78 " (cutoff:3.500A) Processing helix chain 'z' and resid 84 through 105 removed outlier: 4.322A pdb=" N VAL z 88 " --> pdb=" O ASN z 84 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN z 89 " --> pdb=" O LEU z 85 " (cutoff:3.500A) Processing helix chain 'z' and resid 129 through 134 removed outlier: 5.010A pdb=" N ILE z 133 " --> pdb=" O ALA z 129 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER z 134 " --> pdb=" O LEU z 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 129 through 134' Processing helix chain 'z' and resid 151 through 165 removed outlier: 3.831A pdb=" N THR z 155 " --> pdb=" O PHE z 151 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA z 156 " --> pdb=" O PRO z 152 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU z 164 " --> pdb=" O LYS z 160 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER z 165 " --> pdb=" O ALA z 161 " (cutoff:3.500A) Processing helix chain 'z' and resid 186 through 224 removed outlier: 5.980A pdb=" N ARG z 190 " --> pdb=" O THR z 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS z 223 " --> pdb=" O LEU z 219 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP z 224 " --> pdb=" O LYS z 220 " (cutoff:3.500A) Processing helix chain 'z' and resid 227 through 262 removed outlier: 3.800A pdb=" N ILE z 231 " --> pdb=" O SER z 227 " (cutoff:3.500A) Processing helix chain 'z' and resid 112 through 118 removed outlier: 3.606A pdb=" N LEU z 116 " --> pdb=" O PRO z 113 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP z 117 " --> pdb=" O GLY z 114 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS z 118 " --> pdb=" O SER z 115 " (cutoff:3.500A) Processing helix chain 'w' and resid 66 through 71 removed outlier: 5.084A pdb=" N ILE w 70 " --> pdb=" O PRO w 66 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ARG w 71 " --> pdb=" O ILE w 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 66 through 71' Processing helix chain 'w' and resid 82 through 95 removed outlier: 4.776A pdb=" N LEU w 86 " --> pdb=" O GLY w 82 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR w 87 " --> pdb=" O LYS w 83 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 120 removed outlier: 5.892A pdb=" N ARG w 117 " --> pdb=" O MET w 113 " (cutoff:3.500A) Processing helix chain 'w' and resid 148 through 159 removed outlier: 3.646A pdb=" N VAL w 152 " --> pdb=" O PHE w 148 " (cutoff:3.500A) Processing helix chain 'w' and resid 173 through 187 removed outlier: 3.579A pdb=" N HIS w 186 " --> pdb=" O GLN w 182 " (cutoff:3.500A) Processing helix chain 'w' and resid 203 through 215 removed outlier: 3.521A pdb=" N ALA w 207 " --> pdb=" O SER w 203 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 288 removed outlier: 4.458A pdb=" N LEU w 270 " --> pdb=" O ASP w 266 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP w 288 " --> pdb=" O VAL w 284 " (cutoff:3.500A) Processing helix chain 'w' and resid 289 through 298 removed outlier: 4.656A pdb=" N ASP w 293 " --> pdb=" O ASP w 289 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU w 294 " --> pdb=" O GLU w 290 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU w 298 " --> pdb=" O LEU w 294 " (cutoff:3.500A) Processing helix chain 'w' and resid 308 through 322 removed outlier: 5.218A pdb=" N GLN w 312 " --> pdb=" O ALA w 308 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA w 321 " --> pdb=" O ARG w 317 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN w 322 " --> pdb=" O VAL w 318 " (cutoff:3.500A) Processing helix chain 'w' and resid 337 through 348 removed outlier: 4.669A pdb=" N LEU w 341 " --> pdb=" O GLY w 337 " (cutoff:3.500A) Processing helix chain 'w' and resid 358 through 364 removed outlier: 4.443A pdb=" N LYS w 364 " --> pdb=" O LEU w 360 " (cutoff:3.500A) Processing helix chain 'w' and resid 498 through 516 removed outlier: 4.402A pdb=" N GLN w 502 " --> pdb=" O SER w 498 " (cutoff:3.500A) Proline residue: w 503 - end of helix Processing helix chain 'w' and resid 536 through 550 removed outlier: 3.885A pdb=" N ILE w 540 " --> pdb=" O GLY w 536 " (cutoff:3.500A) Processing helix chain 'w' and resid 623 through 638 removed outlier: 3.667A pdb=" N GLY w 638 " --> pdb=" O ALA w 634 " (cutoff:3.500A) Processing helix chain 'w' and resid 661 through 682 removed outlier: 4.812A pdb=" N MET w 665 " --> pdb=" O THR w 661 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER w 667 " --> pdb=" O THR w 663 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS w 680 " --> pdb=" O LYS w 676 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA w 681 " --> pdb=" O ALA w 677 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP w 682 " --> pdb=" O LEU w 678 " (cutoff:3.500A) Processing helix chain 'w' and resid 700 through 712 removed outlier: 4.992A pdb=" N VAL w 704 " --> pdb=" O TYR w 700 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG w 712 " --> pdb=" O LEU w 708 " (cutoff:3.500A) Processing helix chain 'w' and resid 732 through 737 removed outlier: 3.714A pdb=" N ILE w 736 " --> pdb=" O PRO w 732 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET w 737 " --> pdb=" O LEU w 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 732 through 737' Processing helix chain 'w' and resid 738 through 748 removed outlier: 3.973A pdb=" N VAL w 742 " --> pdb=" O GLY w 738 " (cutoff:3.500A) Processing helix chain 'w' and resid 764 through 777 Processing sheet with id= 1, first strand: chain 'D' and resid 128 through 131 removed outlier: 3.972A pdb=" N ILE D 139 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY D 179 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU D 164 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 190 through 194 removed outlier: 4.371A pdb=" N THR D 191 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 295 " --> pdb=" O GLN D 235 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 139 through 143 Processing sheet with id= 4, first strand: chain 'F' and resid 47 through 50 removed outlier: 4.395A pdb=" N VAL F 47 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG F 49 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY F 78 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 186 through 189 removed outlier: 3.739A pdb=" N LEU F 259 " --> pdb=" O ASP F 186 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 217 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.201A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'H' and resid 96 through 99 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'K' and resid 55 through 60 removed outlier: 4.791A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU K 20 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'K' and resid 77 through 81 removed outlier: 5.125A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'L' and resid 38 through 41 removed outlier: 5.516A pdb=" N LEU L 107 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS L 83 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP L 71 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'L' and resid 87 through 90 removed outlier: 3.705A pdb=" N GLY L 88 " --> pdb=" O ASN L 104 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N CYS L 90 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N SER L 102 " --> pdb=" O CYS L 90 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 13, first strand: chain 'M' and resid 273 through 276 Processing sheet with id= 14, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.048A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 16, first strand: chain 'S' and resid 112 through 117 removed outlier: 4.006A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'S' and resid 162 through 166 removed outlier: 3.823A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR S 188 " --> pdb=" O SER S 166 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'S' and resid 168 through 175 removed outlier: 3.515A pdb=" N LYS S 182 " --> pdb=" O ARG S 173 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'T' and resid 71 through 78 removed outlier: 5.049A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'W' and resid 98 through 102 Processing sheet with id= 22, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.368A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU X 60 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'X' and resid 85 through 92 removed outlier: 7.563A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id= 25, first strand: chain 'Z' and resid 97 through 102 removed outlier: 3.523A pdb=" N HIS Z 100 " --> pdb=" O HIS Z 67 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Z 65 " --> pdb=" O ASN Z 102 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '0' and resid 155 through 159 Processing sheet with id= 27, first strand: chain '1' and resid 17 through 22 removed outlier: 5.711A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '1' and resid 41 through 46 removed outlier: 5.915A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '3' and resid 122 through 125 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain '4' and resid 66 through 69 removed outlier: 5.643A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'b' and resid 61 through 68 removed outlier: 6.307A pdb=" N VAL b 33 " --> pdb=" O ASN b 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 174 through 178 removed outlier: 3.909A pdb=" N TRP e 178 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.155A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU e 227 " --> pdb=" O PHE e 217 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE e 215 " --> pdb=" O ALA e 229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR e 213 " --> pdb=" O VAL e 231 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 44 through 55 removed outlier: 4.117A pdb=" N LYS e 230 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU e 48 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE e 232 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA e 236 " --> pdb=" O CYS e 52 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'g' and resid 96 through 101 removed outlier: 3.707A pdb=" N THR g 101 " --> pdb=" O ARG g 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG g 105 " --> pdb=" O THR g 101 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR g 146 " --> pdb=" O ASN g 141 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN g 141 " --> pdb=" O THR g 146 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'm' and resid 62 through 67 removed outlier: 4.545A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU m 75 " --> pdb=" O LEU m 55 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'r' and resid 35 through 42 Processing sheet with id= 38, first strand: chain 'J' and resid 18 through 24 removed outlier: 4.158A pdb=" N GLY J 18 " --> pdb=" O VAL J 72 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.757A pdb=" N HIS I 150 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE I 96 " --> pdb=" O CYS I 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY I 178 " --> pdb=" O VAL I 98 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 41, first strand: chain 'N' and resid 119 through 123 removed outlier: 3.930A pdb=" N PHE N 119 " --> pdb=" O GLY N 164 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 80 through 85 removed outlier: 3.880A pdb=" N VAL P 103 " --> pdb=" O VAL P 94 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.575A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA U 67 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.894A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.365A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'E' and resid 98 through 101 removed outlier: 3.575A pdb=" N VAL E 299 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 273 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.863A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'E' and resid 174 through 181 removed outlier: 5.612A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '5' and resid 125 through 128 removed outlier: 3.583A pdb=" N VAL 5 375 " --> pdb=" O ILE 5 128 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL 5 350 " --> pdb=" O ASP 5 347 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '5' and resid 207 through 213 removed outlier: 4.594A pdb=" N LEU 5 218 " --> pdb=" O ALA 5 102 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '5' and resid 349 through 352 removed outlier: 8.570A pdb=" N ARG 5 349 " --> pdb=" O LEU 5 381 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '6' and resid 173 through 177 Processing sheet with id= 53, first strand: chain '6' and resid 189 through 193 removed outlier: 6.169A pdb=" N CYS 6 189 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE 6 318 " --> pdb=" O CYS 6 189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN 6 191 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARG 6 322 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '6' and resid 272 through 275 removed outlier: 6.590A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '7' and resid 77 through 82 removed outlier: 4.522A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 7 126 " --> pdb=" O LEU 7 107 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '7' and resid 178 through 184 removed outlier: 6.838A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain '9' and resid 42 through 45 removed outlier: 4.372A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'a' and resid 45 through 52 removed outlier: 6.024A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'c' and resid 254 through 258 removed outlier: 6.585A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'd' and resid 192 through 195 removed outlier: 6.706A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR d 209 " --> pdb=" O SER d 200 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'd' and resid 262 through 265 removed outlier: 4.313A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'd' and resid 208 through 217 removed outlier: 6.855A pdb=" N VAL d 208 " --> pdb=" O LEU d 252 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 78 through 81 removed outlier: 7.053A pdb=" N ARG f 78 " --> pdb=" O GLY f 89 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY f 89 " --> pdb=" O ARG f 78 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 126 through 138 removed outlier: 3.583A pdb=" N THR f 96 " --> pdb=" O ARG f 183 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'k' and resid 49 through 56 removed outlier: 3.583A pdb=" N SER k 50 " --> pdb=" O LYS k 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY k 78 " --> pdb=" O PRO k 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 79 through 83 removed outlier: 5.365A pdb=" N LYS p 98 " --> pdb=" O CYS p 82 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE p 103 " --> pdb=" O LEU p 133 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 's' and resid 90 through 93 removed outlier: 4.078A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS s 204 " --> pdb=" O PRO s 237 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 's' and resid 112 through 116 removed outlier: 6.762A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 's' and resid 241 through 244 removed outlier: 6.714A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 129 through 136 removed outlier: 4.775A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Q' and resid 139 through 144 removed outlier: 4.126A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER Q 141 " --> pdb=" O THR Q 148 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ARG Q 143 " --> pdb=" O GLY Q 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ALA Q 147 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'TC' and resid 131 through 135 removed outlier: 5.329A pdb=" N THRTC 131 " --> pdb=" O GLUTC 198 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARGTC 133 " --> pdb=" O VALTC 196 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THRTC 194 " --> pdb=" O THRTC 135 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'z' and resid 142 through 147 removed outlier: 5.749A pdb=" N GLN z 142 " --> pdb=" O ILE z 182 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE z 182 " --> pdb=" O GLN z 142 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE z 178 " --> pdb=" O VAL z 146 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'w' and resid 125 through 129 removed outlier: 3.524A pdb=" N THR w 142 " --> pdb=" O ILE w 75 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA w 77 " --> pdb=" O THR w 142 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET w 76 " --> pdb=" O VAL w 163 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA w 162 " --> pdb=" O PRO w 189 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE w 191 " --> pdb=" O ALA w 162 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG w 190 " --> pdb=" O ALA w 324 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL w 325 " --> pdb=" O LYS w 218 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N CYS w 329 " --> pdb=" O LEU w 222 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'w' and resid 234 through 238 removed outlier: 3.865A pdb=" N GLU w 242 " --> pdb=" O ASP w 237 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'w' and resid 373 through 376 removed outlier: 5.078A pdb=" N LYS w 373 " --> pdb=" O PHE w 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE w 447 " --> pdb=" O ALA w 369 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP w 445 " --> pdb=" O ALA w 371 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'w' and resid 398 through 402 removed outlier: 3.529A pdb=" N ILE w 399 " --> pdb=" O GLU w 408 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS w 406 " --> pdb=" O ASN w 401 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'w' and resid 530 through 534 removed outlier: 3.887A pdb=" N THR w 530 " --> pdb=" O ILE w 494 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N PHE w 491 " --> pdb=" O LEU w 560 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU w 560 " --> pdb=" O PHE w 491 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR w 556 " --> pdb=" O GLU w 495 " (cutoff:3.500A) removed outlier: 39.185A pdb=" N THR w 555 " --> pdb=" O VAL w 696 " (cutoff:3.500A) removed outlier: 35.006A pdb=" N VAL w 696 " --> pdb=" O THR w 555 " (cutoff:3.500A) removed outlier: 30.335A pdb=" N LEU w 557 " --> pdb=" O VAL w 694 " (cutoff:3.500A) removed outlier: 27.102A pdb=" N VAL w 694 " --> pdb=" O LEU w 557 " (cutoff:3.500A) removed outlier: 20.705A pdb=" N LEU w 692 " --> pdb=" O PRO w 559 " (cutoff:3.500A) removed outlier: 16.369A pdb=" N GLN w 561 " --> pdb=" O MET w 690 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N MET w 690 " --> pdb=" O GLN w 561 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA w 563 " --> pdb=" O PRO w 688 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'w' and resid 571 through 575 removed outlier: 3.573A pdb=" N ALA w 574 " --> pdb=" O VAL w 593 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'w' and resid 383 through 387 Processing sheet with id= 81, first strand: chain 'w' and resid 690 through 696 removed outlier: 3.869A pdb=" N GLU w 756 " --> pdb=" O ASN w 691 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU w 693 " --> pdb=" O ALA w 754 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA w 754 " --> pdb=" O GLU w 693 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR w 752 " --> pdb=" O THR w 695 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'w' and resid 686 through 690 No H-bonds generated for sheet with id= 82 2742 hydrogen bonds defined for protein. 8151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 973 hydrogen bonds 1672 hydrogen bond angles 0 basepair planarities 399 basepair parallelities 700 stacking parallelities Total time for adding SS restraints: 74.26 Time building geometry restraints manager: 40.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 14775 1.32 - 1.44: 39887 1.44 - 1.57: 57544 1.57 - 1.70: 3164 1.70 - 1.82: 498 Bond restraints: 115868 Sorted by residual: bond pdb=" C GLU J 188 " pdb=" N ALA J 189 " ideal model delta sigma weight residual 1.335 1.448 -0.113 1.38e-02 5.25e+03 6.71e+01 bond pdb=" C LEU N 230 " pdb=" N SER N 231 " ideal model delta sigma weight residual 1.327 1.190 0.136 1.71e-02 3.42e+03 6.35e+01 bond pdb=" CE1 HIS s 164 " pdb=" NE2 HIS s 164 " ideal model delta sigma weight residual 1.321 1.394 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C ALA J 184 " pdb=" N ALA J 185 " ideal model delta sigma weight residual 1.335 1.247 0.088 1.31e-02 5.83e+03 4.47e+01 bond pdb=" O2B GCP w 801 " pdb=" PB GCP w 801 " ideal model delta sigma weight residual 1.506 1.615 -0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 115863 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.95: 8835 104.95 - 113.19: 66324 113.19 - 121.44: 61245 121.44 - 129.69: 26475 129.69 - 137.93: 1474 Bond angle restraints: 164353 Sorted by residual: angle pdb=" C GLY L 112 " pdb=" N ASN L 113 " pdb=" CA ASN L 113 " ideal model delta sigma weight residual 121.70 132.20 -10.50 1.80e+00 3.09e-01 3.40e+01 angle pdb=" C LEU F 221 " pdb=" N THR F 222 " pdb=" CA THR F 222 " ideal model delta sigma weight residual 121.54 132.67 -11.13 1.91e+00 2.74e-01 3.40e+01 angle pdb=" C THR X 126 " pdb=" N VAL X 127 " pdb=" CA VAL X 127 " ideal model delta sigma weight residual 120.35 128.30 -7.95 1.39e+00 5.18e-01 3.27e+01 angle pdb=" N ARG T 161 " pdb=" CA ARG T 161 " pdb=" C ARG T 161 " ideal model delta sigma weight residual 108.23 100.40 7.83 1.38e+00 5.25e-01 3.22e+01 angle pdb=" CA TRP F 128 " pdb=" CB TRP F 128 " pdb=" CG TRP F 128 " ideal model delta sigma weight residual 113.60 123.93 -10.33 1.90e+00 2.77e-01 2.95e+01 ... (remaining 164348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 66352 35.95 - 71.89: 3306 71.89 - 107.84: 573 107.84 - 143.79: 15 143.79 - 179.73: 53 Dihedral angle restraints: 70299 sinusoidal: 42573 harmonic: 27726 Sorted by residual: dihedral pdb=" CA PHE E 316 " pdb=" C PHE E 316 " pdb=" N PRO E 317 " pdb=" CA PRO E 317 " ideal model delta harmonic sigma weight residual 180.00 95.28 84.72 0 5.00e+00 4.00e-02 2.87e+02 dihedral pdb=" CA ARG p 83 " pdb=" C ARG p 83 " pdb=" N SER p 84 " pdb=" CA SER p 84 " ideal model delta harmonic sigma weight residual 180.00 116.87 63.13 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA LEU h 82 " pdb=" C LEU h 82 " pdb=" N PRO h 83 " pdb=" CA PRO h 83 " ideal model delta harmonic sigma weight residual -180.00 -117.80 -62.20 0 5.00e+00 4.00e-02 1.55e+02 ... (remaining 70296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 17802 0.088 - 0.176: 1462 0.176 - 0.264: 117 0.264 - 0.352: 10 0.352 - 0.440: 7 Chirality restraints: 19398 Sorted by residual: chirality pdb=" CB ILE d 67 " pdb=" CA ILE d 67 " pdb=" CG1 ILE d 67 " pdb=" CG2 ILE d 67 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C3' C A2165 " pdb=" C4' C A2165 " pdb=" O3' C A2165 " pdb=" C2' C A2165 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CB ILE J 70 " pdb=" CA ILE J 70 " pdb=" CG1 ILE J 70 " pdb=" CG2 ILE J 70 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 19395 not shown) Planarity restraints: 15305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR w 142 " 0.033 2.00e-02 2.50e+03 6.43e-02 4.14e+01 pdb=" C THR w 142 " -0.111 2.00e-02 2.50e+03 pdb=" O THR w 142 " 0.042 2.00e-02 2.50e+03 pdb=" N PRO w 143 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU h 82 " -0.082 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO h 83 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO h 83 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO h 83 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 316 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO E 317 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.064 5.00e-02 4.00e+02 ... (remaining 15302 not shown) Histogram of nonbonded interaction distances: 0.50 - 1.38: 34 1.38 - 2.26: 267 2.26 - 3.14: 80960 3.14 - 4.02: 303505 4.02 - 4.90: 529337 Warning: very small nonbonded interaction distances. Nonbonded interactions: 914103 Sorted by model distance: nonbonded pdb=" CB GLN J 41 " pdb=" NH2 ARG w 698 " model vdw 0.505 3.520 nonbonded pdb=" C6 A A2576 " pdb=" CD2 LEU z 128 " model vdw 0.740 3.680 nonbonded pdb=" C4 A A2576 " pdb=" CD ARG w 580 " model vdw 0.836 3.660 nonbonded pdb=" CG LEU z 128 " pdb=" NH2 ARG w 580 " model vdw 0.871 3.550 nonbonded pdb=" OP1 C A2175 " pdb=" CE LYS J 99 " model vdw 0.901 3.440 ... (remaining 914098 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=0.69 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.060 Extract box with map and model: 15.460 Check model and map are aligned: 1.130 Set scattering table: 0.640 Process input model: 314.840 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.330 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: 339.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.007 0.136 115868 Z= 0.436 Angle : 0.866 16.004 164353 Z= 0.479 Chirality : 0.049 0.440 19398 Planarity : 0.008 0.126 15305 Dihedral : 19.411 179.732 52331 Min Nonbonded Distance : 0.505 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.31 % Favored : 92.19 % Rotamer: Outliers : 0.84 % Allowed : 8.07 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.06 % Twisted Proline : 1.57 % 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: -3.38 (0.07), residues: 9334 helix: -1.84 (0.07), residues: 3093 sheet: -2.03 (0.13), residues: 1220 loop : -2.60 (0.07), residues: 5021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 59 HIS 0.033 0.002 HIS p 194 PHE 0.035 0.003 PHE K 67 TYR 0.043 0.003 TYR 5 175 ARG 0.018 0.001 ARG X 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18668 Ramachandran restraints generated. 9334 Oldfield, 0 Emsley, 9334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18668 Ramachandran restraints generated. 9334 Oldfield, 0 Emsley, 9334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 8325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1666 time to evaluate : 7.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET q 128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable